Structural Classification of Proteins

Class: Alpha and beta proteins (a+b)

: Mainly antiparallel beta sheets (segregated alpha and beta regions)

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)

Folds:

Microbial ribonucleases [53932] (1)
single helix packs against antiparallel beta-sheet
1. Microbial ribonucleases [53933] (3)
  uperfamily
  1. Bacterial ribonucleases [81307] (5)
    1. Barnase [81305]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [53945] (60)
    2. Binase [81306]
      1. Bacillus intermedius [TaxId: 1400] [53946] (5)
    3. RNase Sa [53935]
      1. Streptomyces aureofaciens [TaxId: 1894] [53936] (22)
        SQ P05798
    4. Cytotoxic RNase Sa3 [82563]
      1. Streptomyces aureofaciens [TaxId: 1894] [82564] (2)
    5. Ribonuclease Sa2 [110767]
      1. Streptomyces aureofaciens [TaxId: 1894] [110768] (2)
        SQ Q53752
  2. Fungal ribonucleases [81311] (5)
    1. RNase F1 [53937]
      1. Fusarium moniliforme [TaxId: 117187] [53938] (4)
    2. RNase T1 [53939]
      1. Aspergillus oryzae [TaxId: 5062] [53940] (64)
      2. Aspergillus niger [TaxId: 5061] [53941] (1)
    3. RNase U2 [53942]
      1. Ustilago sphaerogena [TaxId: 5271] [53943] (1)
    4. RNase Ms [53947]
      1. Molsin (Aspergillus saitoi) [TaxId: 5063] [53948] (2)
  3. Ribotoxin [81310] (2)
    the fungal cytotoxic ribonucleases with many insertions in the common fold
    1. Restrictocin [81308]
      1. Fungus (Aspergillus restrictus) [TaxId: 5064] [53952] (4)
    2. alpha-Sarcin [81309]
      1. Fungus (Aspergillus giganteus) [TaxId: 5060] [53953] (2)
Lysozyme-like [53954] (1)
common alpha+beta motif for the active site region
1. Lysozyme-like [53955] (11)
  uperfamily
  1. Family 19 glycosidase [53956] (2)
    1. Plant class II chitinase [53957]
      1. Barley (Hordeum vulgare) [TaxId: 4513] [53958] (2)
      2. Jack bean (Canavalia ensiformis) [TaxId: 3823] [53959] (1)
  2. C-type lysozyme [53960] (20)
    1. Lysozyme [53961]
      ubiquitous in a variety of tissues and secretions
      1. Chicken (Gallus gallus) [TaxId: 9031] [53962] (280)
        SQ P00698
      2. Turkey (Meleagris gallopavo) [TaxId: 9103] [53963] (13)
      3. Guinea fowl (Numida meleagris) [TaxId: 8996] [53964] (2)
      4. Pheasant (Phasianus colchicus) [TaxId: 9054] [53965] (2)
      5. Bobwhite quail (Colinus virginianus) [TaxId: 9014] [53966] (3)
      6. Japanese quail (Coturnix coturnix japonica) [TaxId: 93934] [53967] (1)
      7. Human (Homo sapiens) [TaxId: 9606] [53969] (205)
        SQ P00695
      8. Horse (Equus caballus), milk [TaxId: 9796] [53970] (1)
      9. Dog (Canis familiaris), milk [TaxId: 9615] [53971] (5)
      10. Mouse (Mus musculus) [TaxId: 10090] [75329] (1)
      11. Australian echidna (Tachyglossus aculeatus) [TaxId: 9261] [53972] (1)
      12. Rainbow trout (Oncorhynchus mykiss) [TaxId: 8022] [53973] (7)
      13. Silkworm (Bombyx mori) [TaxId: 7091] [64201] (1)
      14. Tasar silkworm (Antheraea mylitta) [TaxId: 34739] [69627] (1)
        induced antibacterial protein
    2. alpha-Lactalbumin [53975]
      expressed only in the lactating mammary gland, strongly binds calcium ion
      1. Yellow baboon (Papio cynocephalus) [TaxId: 9556] [53976] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [53977] (3)
      3. Guinea pig (Cavia porcellus) [TaxId: 10141] [53978] (1)
      4. Goat (Capra hircus) [TaxId: 9925] [53979] (4)
      5. Cow (Bos taurus) [TaxId: 9913] [53980] (9)
      6. Mouse (Mus musculus) [TaxId: 10090] [69628] (15)
  3. Phage lysozyme [53981] (3)
    1. Phage T4 lysozyme [53982]
      1. Bacteriophage T4 [TaxId: 10665] [53983] (446)
        SQ P00720
        many mutant structures
    2. Tail-associated lysozyme gp5, catalytic domain [69629]
      1. Bacteriophage T4 [TaxId: 10665] [69630] (1)
    3. Endolysin Lyz [117758]
      1. Bacteriophage P1 [TaxId: 10678] [117759] (2)
        SQ Q37875 1-185
  4. Lambda lysozyme [53984] (1)
    1. Lambda lysozyme [53985]
      1. Bacteriophage lambda [TaxId: 10710] [53986] (4)
  5. G-type lysozyme [53987] (2)
    1. Lysozyme [53988]
      1. Western graylag goose (Anser anser anser) [TaxId: 8844] [53989] (2)
      2. Australian black swan (Cygnus atratus) [TaxId: 8868] [53990] (2)
  6. Bacterial muramidase, catalytic domain [53991] (2)
    the large N-terminal domain is all-alpha superhelix
    1. 70 kDa soluble lytic transglycosylase, SLT70 [53992]
      1. Escherichia coli [TaxId: 562] [53993] (3)
    2. 36 kDa soluble lytic transglycosylase, SLT35 [53994]
      1. Escherichia coli [TaxId: 562] [53995] (8)
  7. Chitosanase [53996] (2)
    1. Endochitosanase [53997]
      1. Streptomyces sp., strain N174 [TaxId: 1931] [53998] (1)
      2. Bacillus circulans [TaxId: 1397] [53999] (1)
  8. RPF-like [159824] (1)
    Pfam 06737; Transglycosylase-like domain
    1. Probable resuscitation-promoting factor RpfB [159825]
      1. Mycobacterium tuberculosis [TaxId: 1773] [159826] (1)
        SQ O05594 247-362
  9. NMB1012-like [159827] (2)
    Pfam 05838; predicted lysozyme (DUF847)
    1. Hypothetical protein NMB1012 [159828]
      1. Neisseria meningitidis [TaxId: 487] [159829] (8)
        SQ Q7DDI9 1-153
    2. Putative secretion activator PG0293 [159830]
      1. Porphyromonas gingivalis [TaxId: 837] [159831] (1)
        SQ Q7MXB3 1-192
  10. PBP transglycosylase domain-like [159832] (2)
    Pfam 00912; lacking the characteristic beta-sheet; otherwise has a similar fold to the Family 19 glycosidase
    1. Penicillin-binding protein 1a, PBP1a [159833]
      1. Aquifex aeolicus [TaxId: 63363] [159834] (2)
        SQ O66874 57-243
    2. Penicillin-binding protein 2, PBP2 [159835]
      1. Staphylococcus aureus [TaxId: 1280] [159836] (7)
        SQ Q2YY56 67-292
  11. PA2222-like [159837] (1)
    PfamB 104465
    1. Hypothetical protein PA2222 [159838]
      1. Pseudomonas aeruginosa [TaxId: 287] [159839] (8)
        SQ Q9I1P7 4-215
Cysteine proteinases [54000] (1)
consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
1. Cysteine proteinases [54001] (22)
  the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet
  uperfamily
  1. Papain-like [54002] (30)
    1. Actinidin [54003]
      1. Chinese gooseberry or kiwifruit (Actinidia chinensis) [TaxId: 3625] [54004] (2)
    2. Papain [54005]
      1. Papaya (Carica papaya) [TaxId: 3649] [54006] (18)
    3. Caricain (protease omega) [54007]
      1. Papaya (Carica papaya) [TaxId: 3649] [54008] (3)
    4. Chymopapain [54009]
      1. Papaya (Carica papaya) [TaxId: 3649] [54010] (1)
    5. Glycyl endopeptidase [54011]
      1. Papaya (Carica papaya) [TaxId: 3649] [54012] (1)
    6. Proline-specific cysteine protease [54013]
      1. Ginger rhizome (Zingiber officinale) [TaxId: 94328] [54014] (1)
    7. Ervatamin B [89803]
      1. Adam's apple (Ervatamia coronaria) [TaxId: 52861] [89804] (1)
    8. Ervatamin C [102717]
      1. East indian rosebay (Ervatamia coronaria) [TaxId: 52861] [102718] (1)
    9. Vignain (bean endopeptidase) [102719]
      1. Castor bean (Ricinus communis) [TaxId: 3988] [102720] (1)
    10. Bleomycin hydrolase [54017]
      DNA-binding protease that has more insertions in the papain-like fold
      1. Baker's yeast (Saccharomyces cerevisiae), Gal6 [TaxId: 4932] [54018] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [54019] (2)
    11. Cruzain [54020]
      1. Trypanosoma cruzi [TaxId: 5693] [54021] (17)
    12. (Pro)cathepsin B [54022]
      1. Human (Homo sapiens) [TaxId: 9606] [54023] (6)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [54024] (4)
      3. Cow (Bos taurus) [TaxId: 9913] [54025] (11)
    13. Cathepsin C (dipeptidyl peptidase I), catalytic domain [75330]
      1. Human (Homo sapiens) [TaxId: 9606] [75331] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82565] (1)
    14. Cathepsin F [89805]
      1. Human (Homo sapiens) [TaxId: 9606] [89806] (1)
    15. Cathepsin H [81637]
      also contains a disulfide-bound minicathepsin H chain
      1. Pig (Sus scrofa) [TaxId: 9823] [81636] (3)
    16. (Pro)cathepsin K [54028]
      1. Human (Homo sapiens) [TaxId: 9606] [54029] (32)
        SQ P43235 116-329 ! SQ P43235 115-329
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [142845] (1)
        SQ P43236 115-329
    17. (Pro)cathepsin L [54026]
      1. Human (Homo sapiens) [TaxId: 9606] [54027] (4)
    18. (Pro)cathepsin S [82566]
      1. Human (Homo sapiens) [TaxId: 9606] [82567] (36)
    19. (Pro)cathepsin V [64202]
      1. Human (Homo sapiens) [TaxId: 9606] [64203] (1)
    20. (Pro)cathepsin X [54031]
      1. Human (Homo sapiens) [TaxId: 9606] [54032] (2)
    21. Staphopain StpA [54033]
      1. Staphylococcus aureus [TaxId: 1280] [54034] (1)
    22. Staphopain SspB [102721]
      1. Staphylococcus aureus [TaxId: 1280] [102722] (4)
        SQ Q70UQ9 41-393
    23. Streptococcal pyrogenic exotoxin B [54035]
      1. Streptococcus pyogenes [TaxId: 1314] [54036] (2)
        SQ P00788 31-398
    24. Falcipain 2 [142846]
      1. Plasmodium falciparum [TaxId: 5833] [142847] (6)
        SQ Q9N6S8 244-484
    25. Major mite fecal allergen der p 1 [142848]
      1. House-dust mite (Dermatophagoides pteronyssinus) [TaxId: 6956] [142849] (3)
        SQ P08176 19-320! SQ P08176 99-320
  2. Avirulence protein Avrpph3 [102723] (1)
    1. Avirulence protein Avrpph3 [102724]
      1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [102725] (1)
  3. FMDV leader protease [54037] (1)
    1. FMDV leader protease [54038]
      1. Foot-and-mouth disease virus [TaxId: 12110] [54039] (5)
  4. Calpain large subunit, catalytic domain (domain II) [54040] (5)
    1. Calpain large subunit, catalytic domain (domain II) [54041]
      includes the N-terminal 'sequence' domain I
      1. Human (Homo sapiens), M-type [TaxId: 9606] [54042] (2)
      2. Rat (Rattus norvegicus), M-type [TaxId: 10116] [54043] (3)
      3. Rat (Rattus norvegicus), mu-type [TaxId: 10116] [75332] (10)
        SQ P97571 33-353
      4. Human (Homo sapiens), calpain 9 [TaxId: 9606] [142850] (1)
        SQ O14815 28-337
      5. Human(Homo sapiens), mu type [TaxId: 9606] [142851] (3)
        SQ P07384 33-353! SQ P07384 33-354
  5. Transglutaminase core [54044] (6)
    1. Transglutaminase catalytic domain [54045]
      1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [54046] (8)
        Coagulation factor XIII
      2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [75333] (2)
        GDP-binding protein
      3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [75334] (8)
      4. Red sea bream (Chrysophrys major) [TaxId: 143350] [64204] (1)
    2. Peptide:N-glycanase 1, PNG1 [142852]
      1. Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932] [142853] (2)
        SQ Q02890 8-327
      2. Mouse (Mus musculus) [TaxId: 10090] [159840] (2)
        SQ Q9JI78 164-450
  6. Arylamine N-acetyltransferase [54047] (4)
    fold similar to that of the factor XIII catalytic domain
    1. Arylamine N-acetyltransferase [54048]
      1. Salmonella typhimurium [TaxId: 90371] [54049] (1)
      2. Mycobacterium smegmatis [TaxId: 1772] [75335] (7)
      3. Rhizobium loti [TaxId: 381] [142854] (2)
        SQ Q98D42 6-275
      4. Pseudomonas aeruginosa [TaxId: 287] [142855] (1)
        SQ Q9HUY3 1-277
  7. Ubiquitin carboxyl-terminal hydrolase UCH-L [54050] (3)
    1. Ubiquitin carboxyl-terminal hydrolase UCH-l3 [54051]
      1. Human (Homo sapiens) [TaxId: 9606] [54052] (2)
        SQ P15374
      2. Synthetic, based on Saccharomyces cerevisiae sequence [54053] (1)
    2. Ubiquitin carboxyl-terminal hydrolase isozyme l1 [142856]
      1. Human (Homo sapiens) [TaxId: 9606] [142857] (2)
        SQ P09936 1-223
  8. Ubiquitin carboxyl-terminal hydrolase, UCH [82568] (5)
    Pfam 00443
    1. Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAUSP) [82569]
      1. Human (Homo sapiens) [TaxId: 9606] [82570] (2)
    2. Ubiquitin carboxyl-terminal hydrolase 6 [110769]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110770] (1)
        SQ P43593 103-499
    3. Ubiquitin carboxyl-terminal hydrolase 8 [142858]
      1. Human (Homo sapiens) [TaxId: 9606] [142859] (1)
        SQ P40818 762-1109
    4. Ubiquitin carboxyl-terminal hydrolase 14 [142860]
      1. Human (Homo sapiens) [TaxId: 9606] [142861] (4)
        SQ P54578 100-482
    5. Ubiquitin carboxyl-terminal hydrolase 2, USP2 [159841]
      1. Human (Homo sapiens) [TaxId: 9606] [159842] (2)
        SQ O75604 263-600! SQ O75604 264-599
  9. Adenain-like [54054] (5)
    Pfam 02902; Ulp1 protease family
    1. Human adenovirus 2 proteinase, adenain [54055]
      1. Mastadenovirus H2 [TaxId: 10515] [54056] (2)
    2. Ulp1 protease C-terminal domain [54057]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54058] (4)
    3. Sentrin-specific protease 2, SENP2 [110771]
      1. Human (Homo sapiens) [TaxId: 9606] [110772] (8)
        SQ Q9HC62 366-589
    4. Sentrin-specific protease 8, SENP8 [117760]
      1. Human (Homo sapiens) [TaxId: 9606] [117761] (6)
        SQ Q96LD8
    5. Sentrin-specific protease 1 [142862]
      1. Human (Homo sapiens) [TaxId: 9606] [142863] (6)
        SQ Q9P0U3 419-643
  10. Microbial transglutaminase [75336] (1)
    inverted positions of the catalytic triad Asp and His residues
    1. Microbial transglutaminase [75337]
      1. Streptoverticillium mobaraense [TaxId: 35621] [75338] (1)
  11. Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [110773] (1)
    probably the same as Pfam 02338, OTU-like cysteine protease, but 1TFF (SQ Q96DC9) was not detected by the Pfam model
    1. Ubiquitin thiolesterase protein OTUB2 (Otubain-2) [110774]
      1. Human (Homo sapiens) [TaxId: 9606] [110775] (1)
        SQ Q96DC9
  12. IgG-specific endopeptidase IdeS (Sib38) [117762] (1)
    1. IgG-specific endopeptidase IdeS (Sib38) [117763]
      1. Streptococcus pyogenes [TaxId: 1314] [117764] (1)
        SQ Q9F1R7 38-339 # SPy0861
  13. Lpg0564-like [142864] (1)
    Pfam 07313, DUF1460; contains new PDB entry 2p1g, annotated as putative xylanase
    1. Hypothetical protein Lpg0564 [142865]
      1. Legionella pneumophila [TaxId: 446] [142866] (1)
        SQ Q5ZY11 49-352
  14. Phytochelatin synthase [142867] (1)
    Pfam 05023; assosiated Pfam 09328 (DUF1984) is a part of the same functional unit
    1. Primitive phytochelatin synthase [142868]
      1. Nostoc sp. pcc 7120 [TaxId: 103690] [142869] (4)
        SQ Q8YY76 29-238
  15. CHAP domain [142870] (1)
    Pfam 05257
    1. Glutathionylspermidine synthase, amidase domain [142871]
      1. Escherichia coli [TaxId: 562] [142872] (10)
        SQ P0AES0 10-200
  16. NlpC/P60 [142873] (1)
    Pfam 00877
    1. Cell wall-associated hydrolase Spr C-terminal domain [142874]
      1. Nostoc punctiforme [TaxId: 272131] [142875] (3)
        SQ Q8YRR4 87-234
  17. PMT C-terminal domain like [159843] (1)
    displays a minimal thiol-protease fold and its catalytic triad; potential redox regulation: the catalytic cysteine can form a disulfide bond with an N-terminal cysteine
    1. Dermonecrotic toxin, ToxA [159844]
      Synonym: Mitogenic toxin PMT
      1. Pasteurella multocida [TaxId: 747] [159845] (4)
        SQ P17452 1094-1285
  18. MOA C-terminal domain-like [159846] (1)
    PfamB 070855
    1. Agglutinin MOA [159847]
      1. Fairy-ring mushroom (Marasmius oreades) [TaxId: 181124] [159848] (1)
        SQ Q8X123 156-293
  19. Atu2299-like [159849] (1)
    Pfam 09641; DUF2026; putative Cys/Ser-His-Asp catalytic triad
    1. Hypothetical protein Atu2299 [159850]
      Serine catalytic nucleophile
      1. Agrobacterium tumefaciens [TaxId: 358] [159851] (1)
        SQ Q8UD29 1-202
  20. M48USP-like [159852] (1)
    Pfam 04843; Herpesvirus tegument protein, N-terminal conserved region
    1. Tegument protein M48; N-terminal domain [159853]
      1. Murine cytomegalovirus (MCMV) [TaxId: 10366] [159854] (2)
        SQ A8E1C4 1-232
  21. YiiX-like [159855] (1)
    Pfam 06520; DUF1105; circularly permuted active site residues compare to papain
    1. Hypothetical protein YiiX [159856]
      1. Escherichia coli [TaxId: 562] [159857] (2)
        SQ Q8X778 19-200
  22. Autophagin-like [159858] (2)
    Pfam 03416
    1. Cysteine protease ATG4A [159859]
      Autophagin-2
      1. Human (Homo sapiens) [TaxId: 9606] [159860] (4)
        SQ Q8WYN0 26-359
    2. Cysteine protease ATG4B [159861]
      Autophagin-1
      1. Human (Homo sapiens) [TaxId: 9606] [159862] (5)
        SQ Q9Y4P1 10-373! SQ Q9Y4P1 5-354
His-Me finger endonucleases [54059] (1)
core: (alpha)-beta-omega_loop-beta-alpha; embeded in larger different structures
1. His-Me finger endonucleases [54060] (6)
  common motif contains conserved histidine residue and metal-binding site
  uperfamily
  1. Endonuclease I [102726] (1)
    1. Periplasmic endonuclease Vvn [102727]
      1. Vibrio vulnificus [TaxId: 672] [102728] (6)
  2. HNH-motif [54061] (2)
    1. DNase domain of colicin E7 [54062]
      1. Escherichia coli [TaxId: 562] [54063] (10)
    2. DNase domain of colicin E9 [54064]
      1. Escherichia coli [TaxId: 562] [54065] (15)
        SQ P09883 456-581
  3. DNA/RNA non-specific endonuclease [54066] (2)
    the core motif is inserted in a six-stranded meander beta-sheet domain
    1. Sm endonuclease [54067]
      1. Serratia marcescens [TaxId: 615] [54068] (4)
    2. Nuclease NucA [159863]
      1. Anabaena sp., PCC 7120 [TaxId: 1167] [159864] (1)
        SQ P38446 35-274
  4. Intron-encoded homing endonucleases [54069] (2)
    1. Intron-encoded homing endonuclease I-PpoI [54070]
      1. Physarum polycephalum [TaxId: 5791] [54071] (7)
    2. Intron-encoded homing endonuclease I-HmuI [110776]
      1. Bacteriophage SP01 [TaxId: 10685] [110777] (1)
        SQ P34081
  5. Recombination endonuclease VII, N-terminal domain [68915] (1)
    1. Recombination endonuclease VII, N-terminal domain [68916]
      1. Bacteriophage T4 [TaxId: 10665] [68917] (7)
  6. Caspase-activated DNase, CAD (DffB, DFF40) [110778] (1)
    1. Caspase-activated DNase, CAD (DffB, DFF40) [110779]
      1. Mouse (Mus musculus) [TaxId: 10090] [110780] (1)
        SQ O54788 85-329 # structure of the N-terminal, CAD domain (1-87) is solved separately; scop_sp 54282
RNase A-like [54075] (1)
contains long curved beta-sheet and 3 helices
1. RNase A-like [54076] (1)
  can be classified as disulfide-rich
  uperfamily
  1. Ribonuclease A-like [54077] (15)
    1. Ribonuclease A (also ribonuclease B, S) [54078]
      1. Cow (Bos taurus) [TaxId: 9913] [54079] (167)
      2. Human (Homo sapiens), des1-7 [TaxId: 9606] [54080] (7)
      3. Rat (Rattus norvegicus) [TaxId: 10116] [54081] (1)
    2. Amphibian cytotoxic ribonuclease [54084]
      1. Frog (Rana pipiens), P-30 [TaxId: 8404] [54083] (3)
      2. Bullfrog (Rana catesbeiana) [TaxId: 8400] [54085] (4)
      3. Bullfrog (Rana catesbeiana), RNase2 [TaxId: 8400] [82571] (1)
      4. Bullfrog (Rana catesbeiana), RNase4 [TaxId: 8400] [75339] (1)
      5. Bullfrog (Rana catesbeiana), RNase6 [TaxId: 8400] [110781] (2)
        SQ Q9DFY5
    3. Seminal ribonucleasease [54086]
      1. Cow (Bos taurus) [TaxId: 9913] [54087] (12)
        SQ P00669 27-150
    4. Hybrid between ribonuclease A and seminal ribonuclease [54088]
      1. Cow (Bos taurus) [TaxId: 9913] [54089] (1)
    5. Eosinophil cationic protein (ECP), ribonuclease 3 [54090]
      1. Human (Homo sapiens) [TaxId: 9606] [54091] (3)
    6. Eosinophil-derived neurotoxin (EDN) [64205]
      1. Human (Homo sapiens) [TaxId: 9606] [64206] (12)
    7. Ribonuclease 4 [54092]
      1. Human (Homo sapiens) [TaxId: 9606] [54093] (2)
    8. Angiogenin [54094]
      1. Human (Homo sapiens) [TaxId: 9606] [54095] (19)
      2. Cow (Bos taurus) [TaxId: 9913] [54096] (2)
EndoU-like [142876] (1)
comprises several helices and two three-stranded antiparallel beta-sheets; similar architecture to the RNase A-like fold (scop_cf 54075)
1. EndoU-like [142877] (2)
  similarity to the RNase A-like superfamily (scop_sf 54076) extends to the active site location and architecture; the two structural cores of the RNase A and EndoU superfamilies are interrelated by a topological permutation - transposition of two pereferial beta-strands, suggesting possible distant homology of the two superfamilies (and their unification in a hyperfamily)
  uperfamily
  1. Eukaryotic EndoU ribonuclease [142878] (1)
    PfamB 010233; common fold decorated with additional structures
    1. EndoU [142879]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [142880] (3)
        SQ Q8JFY9 6-289
  2. Nsp15 C-terminal domain-like [142881] (2)
    PfamB 001946
    1. Nsp15, C-terminal domain [142882]
      1. SARS coronavirus [TaxId: 227859] [142883] (11)
        SQ Q6VA80 6620-6774
      2. Murine hepatitis virus, MHV [TaxId: 11138] [142884] (2)
        SQ P16342 6720-6872
Prion-like [54097] (1)
beta-alpha-beta-alpha(2); antiparallel beta-ribbon
1. Prion-like [54098] (1)
  uperfamily
  1. Prion-like [54099] (14)
    1. Prion protein domain [54100]
      1. Mouse (Mus musculus) [TaxId: 10090] [54101] (3)
        SQ P04925 120-231
      2. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [54102] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [54103] (18)
      4. Cow (Bos taurus) [TaxId: 9913] [54104] (4)
      5. Sheep (Ovis aries) [TaxId: 9940] [102729] (6)
        SQ P23907 124-234 ! SQ P23907 122-234 ! SQ P23907 127-228
      6. American elk (Cervus elaphus nelsoni) [TaxId: 9864] [117765] (1)
        SQ 67986 124-234
      7. Chicken (Gallus gallus) [TaxId: 9031] [117766] (1)
        SQ P27177 132-248
      8. Red-eared slider turtle (Trachemys scripta) [TaxId: 34903] [117767] (1)
        SQ Q9I9C0 141-248
      9. African clawed frog (Xenopus laevis) [TaxId: 8355] [117768] (1)
        SQ Q5S1W7 43-171
      10. Cat (Felis silvestris catus) [TaxId: 9685] [117769] (1)
        SQ O18754 104-214
      11. Dog (Canis familiaris) [TaxId: 9615] [117770] (1)
        SQ O46501 124-233
      12. Pig (Sus scrofa) [TaxId: 9823] [117771] (1)
        SQ P49927 125-235
    2. Prion-like protein Doppel [64207]
      1. Human (Homo sapiens) [TaxId: 9606] [82572] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [64208] (1)
LysM domain [54105] (1)
beta-alpha(2)-beta; antiparallel strands
1. LysM domain [54106] (1)
  uperfamily
  1. LysM domain [54107] (2)
    1. Membrane-bound lytic murein transclycosylase D, MltD [54108]
      1. Escherichia coli [TaxId: 562] [54109] (1)
    2. Hypothetical protein YkuD, N-terminal domain [142885]
      1. Bacillus subtilis [TaxId: 1423] [142886] (2)
        SQ O34816 1-48
gpW/XkdW-like [64209] (2)
alpha-beta(2)-alpha; antiparallel hairpin
1. Head-to-tail joining protein W, gpW [64210] (1)
  uperfamily
  1. Head-to-tail joining protein W, gpW [64211] (1)
    1. Head-to-tail joining protein W, gpW [64212]
      1. Bacteriophage lambda [TaxId: 10710] [64213] (1)
2. XkdW-like [159865] (1)
  different packing of secondary structures than in gpW
  1. XkdW-like [159866] (1)
    Pfam 09636
    1. Phage-like element PbsX protein XkdW [159867]
      1. Bacillus subtilis [TaxId: 1423] [159868] (1)
        SQ P54342 1-60
Hypothetical protein MTH677 [110782] (1)
alpha-beta(2)-alpha; 2 layers a/b; antiparallel beta-hairpin
1. Hypothetical protein MTH677 [110783] (1)
  uperfamily
  1. Hypothetical protein MTH677 [110784] (1)
    1. Hypothetical protein MTH677 [110785]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [110786] (1)
        SQ O26773
GTF2I-like repeat [117772] (1)
alpha(2)-beta-alpha-beta-alpha; 2 layers: a/b; antiparallel beta-ribbon
1. GTF2I-like repeat [117773] (1)
  uperfamily
  1. GTF2I-like repeat [117774] (1)
    Pfam 02946
    1. General transcription factor II-I [117775]
      there are six GTF2I-like repeats in this protein
      1. Mouse (Mus musculus) [TaxId: 10090] [117776] (1)
        SQ Q9ESZ8
Urease, gamma-subunit [54110] (1)
alpha(3)-beta(2); antiparallel hairpin
1. Urease, gamma-subunit [54111] (1)
  uperfamily
  1. Urease, gamma-subunit [54112] (3)
    1. Urease, gamma-subunit [54113]
      1. Klebsiella aerogenes [TaxId: 28451] [54114] (27)
      2. Bacillus pasteurii [TaxId: 1474] [54115] (6)
      3. Helicobacter pylori [TaxId: 210] [69631] (2)
        fused with beta subunit
IL8-like [54116] (2)
beta(3)-alpha
1. Interleukin 8-like chemokines [54117] (1)
  form dimers with different dimerisation modes
  uperfamily
  1. Interleukin 8-like chemokines [54118] (29)
    1. Interleukin-8, IL-8 [54119]
      1. Human (Homo sapiens) [TaxId: 9606] [54120] (9)
    2. Platelet factor 4, PF4 [54121]
      1. Cow (Bos taurus) [TaxId: 9913] [54122] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [54123] (6)
    3. IP-10/CXCL10 [82573]
      1. Human (Homo sapiens) [TaxId: 9606] [82574] (4)
    4. Melanoma growth stimulating activity (MGSA) [54124]
      1. Human (Homo sapiens) [TaxId: 9606] [54125] (3)
    5. IL-8/MGSA chimeric protein CIL-8M [54126]
      IL-8: residues 1-53; MGSA: residues 54-72
      1. Human (Homo sapiens) [TaxId: 9606] [54127] (1)
    6. Macrophage inflammatory protein, MIP [54128]
      has different dimerisation mode
      1. Human (Homo sapiens), 1-beta [TaxId: 9606] [54129] (3)
      2. Human (Homo sapiens), 1-alpha [TaxId: 9606] [54130] (2)
      3. Human (Homo sapiens), ccl20/mip-3a [TaxId: 9606] [75340] (4)
      4. Mouse (Mus musculus), ccl20/mip-3a [TaxId: 10090] [64214] (1)
      5. Kaposi's sarcoma-associated herpesvirus, VMIP-II [TaxId: 37296] [54131] (10)
        anti-HIV chemokine
    7. RANTES (regulated upon activation, normal T-cell expressed and secreted) [54132]
      has different dimerisation mode
      1. Human (Homo sapiens) [TaxId: 9606] [54133] (9)
        SQ P13501 25-91
    8. Monocyte chemoattractant protein-1 (MCP-1, MCAF) [54134]
      1. Human (Homo sapiens) [TaxId: 9606] [54135] (9)
    9. Monocyte chemoattractant protein-2 (MCP-2) [54136]
      1. Human (Homo sapiens) [TaxId: 9606] [54137] (1)
    10. CC chemokine I-309 [54138]
      1. Human (Homo sapiens) [TaxId: 9606] [54139] (1)
    11. Eotaxin [54140]
      1. Human (Homo sapiens) [TaxId: 9606] [54141] (2)
    12. Eotaxin-2 [54142]
      1. Human (Homo sapiens) [TaxId: 9606] [54143] (2)
    13. Eotaxin-3 [75341]
      1. Human (Homo sapiens) [TaxId: 9606] [75342] (2)
    14. Lymphotactin [69632]
      1. Human (Homo sapiens) [TaxId: 9606] [69633] (2)
    15. Monocyte chemoattractant protein-3 (MCP-3) [54144]
      1. Human (Homo sapiens) [TaxId: 9606] [54145] (2)
    16. Chemokine domain of fractalkine [54146]
      1. Human (Homo sapiens) [TaxId: 9606] [54147] (2)
    17. Platelet basic protein, PBP [54148]
      synonym: Small inducible cytokine B7; Neutrophil-activating peptide-2 (NAP-2), Connective tissue activating peptide-III (CTAP-III)
      1. Human (Homo sapiens) [TaxId: 9606] [54149] (3)
    18. Stromal cell-derived factor-1 (SDF-1) [54150]
      1. Human (Homo sapiens) [TaxId: 9606] [54151] (7)
    19. Macrophage inflammatory protein-2 [54152]
      1. Mouse (Mus musculus) [TaxId: 10090] [54153] (1)
    20. Chemokine hcc-2 (macrophage inflammatory protein-5) [54154]
      1. Human (Homo sapiens) [TaxId: 9606] [54155] (1)
    21. Gro beta [54156]
      1. Human (Homo sapiens) [TaxId: 9606] [54157] (1)
    22. Myeloid progenitor inhibitory factor-1 (MPIF-1) [64215]
      1. Human (Homo sapiens) [TaxId: 9606] [64216] (1)
    23. Thymus and activation-regulated chemokine, TRAC [102730]
      1. Human (Homo sapiens) [TaxId: 9606] [102731] (2)
    24. Small inducible cytokine b11 (CXCL11/I-TAC) [102732]
      1. Human (Homo sapiens) [TaxId: 9606] [102733] (1)
2. PhtA domain-like [142887] (1)
  contains extra N-terminal beta-hairpin, like structurally similar archaeal "histone-like" proteins (scop_fa 54161), but does not adopt its SH3-like barrel fold
  uperfamily
  1. PhtA domain-like [142888] (1)
    Pfam 04270; Streptococcal histidine triad protein
    1. Pneumococcal histidine triad protein A, PhtA [142889]
      1. Streptococcus pneumoniae [TaxId: 1313] [142890] (3)
        SQ Q97QM8 166-220
DNA-binding domain [54170] (1)
beta(3)-alpha; 2 layers: alpha/beta
1. DNA-binding domain [54171] (4)
  uperfamily
  1. DNA-binding domain from tn916 integrase [54172] (1)
    1. DNA-binding domain from tn916 integrase [54173]
      1. Enterococcus faecalis [TaxId: 1351] [54174] (4)
  2. lambda integrase N-terminal domain [75344] (1)
    1. lambda integrase N-terminal domain [75345]
      1. Bacteriophage lambda [TaxId: 10710] [75346] (7)
  3. GCC-box binding domain [54175] (1)
    1. GCC-box binding domain [54176]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [54177] (3)
  4. Methyl-CpG-binding domain, MBD [54178] (3)
    1. Methyl-CpG-binding protein 2, MECP2 [54179]
      1. Human (Homo sapiens) [TaxId: 9606] [54180] (1)
      2. Chicken (Gallus gallus) [TaxId: 9031] [102734] (1)
    2. Methylation-dependent transcriptional repressor MBD1/PCM1 [54181]
      1. Human (Homo sapiens) [TaxId: 9606] [54182] (2)
Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54183] (1)
alpha1-beta3; 2 layers: alpha/beta; order 132
1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54184] (1)
  duplication: consists of 2 subdomains of this fold
  uperfamily
  1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54185] (1)
    1. Penicillin-binding protein 2x (pbp-2x), c-terminal domain [54186]
      1. Streptococcus pneumoniae [TaxId: 1313] [54187] (22)
Dodecin subunit-like [88797] (6)
beta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132
1. Dodecin-like [89807] (1)
  uperfamily
  1. Dodecin-like [89808] (2)
    Subunit assembly and a probable biological unit is a dodecamer, hence the name
    1. Flavin-binding protein dodecin [89809]
      1. Archaeon Halobacterium salinarum [TaxId: 2242] [89810] (12)
    2. Uncharacterized protein TTHA1431 [159869]
      1. Thermus thermophilus [TaxId: 274] [159870] (62)
        SQ Q5SIE3 2-67! SQ Q5SIE3 2-68
2. Amyloid beta a4 protein copper binding domain (domain 2) [89811] (1)
  uperfamily
  1. Amyloid beta a4 protein copper binding domain (domain 2) [89812] (1)
    1. Amyloid beta a4 protein copper binding domain (domain 2) [89813]
      1. Human (Homo sapiens) [TaxId: 9606] [89814] (3)
3. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88798] (1)
  uperfamily
  1. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88799] (3)
    1. N-terminal, heterodimerisation domain of RBP7 (RpoE) [88800]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88801] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117777] (7)
        SQ P34087
      3. Human (Homo sapiens) [TaxId: 9606] [142891] (4)
        SQ P62487 1-77
4. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117778] (1)
  uperfamily
  1. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117779] (1)
    1. D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain [117780]
      homo-dimerisation domain
      1. Clostridium sticklandii [TaxId: 1511] [117781] (1)
        SQ Q9ZFE5
5. YbjQ-like [117782] (1)
  pentamer, beta/alpha-propeller; additional short beta-strands promote oligomeric assembly
  uperfamily
  1. YbjQ-like [117783] (2)
    Pfam 01906; DUF 74, UPF0145
    1. Hypothetical protein YbjQ [117784]
      1. Shigella flexneri [TaxId: 623] [117785] (1)
        SQ Q83LS2
    2. Hypothetical protein BC1012 [142892]
      1. Bacillus cereus [TaxId: 1396] [142893] (5)
        SQ Q81H14 1-103
6. YdgH-like [159871] (1)
  extra N-terminal structures: short strand and short helix; topological similarity to the YbjQ-like superfamily
  1. YdgH-like [159872] (2)
    Pfam 07338; DUF1471
    1. Hypothetical protein STM0082 [159873]
      1. Salmonella typhimurium [TaxId: 90371] [159874] (2)
        SQ Q7CR88 1-96
    2. Putative periplasmic protein YahO [159875]
      SCH_0407
      1. Salmonella choleraesuis [TaxId: 28901] [159876] (1)
        SQ Q57SJ8 1-91
Ribosomal proteins S24e, L23 and L15e [54188] (1)
beta-(alpha)-beta-alpha-beta(2); 3 layers: alpha/beta/alpha; antiparallel beta-sheet: order 1243
1. Ribosomal proteins S24e, L23 and L15e [54189] (3)
  uperfamily
  1. L23p [54190] (4)
    1. Ribosomal protein L23 [54191]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [54192] (62)
        SQ P12732
      2. Thermus thermophilus [TaxId: 274] [89815] (7)
      3. Deinococcus radiodurans [TaxId: 1299] [159877] (8)
        SQ Q9RXK0 2-94
      4. Escherichia coli [TaxId: 562] [159878] (28)
        SQ P02424 1-99
  2. L15e [54193] (1)
    elaborated with additional structures
    1. Ribosomal protein L15e [54194]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [54195] (42)
        SQ P60618
  3. Ribosomal protein S24e [117786] (4)
    Pfam 01282
    1. Ribosomal protein S24e [117787]
      1. Methanosarcina mazei [TaxId: 2209] [117788] (1)
        SQ Q8PZ95
      2. Thermoplasma acidophilum [TaxId: 2303] [142894] (1)
        SQ Q9HJ79 1-98
      3. Methanococcus maripaludis [TaxId: 39152] [142895] (1)
        SQ P61193 1-102
      4. Pyrococcus abyssi [TaxId: 29292] [159879] (2)
        SQ Q9UY20 1-93
Ribosome binding domain-like [100965] (2)
beta-(2)-alpha(2)-beta(2); 2 layers: beta/alpha; antiparallel beta-sheet: order 1243; topological similarity to the common core of ribosomal proteins L23 and L15e
1. Trigger factor ribosome-binding domain [102735] (1)
  uperfamily
  1. Trigger factor ribosome-binding domain [102736] (2)
    1. Trigger factor ribosome-binding domain [102737]
      1. Escherichia coli [TaxId: 562] [102738] (4)
        SQ P22257
      2. Vibrio cholerae [TaxId: 666] [110787] (1)
        SQ Q9KQS5
2. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100966] (1)
  uperfamily
  1. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100967] (2)
    1. Translation initiation factor 2 beta, aIF2beta, N-terminal domain [100968]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102739] (1)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [100969] (1)
TFB5-like [142896] (1)
beta-alpha-beta(2)-alpha; 2 layers, a/b; antiparallel sheet, order: 132; dimerises in solution (PDB 2jnj) via extended N-terminal strand
1. TFB5-like [142897] (1)
  uperfamily
  1. TFB5-like [142898] (1)
    Pfam 06331
    1. General transcription factor IIH polypeptide 5, TFB5 [142899]
      1. Human (Homo sapiens) [TaxId: 9606] [142900] (1)
        SQ Q6ZYL4 6-71
Obg GTP-binding protein C-terminal domain [102740] (1)
beta-(2)-alpha(3)-beta(2); 2 layers: beta/alpha; mixed beta-sheet: order 1234; strands 2 and 3 a parallel to each other
1. Obg GTP-binding protein C-terminal domain [102741] (1)
  uperfamily
  1. Obg GTP-binding protein C-terminal domain [102742] (1)
    1. Obg GTP-binding protein C-terminal domain [102743]
      1. Thermus thermophilus [TaxId: 274] [102744] (1)
        TT1381
HIT-like [54196] (2)
alpha-beta(3)-alpha-beta(2); 3 layers: alpha/beta/alpha
1. HIT-like [54197] (4)
  uperfamily
  1. HIT (HINT, histidine triad) family of protein kinase-interacting proteins [54198] (7)
    Pfam 01230
    topologically similar to the N-terminal domain of protein kinases
    1. Histidine triad nucleotide-binding protein (HINT) [54199]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [54200] (5)
    2. FHIT (fragile histidine triad protein) [54201]
      1. Human (Homo sapiens) [TaxId: 9606] [54202] (8)
    3. Protein kinase C inhibitor-1, PKCI-1 [54203]
      1. Human (Homo sapiens) [TaxId: 9606] [54204] (6)
    4. NIT-FHIT fusion protein, C-terminal domain [54205]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [54206] (1)
    5. Hit [117789]
      1. Bacillus subtilis [TaxId: 1423] [117790] (1)
        SQ O07513
    6. Putative hydrolase [117791]
      1. Clostridium thermocellum [TaxId: 1515] [117792] (1)
        SQ Q4CCR3
    7. Histidine triad protein Mfla2506 [159880]
      1. Methylobacillus flagellatus [TaxId: 405] [159881] (4)
        SQ Q1GYB6 6-144
  2. Hexose-1-phosphate uridylyltransferase [54207] (2)
    duplication: consists of 2 HIT-like motifs
    binds zinc and iron ions
    1. Galactose-1-phosphate uridylyltransferase [54208]
      1. Escherichia coli [TaxId: 562] [54209] (4)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110788] (20)
        SQ Q9FK51
  3. mRNA decapping enzyme DcpS C-terminal domain [102745] (2)
    1. mRNA decapping enzyme DcpS C-terminal domain [102746]
      1. Human (Homo sapiens) [TaxId: 9606] [102747] (14)
      2. Mouse (Mus musculus) [TaxId: 10090] [110789] (1)
        SQ Q9DAR7
  4. CDH-like [159882] (1)
    Pfam 02611; CDP-diacylglycerol pyrophosphatase; duplication: consists of the N-terminal HIT subdomain and C-terminal rudiment HIT-like subdomain
    1. CDP-diacylglycerol pyrophosphatase CDH [159883]
      1. Escherichia coli [TaxId: 562] [159884] (2)
        SQ Q8X7A5 31-250
2. Rotavirus NSP2 fragment, C-terminal domain [75347] (1)
  uperfamily
  1. Rotavirus NSP2 fragment, C-terminal domain [75348] (1)
    1. Rotavirus NSP2 fragment, C-terminal domain [75349]
      1. Simian 11 rotavirus [TaxId: 10923] [75350] (5)
Secretion chaperone-like [69634] (5)
alpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/beta
1. Type III secretory system chaperone-like [69635] (2)
  uperfamily
  1. Type III secretory system chaperone [69636] (11)
    the family sequences are very divergent
    1. YopE chaperone SycE [69637]
      1. Yersinia pestis [TaxId: 632] [69638] (3)
      2. Yersinia enterocolitica [TaxId: 630] [75351] (1)
    2. Virulence effector SptP secretion chaperone SicP [69639]
      1. Salmonella typhimurium [TaxId: 90371] [69640] (1)
    3. Secretion chaperone CesT [69641]
      1. Escherichia coli [TaxId: 562] [69642] (1)
    4. Secretion chaperone SigE [69643]
      1. Salmonella enterica [TaxId: 28901] [69644] (1)
    5. Surface presentation of antigens protein SpaK (Spa15) [102748]
      1. Shigella flexneri [TaxId: 623] [102749] (1)
      2. Salmonella typhimurium [TaxId: 90371] [142901] (2)
        SQ P0A1N0 1-134
    6. Putative YopH chaperone SycH [110790]
      1. Yersinia pestis [TaxId: 632] [110791] (1)
        SQ Q7ARG9
    7. AvrPphF ORF1, chaperone of AvrPphF ORF2 [110792]
      1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [110793] (1)
        SQ Q9K2L2 1-125
    8. Chaperone protein YscB [142902]
      1. Yersinia pestis [TaxId: 632] [142903] (1)
        SQ Q56973 2-127
    9. Chaperone protein SycN [142904]
      1. Yersinia pestis [TaxId: 632] [142905] (1)
        SQ P61380 2-122
  2. Tll0839-like [159885] (1)
    Pfam 08851; DUF1821; cyanobacterial family of similar subunit and dimer structures to the Type III secretory system chaperone from proteobacteria
    1. Uncharacterized protein Tll0839 [159886]
      1. Synechococcus elongatus [TaxId: 32046] [159887] (2)
        SQ Q8DKM0 1-152
2. Arp2/3 complex subunits [69645] (1)
  uperfamily
  1. Arp2/3 complex subunits [69646] (2)
    1. ARPC4 (20 kDa subunit) [69647]
      1. Cow (Bos taurus) [TaxId: 9913] [69648] (10)
        SQ P59998 # 100% sequence identity
    2. ARPC2 (34 kDa subunit) [69649]
      duplication: tandem repeat of two domains of this fold
      1. Cow (Bos taurus) [TaxId: 9913] [69650] (17)
        SQ O15144 1-282 # 100% sequence identity
3. YjbR-like [142906] (1)
  overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
  uperfamily
  1. YjbR-like [142907] (2)
    Pfam 04237; DUF419
    1. Hypothetical protein DR2400 [142908]
      1. Deinococcus radiodurans [TaxId: 1299] [142909] (1)
        SQ Q9RRT5 2-132
    2. Hypothetical protein YjbR [142910]
      1. Escherichia coli [TaxId: 562] [142911] (1)
        SQ P0AF50 1-118
4. YdhG-like [159888] (1)
  some similarity to YjbR-like (scop_sf 136320)
  1. YdhG-like [159889] (2)
    Pfam 08818; DUF1801
    1. Uncharacterized protein LSEI2283 [159890]
      1. Lactobacillus casei [TaxId: 1582] [159891] (2)
        SQ Q035U5 2-122
    2. Uncharacterized protein YdhG [159892]
      1. Bacillus subtilis [TaxId: 1423] [159893] (2)
        SQ Q797E6 1-123
5. YgaC/TfoX-N like [159894] (2)
  overall similar to the Type III secretory system chaperone subunits; different shape of the beta-sheet
  1. YgaC-like [159895] (1)
    Pfam 09400; DUF2002
    1. Putative cytoplasmic protein YgaC [159896]
      1. Salmonella typhimurium [TaxId: 90371] [159897] (1)
        SQ Q8ZML5 1-112
  2. TfoX N-terminal domain-like [159898] (1)
    Pfam 04993
    1. Hypothetical protein VP1028 [159899]
      1. Vibrio parahaemolyticus [TaxId: 670] [159900] (2)
        SQ Q87QX1 3-105
DNA-binding domain of intron-encoded endonucleases [64495] (1)
beta(2)-alpha(2)-beta; 2 layers; 3-stranded antiparallel beta-sheet, order 213; HTH motif; also includes the extra N-terminal, DNA minor groove-binding helix
1. DNA-binding domain of intron-encoded endonucleases [64496] (1)
  uperfamily
  1. DNA-binding domain of intron-encoded endonucleases [64497] (2)
    1. DNA-binding domain of intron endonuclease I-TevI [64498]
      contains extra N-terminal zinc-finger domain
      1. Bacteriophage T4 [TaxId: 10665] [64499] (2)
        SQ P13299 149-244
    2. Intron-encoded homing endonuclease I-HmuI [110794]
      1. Bacteriophage SP01 [TaxId: 10685] [110795] (1)
        SQ P34081
MotA C-terminal domain-like [69651] (1)
alpha-beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta
1. DNA-binding C-terminal domain of the transcription factor MotA [69652] (1)
  uperfamily
  1. DNA-binding C-terminal domain of the transcription factor MotA [69653] (1)
    1. DNA-binding C-terminal domain of the transcription factor MotA [69654]
      1. Bacteriophage T4 [TaxId: 10665] [69655] (1)
YktB/PF0168-like [142912] (1)
alpha-beta(4)-alpha-beta(2)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order: 1234756; half-barrel shape; topological similarity to the MotA C-terminal domain-like fold (scop_cf 69651) and the Secretion chaperone-like fold (scop_cf 69634)
1. YktB/PF0168-like [142913] (2)
  uperfamily
  1. YktB-like [142914] (1)
    Pfam 06335; DUF1054
    1. Hypothetical protein YktB [142915]
      1. Bacillus subtilis [TaxId: 1423] [142916] (1)
        SQ Q45498 2-211
  2. PF0168-like [142917] (1)
    1. Hypothetical protein PF0168 [142918]
      1. Pyrococcus furiosus [TaxId: 2261] [142919] (1)
        SQ Q8U4C0 2-167
Mago nashi protein [89816] (1)
beta(4)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, order: 651234
1. Mago nashi protein [89817] (1)
  uperfamily
  1. Mago nashi protein [89818] (2)
    1. Mago nashi protein [89819]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89820] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [102750] (6)
WGR domain-like [142920] (1)
beta(4)-alpha-X-beta; 2 layers, a/b; antiparallel beta-sheet, order 51234; the beta-hairpin insetrion in strand 1 results in the formation of a beta-triangle structure
1. WGR domain-like [142921] (1)
  uperfamily
  1. WGR domain [142922] (1)
    Pfam 05406; the conserved WGR motif maps to the C-end of strand 3, both large sidechains are exposed
    1. Poly [ADP-ribose] polymerase-1, PARP-1 [142923]
      1. Human (Homo sapiens) [TaxId: 9606] [142924] (1)
        SQ P09874 517-642
PH1570-like [159901] (1)
duplication: two beta(4)-alpha structural repeats, related by pseudo twofold symmetry; two extra helices in the linker region; single 8-standed antiparallel beta-sheet, order: 12348765
1. PH1570-like [159902] (1)
  1. PH1570-like [159903] (1)
    Pfam 09638
    1. Hypothetical protein PH1570 [159904]
      1. Pyrococcus horikoshii [TaxId: 53953] [159905] (2)
        SQ O59278 1-152
Ribosomal protein S5 domain 2-like [54210] (1)
core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
1. Ribosomal protein S5 domain 2-like [54211] (12)
  uperfamily
  1. Translational machinery components [54212] (8)
    1. Elongation factor G (EF-G), domain IV [54213]
      1. Thermus thermophilus [TaxId: 274] [54214] (9)
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [142925] (2)
        SQ Q5SI76 448-562
        TTHA1498
    2. Elongation factor 2 (eEF-2), domain IV [82575]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82576] (22)
        SQ P32324
    3. Ribosomal protein S5, C-terminal domain [54215]
      1. Bacillus stearothermophilus [TaxId: 1422] [54216] (1)
      2. Thermus thermophilus [TaxId: 274] [54217] (36)
        SQ P27152 ! SQ P80373
      3. Escherichia coli [TaxId: 562] [159906] (24)
        SQ P0A7W1 78-158
    4. Ribosomal protein S9 [54218]
      1. Thermus thermophilus [TaxId: 274] [54219] (39)
        SQ P80374
      2. Escherichia coli [TaxId: 562] [159907] (26)
        SQ P0A7X3 3-129
  2. RNase P protein [54220] (3)
    1. RNase P protein [54221]
      1. Bacillus subtilis [TaxId: 1423] [54222] (1)
      2. Staphylococcus aureus [TaxId: 1280] [54223] (1)
      3. Thermotoga maritima [TaxId: 2336] [89821] (1)
  3. DNA gyrase/MutL, second domain [54224] (7)
    1. DNA mismatch repair protein MutL [54225]
      1. Escherichia coli [TaxId: 562] [54226] (6)
    2. DNA mismatch repair protein PMS2 [69656]
      1. Human (Homo sapiens) [TaxId: 9606] [69657] (3)
    3. DNA gyrase B [54227]
      1. Escherichia coli [TaxId: 562] [54228] (1)
      2. Thermus thermophilus [TaxId: 274] [75352] (1)
    4. DNA topoisomerase II [102751]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102752] (2)
    5. Topoisomerase IV subunit B [102753]
      1. Escherichia coli [TaxId: 562] [102754] (1)
    6. Topoisomerase VI-B subunit [82577]
      contains an H2TH domain inserted in front of this domain and after the N-terminal ATPase domain
      1. Archaeon Sulfolobus shibatae [TaxId: 2286] [82578] (10)
  4. Hsp90 middle domain [102755] (1)
    related to the DNA gyrase/MutL family; contains extra C-terminal alpha/beta subdomain
    1. Heat shock protein hsp82 [102756]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102757] (3)
  5. Ribonuclease PH domain 1-like [54229] (14)
    1. Ribonuclease PH, domain 1 [102758]
      1. Aquifex aeolicus [TaxId: 63363] [102759] (4)
      2. Pseudomonas aeruginosa [TaxId: 287] [102760] (2)
      3. Bacillus subtilis [TaxId: 1423] [102761] (3)
    2. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4 [54230]
      duplication of two-domain units formed by domains 1-2 and 4-5
      1. Streptomyces antibioticus [TaxId: 1890] [54231] (2)
    3. Exosome complex exonuclease RRP42 [159908]
      1. Human (Homo sapiens) [TaxId: 9606] [159909] (1)
        SQ Q15024 5-191
    4. Exosome complex exonuclease RRP46 [159910]
      1. Human (Homo sapiens) [TaxId: 9606] [159911] (1)
        SQ Q9NQT4 25-146
    5. Exosome complex exonuclease RRP45 [159912]
      1. Human (Homo sapiens) [TaxId: 9606] [159913] (1)
        SQ Q86Y41 1-184
    6. Exosome complex exonuclease RRP43 [159914]
      1. Human (Homo sapiens) [TaxId: 9606] [159915] (1)
        SQ Q96B26 7-187
    7. Exosome complex exonuclease MTR3 [159916]
      1. Human (Homo sapiens) [TaxId: 9606] [159917] (1)
        SQ Q5RKV6 29-175
    8. Exosome complex exonuclease RRP41 [159918]
      1. Human (Homo sapiens) [TaxId: 9606] [159919] (1)
        SQ Q9NPD3 7-151
    9. Exosome complex exonuclease 2,ECX2 [159920]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159921] (6)
        SQ O29756 3-178
      2. Sulfolobus solfataricus [TaxId: 2287] [159922] (51)
        SQ Q9UXC0 1-191
    10. Exosome complex exonuclease 1, ECX1 [159923]
      1. Sulfolobus solfataricus [TaxId: 2287] [159924] (50)
        SQ Q9UXC2 8-155
      2. Archaeoglobus fulgidus [TaxId: 2234] [159925] (6)
        SQ O29757 10-153
  6. GHMP Kinase, N-terminal domain [54232] (10)
    1. Galactokinase [102762]
      1. Lactococcus lactis [TaxId: 1358] [102763] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [102764] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [117793] (1)
        SQ P51570
    2. Homoserine kinase [54233]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [54234] (5)
    3. Mevalonate kinase [75353]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75354] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [75355] (2)
    4. Phosphomevalonate kinase (PMK) [75356]
      1. Streptococcus pneumoniae r6 [TaxId: 171101] [75357] (1)
    5. Mevalonate 5-diphosphate decarboxylase [64219]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64220] (1)
    6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89822]
      1. Thermus thermophilus [TaxId: 274] [89823] (1)
      2. Escherichia coli [TaxId: 562] [102765] (1)
  7. Early switch protein XOL-1, N-terminal domain [89824] (1)
    diverged from the GHMP Kinase family; lost the ATP-binding site
    1. Early switch protein XOL-1, N-terminal domain [89825]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89826] (1)
  8. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89827] (1)
    duplication; there are two structural repeats of this fold; each repeat is elaborated with additional structures forming the active site
    1. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC [89828]
      1. Aquifex aeolicus [TaxId: 63363] [89829] (34)
        SQ O67648 3-270
  9. Imidazole glycerol phosphate dehydratase [102766] (3)
    duplication; there are two structural repeats of this fold
    1. Imidazole glycerol phosphate dehydratase [102767]
      1. Fungus (Filobasidiella neoformans) [TaxId: 5207] [102768] (1)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142926] (32)
        SQ P34047 159-255! SQ P34047 73-158
      3. Staphylococcus aureus [TaxId: 1280] [142927] (12)
        SQ P64373 1-84! SQ P64373 85-179
  10. ATP-dependent protease Lon (La), catalytic domain [102769] (2)
    contains extra C-terminal alpha/beta subdomain
    1. ATP-dependent protease Lon (La), catalytic domain [102770]
      1. Escherichia coli [TaxId: 562] [102771] (2)
      2. Methanococcus jannaschii [TaxId: 2190] [117794] (1)
        SQ Q58812 456-640 # MJ1417
  11. YigZ N-terminal domain-like [102772] (2)
    modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand is inserted between strands 3 and 4
    1. Hypothetical protein YigZ, N-terminal domain [102773]
      1. Escherichia coli [TaxId: 562] [102774] (1)
        two-domain structure is similar to the C-terminal region of EF-G (domains IV and V)
    2. Hypothetical protein TTHA1053, N-terminal domain [142928]
      1. Thermus thermophilus [TaxId: 274] [142929] (1)
        SQ Q5SJF5 2-124
  12. Formaldehyde-activating enzyme, FAE [117795] (1)
    modification of the common fold; contains extra alpha-beta unit after strand 2, the extra strand extends beta-sheet antiparallel to strand 3
    1. Formaldehyde-activating enzyme, FAE [117796]
      1. Methylobacterium extorquens [TaxId: 408] [117797] (2)
        SQ Q9FA38
beta-Grasp (ubiquitin-like) [54235] (14)
core: beta(2)-alpha-beta(2); mixed beta-sheet 2143
1. Ubiquitin-like [54236] (8)
  uperfamily
  1. Ubiquitin-related [54237] (47)
    Pfam 00240
    1. Ubiquitin [54238]
      1. Human (Homo sapiens) [TaxId: 9606] [54239] (102)
        SQ P62988
        identical sequence in many other species
      2. Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932] [89830] (7)
      3. Synthetic, based on Saccharomyces cerevisiae sequence [54240] (1)
    2. SUMO-1 (smt3 homologue) [54241]
      1. Human (Homo sapiens) [TaxId: 9606] [54242] (17)
        SQ Q93068
      2. Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932] [54243] (4)
    3. Nedd8 [54244]
      1. Human (Homo sapiens) [TaxId: 9606] [54245] (7)
        SQ Q15843
    4. Elongin B [54246]
      1. Human (Homo sapiens) [TaxId: 9606] [54247] (7)
      2. Mouse (Mus musculus) [TaxId: 10090] [142930] (1)
        SQ P62869 1-98
    5. Rub1 [54248]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [54249] (1)
    6. Ubiquitin-like modifier protein hub1 [82579]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82580] (1)
    7. Ubiquitin-like N-terminal domain of PLIC-2 [75358]
      1. Human (Homo sapiens) [TaxId: 9606] [75359] (1)
    8. Ubiquitin-like domain of parkin [89831]
      1. Human (Homo sapiens) [TaxId: 9606] [89832] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [89833] (2)
    9. Ubiquitin-like domain of Rad23 homolog A (Hhr23a) [102775]
      1. Human (Homo sapiens) [TaxId: 9606] [102776] (4)
    10. Ubiquitin-like domain of Rad23 homolog B (Hhr23B) [102777]
      1. Human (Homo sapiens) [TaxId: 9606] [102778] (2)
        SQ P54727 1-82
    11. Ubiquitin-like protein 5, ubl5 [102779]
      1. Human (Homo sapiens) [TaxId: 9606] [102780] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [102781] (1)
    12. Hypothetical protein At3g01050 [102782]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102783] (1)
    13. Ubiquitin-like protein 3300001g02rik [102784]
      1. Mouse (Mus musculus) [TaxId: 10090] [102785] (1)
    14. Ubiquitin-like domain of tubulin folding cofactor B [102786]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [102787] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [117798] (1)
        SQ Q9D1E6 11-92
    15. 1700011n24rik protein [110796]
      1. Mouse (Mus musculus) [TaxId: 10090] [110797] (1)
        SQ Q9DAF3 1-89
    16. 8430435i17rik protein [110798]
      1. Mouse (Mus musculus) [TaxId: 10090] [110799] (1)
        SQ Q8BGR9 3-79
    17. hypothetical D7wsu128e protein [110800]
      1. Mouse (Mus musculus) [TaxId: 10090] [110801] (1)
        SQ Q78JW9 76-157
    18. Splicing factor 3 subunit 1, C-terminal domain [117799]
      1. Mouse (Mus musculus) [TaxId: 10090] [117800] (1)
        SQ Q8K4Z5 685-786
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117801] (1)
        SQ Q8RXF1 683-780; T5E21.13/At1g14650
      3. Human (Homo sapiens) [TaxId: 9606] [142931] (1)
        SQ Q15459 704-789
    19. Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 [117802]
      1. Human (Homo sapiens) [TaxId: 9606] [117803] (1)
        SQ Q15011 10-90
    20. Ubiquitin carboxyl-terminal hydrolase 14 [117804]
      1. Mouse (Mus musculus) [TaxId: 10090] [117805] (1)
        SQ Q9JMA1 3-85
    21. Ubiquitin-like protein 3, Ubl3 [117806]
      1. Mouse (Mus musculus) [TaxId: 10090] [117807] (1)
        SQ Q9Z2M6 1-103
    22. 2'-5'-oligoadenylate synthetase-like protein, OASL [117808]
      1. Human (Homo sapiens) [TaxId: 9606] [117809] (1)
        SQ Q15646 434-507
    23. Ubiquitin-like protein bab25500 (2010008E23Rik) [117810]
      1. Mouse (Mus musculus) [TaxId: 10090] [117811] (1)
        SQ Q9D8C5 163-244
    24. Tubulin-folding protein TbcE [117812]
      1. Mouse (Mus musculus) [TaxId: 10090] [117813] (1)
        SQ Q8CIV8 441-524
    25. NEDD8 ultimate buster-1, NUB1 [117814]
      1. Human (Homo sapiens) [TaxId: 9606] [117815] (1)
        SQ Q9Y5A7 75-161
    26. SUMO-2 [117816]
      1. Human (Homo sapiens) [TaxId: 9606] [117817] (13)
        SQ P61956
    27. Bag-family molecular chaperone regulator-1 [142932]
      1. Human (Homo sapiens) [TaxId: 9606] [142933] (1)
        SQ Q99933 72-152
        the BAG domain structure is also known (scop_sp 63494)
    28. NPL4-like protein 1 [142934]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142935] (1)
        SQ Q9LYC2 2-95
    29. Interferon-induced 15 kDa protein [142936]
      1. Human (Homo sapiens) [TaxId: 9606] [142937] (2)
        SQ P05161 2-77! SQ P05161 78-153
    30. Ubiquitin-like protein smt3a, SUMO-3 [142938]
      1. Human (Homo sapiens) [TaxId: 9606] [142939] (1)
        SQ P55854 14-92
    31. DSK2 [142940]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [142941] (5)
        SQ P48510 2-74
    32. Ubiquitin-like protein 7 [142942]
      1. Mouse (Mus musculus) [TaxId: 10090] [142943] (1)
        SQ Q91W67 1-94
    33. Ubiquitin-like PHD and RING finger domain-containing protein 2 [142944]
      1. Human (Homo sapiens) [TaxId: 9606] [142945] (1)
        SQ Q96PU4 1-76
    34. Ubiquilin-3 [142946]
      1. Human (Homo sapiens) [TaxId: 9606] [142947] (2)
        SQ Q9H347 11-104! SQ Q9H347 15-98
    35. Ubiquitin-like PHD and RING finger domain-containing protein 1 [142948]
      1. Human (Homo sapiens) [TaxId: 9606] [142949] (2)
        SQ Q96T88 1-76
    36. 4931431F19Rik [142950]
      1. Mouse (Mus musculus) [TaxId: 10090] [142951] (1)
        SQ Q9D4I8 14-96
        structure of the C-terminal UBA domain is also known (PDB 1vej)
    37. Large proline-rich protein BAT3 [142952]
      1. Human (Homo sapiens) [TaxId: 9606] [142953] (1)
        SQ P46379 17-89
    38. Dendritic cell-derived ubiquitin-like protein [142954]
      1. Human (Homo sapiens) [TaxId: 9606] [142955] (1)
        SQ Q8WUN7 149-228
  2. UBX domain [54250] (5)
    Pfam 00789
    1. Fas-associated factor 1, Faf1 [54251]
      1. Human (Homo sapiens) [TaxId: 9606] [54252] (1)
    2. p47 [64221]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [64222] (3)
    3. Hypothetical protein KIAA0794 [117818]
      1. Human (Homo sapiens) [TaxId: 9606] [117819] (1)
        SQ O94888 376-487
    4. UBX domain-containing protein 6 (Reproduction 8) [142956]
      1. Mouse (Mus musculus) [TaxId: 10090] [142957] (1)
        SQ Q9QZ49 182-277
    5. Tether containing UBX domain for GLUT4 (Tug) [142958]
      1. Mouse (Mus musculus) [TaxId: 10090] [142959] (1)
        SQ Q8VBT9 10-85
  3. GABARAP-like [54253] (5)
    intracellular membrane trafficking and fusion proteins
    1. Golgi-associated ATPase enhancer of 16 kD, Gate-16 [54254]
      1. Cow (Bos taurus) [TaxId: 9913] [54255] (1)
    2. GABA(A) receptor associated protein GABARAP [69658]
      1. Human (Homo sapiens) [TaxId: 9606] [69659] (6)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [75360] (1)
    3. Microtubule-associated proteins 1A/1B light chain 3B [110802]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110803] (4)
        SQ Q62625 4-116
      2. Human (Homo sapiens) [TaxId: 9606] [117820] (3)
        SQ Q9GZQ8
  4. First domain of FERM [54256] (7)
    1. Moesin [54257]
      1. Human (Homo sapiens) [TaxId: 9606] [54258] (3)
        SQ P26038 4-297
    2. Radixin [54259]
      1. Mouse (Mus musculus) [TaxId: 10090] [54260] (20)
    3. Ezrin [82581]
      1. Human (Homo sapiens) [TaxId: 9606] [82582] (1)
    4. Erythroid membrane protein 4.1R [54261]
      1. Human (Homo sapiens) [TaxId: 9606] [54262] (1)
    5. Merlin [69660]
      the neurofibromatosis 2 tumor suppressor protein
      1. Human (Homo sapiens) [TaxId: 9606] [69661] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [75361] (1)
    6. Focal adhesion kinase 1 [142960]
      1. Chicken (Gallus gallus) [TaxId: 9031] [142961] (5)
        SQ Q00944 31-130
  5. Ras-binding domain, RBD [54263] (16)
    contains Pfam 00788 and Pfam 02196
    1. c-Raf1 RBD [54264]
      1. Human (Homo sapiens) [TaxId: 9606] [54265] (3)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [54266] (1)
    2. Ral guanosine-nucleotide exchange factor, RalGDS [54267]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [54268] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [54269] (3)
    3. RalGDS-like factor, Rlf [54270]
      1. Mouse (Mus musculus) [TaxId: 10090] [54271] (1)
    4. Rgl [54272]
      1. Mouse (Mus musculus) [TaxId: 10090] [54273] (1)
    5. Phoshoinositide 3-kinase (PI3K) [54274]
      includes parts of the flanking linkers
      1. Pig (Sus scrofa) [TaxId: 9823] [54275] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [54276] (3)
    6. Protein kinase byr2 [69662]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [69663] (2)
    7. Regulator of G-protein signaling 14, RGS14 [117821]
      1. Mouse (Mus musculus) [TaxId: 10090] [117822] (1)
        SQ P97492 366-456
    8. Growth factor receptor-bound protein 7, GRB-7 [117823]
      1. Human (Homo sapiens) [TaxId: 9606] [117824] (1)
        SQ Q14451 100-186
    9. Rap guanine nucleotide exchange factor 5, RapGEF5 [117825]
      1. Human (Homo sapiens) [TaxId: 9606] [117826] (1)
        SQ Q92565 241-331
    10. Ras association domain-containing protein 8 [142962]
      1. Human (Homo sapiens) [TaxId: 9606] [142963] (1)
        SQ Q8NHQ8 1-83
    11. Afadin [142964]
      1. Mouse (Mus musculus) [TaxId: 10090] [142965] (1)
        SQ Q9QZQ1 246-348
        The FHA domain structure is also known (PDB 1wln)
    12. Phospholipase C-epsilon-1 [142966]
      contains several Ras-binding domains; some are 'hidden' in the sequence
      1. Human (Homo sapiens) [TaxId: 9606] [142967] (4)
        SQ Q9P212 2006-2114! SQ Q9P212 2131-2246! SQ Q9P212 2134-2239
    13. A-Raf proto-oncogene serine/threonine-protein kinase [142968]
      1. Human (Homo sapiens) [TaxId: 9606] [142969] (1)
        SQ P10398 19-91
  6. BM-002-like [75362] (3)
    Pfam 03671; UPF0185; this family comprises small uncharacterized proteins including human protein BM-002
    1. Hypothetical protein zk652.3 [75363]
      1. Caenorhabditis elegans [TaxId: 6239] [75364] (1)
    2. Hypothetical protein 1810045k17 [102788]
      1. Mouse (Mus musculus) [TaxId: 10090] [102789] (1)
    3. Ubiquitin-fold modifier 1 [142970]
      1. Human (Homo sapiens) [TaxId: 9606] [142971] (1)
        SQ P61960 1-83
  7. APG12-like [142972] (1)
    Pfam 04110
    1. Autophagy-related protein 12b (APG12b) [142973]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [142974] (2)
        SQ Q9LVK3 10-93
  8. DIX domain [159926] (1)
    Pfam 00778
    1. Axin 1 [159927]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [159928] (9)
        SQ O70239 745-827
2. CAD & PB1 domains [54277] (2)
  contain extra helix; similar heterodimerization modes; possibly related to the ubiquitin-like superfamily
  uperfamily
  1. CAD domain [54278] (5)
    1. Cell death-inducing effector B (CIDE-B), N-terminal domain [54279]
      1. Human (Homo sapiens) [TaxId: 9606] [54280] (1)
    2. Caspase-activated DNase (CAD), DFF40, N-terminal domain [54281]
      1. Mouse (Mus musculus) [TaxId: 10090] [54282] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [64223] (1)
    3. Inhibitor of caspase-activated DNase (ICAD), DFF45, N-terminal domain [54283]
      1. Mouse (Mus musculus) [TaxId: 10090] [54284] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [64224] (1)
  2. PB1 domain [64225] (11)
    Pfam 00564
    forms heterodimers, although not all PB1 domain pairs associate.
    1. Neutrophil cytosol factor 2 (p67phox component of NADPH oxidase) [102790]
      1. Human (Homo sapiens) [TaxId: 9606] [102791] (1)
    2. Neutrophil cytosol factor 4 (p40phox component of NADPH oxidase) [102792]
      1. Human (Homo sapiens) [TaxId: 9606] [102793] (1)
    3. Bud emergence mediator Bemp1 [64226]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64227] (2)
    4. Cell division control protein 24, CDC24, C-terminal domain [89834]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89835] (3)
    5. Protein kinase C, iota type [110804]
      1. Human (Homo sapiens) [TaxId: 9606] [110805] (2)
        SQ P41743 16-98 ! SQ P41743 16-99
    6. Mitogen activated protein kinase kinase 5, Map2k5 [117827]
      1. Mouse (Mus musculus) [TaxId: 10090] [117828] (1)
        SQ Q9D222 7-107
      2. Human (Homo sapiens) [TaxId: 9606] [142975] (2)
        SQ Q13163 4-108
    7. Next to BRCA1 gene 1 protein, NBR1 (KIAA0049) [117829]
      1. Human (Homo sapiens) [TaxId: 9606] [117830] (2)
        SQ Q14596 1-85
    8. Partitioning defective-6 homolog alpha, PAR-6 alpha [117831]
      1. Human (Homo sapiens) [TaxId: 9606] [117832] (1)
        SQ Q9NPB6 14-95
    9. Mitogen-activated protein kinase kinase kinase 2, MEKK 2 [142976]
      1. Human (Homo sapiens) [TaxId: 9606] [142977] (3)
        SQ Q9Y2U5 42-123! SQ Q9Y2U5 43-132
    10. Mitogen-activated protein kinase kinase kinase 3, MEKK 3 [142978]
      1. Human (Homo sapiens) [TaxId: 9606] [142979] (2)
        SQ Q99759 42-123! SQ Q99759 43-122
3. MoaD/ThiS [54285] (4)
  possible link between the ubiquitin-like and 2Fe-2S ferredoxin-like superfamilies
  uperfamily
  1. MoaD [54286] (3)
    1. Molybdopterin synthase subunit MoaD [54287]
      1. Escherichia coli [TaxId: 562] [54288] (7)
      2. Pyrococcus furiosus [TaxId: 2261] [110806] (1)
        SQ Q8U3C7
    2. MoaD-related protein, N-terminal domain [102794]
      1. Thermus thermophilus [TaxId: 274] [102795] (1)
  2. ThiS [54289] (5)
    1. Thiamin biosynthesis sulfur carrier protein ThiS [54290]
      1. Escherichia coli [TaxId: 562] [54291] (3)
      2. Bacillus subtilis [TaxId: 1423] [110807] (1)
        SQ O31617
    2. Hypothetical protein MTH1743 [69664]
      probable ThiS homologue
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69665] (1)
    3. Hypothetical protein PF1061 [102796]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [102797] (2)
    4. Uncharacterised protein TTHA0675 [159929]
      probable ThiS homologue
      1. Thermus thermophilus [TaxId: 274] [159930] (6)
        SQ Q5SKG8 1-63
  3. C9orf74 homolog [117833] (1)
    1. C9orf74 homolog [117834]
      1. Mouse (Mus musculus) [TaxId: 10090] [117835] (2)
        SQ Q9D2P4 #
  4. HI0395-like [159931] (1)
    Pfam 03658; UPF0125
    1. Hypothetical protein HI0395 [159932]
      NTHI0516
      1. Haemophilus influenzae [TaxId: 727] [159933] (2)
        SQ Q4QNE7 2-78
4. TGS-like [81271] (2)
  possibly related to the ubiquitin-like and MoaD/ThiS superfamilies; some similarity to the alpha-L RNA-binding motif
  uperfamily
  1. TGS domain [81270] (2)
    1. Threonyl-tRNA synthetase (ThrRS), N-terminal 'additional' domain [55176]
      1. Escherichia coli [TaxId: 562] [55177] (5)
        SQ P0A8M3
      2. Staphylococcus aureus [TaxId: 1280] [102798] (2)
  2. G domain-linked domain [82583] (3)
    1. YchF GTP-binding protein, C-terminal domain [82584]
      N-terminal domain belongs to the Obg family of GTPases some members of which contain a C-terminal TGS domain
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82585] (1)
      2. Haemophilus influenzae [TaxId: 727] [89836] (1)
        HI0393
    2. GTP-binding protein PH0525 [142980]
      1. Pyrococcus horikoshii [TaxId: 53953] [142981] (1)
        SQ O58261 320-395
5. 2Fe-2S ferredoxin-like [54292] (2)
  uperfamily
  1. 2Fe-2S ferredoxin-related [54293] (19)
    1. 2Fe-2S ferredoxin [54294]
      1. Cyanobacterium (Anabaena sp.), pcc 7119 and 7120 [TaxId: 1167] [54295] (12)
      2. Spirulina platensis [TaxId: 118562] [54296] (1)
      3. Cyanobacterium (Aphanothece sacrum) [TaxId: 1122] [54297] (1)
      4. Synechocystis sp., pcc 6803 [TaxId: 1143] [54298] (3)
      5. Synechococcus elongatus [TaxId: 32046] [54299] (3)
      6. Chlorella fusca [TaxId: 3073] [54300] (1)
      7. Equisetum arvense [TaxId: 3258] [54301] (2)
        SQ P00237 # isoform II
      8. Archaeon Haloarcula marismortui [TaxId: 2238] [54302] (1)
      9. Archaeon Halobacterium halobium [TaxId: 2242] [64228] (2)
      10. Parsley (Petroselinum crispum) [TaxId: 4043] [54303] (1)
      11. Spinach (Spinacia oleracea) [TaxId: 3562] [54304] (1)
      12. Maize (Zea mays) [TaxId: 4577] [54305] (1)
      13. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [102799] (1)
      14. Trichomonas vaginalis [TaxId: 5722] [75365] (1)
      15. Rhodobacter capsulatus, ferredoxin VI [TaxId: 1061] [64230] (2)
      16. Pseudomonas putida, putidaredoxin [TaxId: 303] [54307] (18)
      17. Pseudomonas sp., terpredoxin [TaxId: 306] [54309] (1)
    2. Adrenodoxin-like ferredoxin [75366]
      1. Escherichia coli [TaxId: 562] [75367] (1)
    3. Adrenodoxin [54310]
      1. Cow (Bos taurus) [TaxId: 9913] [54311] (7)
  2. 2Fe-2S ferredoxin domains from multidomain proteins [54312] (16)
    1. Fe-only hydrogenase, N-terminal domain [54313]
      1. Clostridium pasteurianum [TaxId: 1501] [54314] (4)
    2. Aldehyde oxidoreductase, N-terminal domain [54315]
      1. Desulfovibrio gigas [TaxId: 879] [54316] (3)
        SQ Q46509
      2. Desulfovibrio desulfuricans [TaxId: 876] [54317] (1)
    3. Xanthine oxidase, N-terminal domain [54318]
      1. Cow (Bos taurus) [TaxId: 9913] [54319] (7)
        SQ P80457
    4. Xanthine dehydrogenase chain A, N-terminal domain [69666]
      1. Rhodobacter capsulatus [TaxId: 1061] [69667] (2)
    5. Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain [54320]
      1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [54321] (5)
      2. Hydrogenophaga pseudoflava [TaxId: 47421] [54322] (4)
    6. Phthalate dioxygenase reductase, C-terminal domain [54323]
      two other domains are common to ferredoxin reductase
      1. Pseudomonas cepacia, db01 [TaxId: 292] [54324] (1)
    7. Benzoate dioxygenase reductase, N-terminal domain [75368]
      1. Acinetobacter sp. [TaxId: 472] [75369] (1)
    8. Succinate dehydogenase iron-sulfur protein, N-terminal domain [82586]
      1. Escherichia coli [TaxId: 562] [82587] (3)
    9. Fumarate reductase iron-sulfur protein, N-terminal domain [54325]
      1. Escherichia coli [TaxId: 562] [54326] (7)
      2. Wolinella succinogenes [TaxId: 844] [54327] (8)
    10. Methane monooxygenase reductase N-terminal domain [69668]
      1. Methylococcus capsulatus [TaxId: 414] [69669] (1)
    11. Quinoline 2-oxidoreductase small subunit QorS, N-domain [110808]
      1. Pseudomonas putida [TaxId: 303] [110809] (1)
        SQ P72223
    12. 4-hydroxybenzoyl-CoA reductase gamma subunit HrcC, N-terminal domain [117836]
      1. Thauera aromatica [TaxId: 59405] [117837] (2)
        SQ O33818
    13. Nadh-quinone oxidoreductase chain 3, Nqo3, N-terminal domain [142982]
      1. Thermus thermophilus [TaxId: 274] [142983] (4)
        SQ Q56223 1-95
6. Staphylokinase/streptokinase [54328] (1)
  uperfamily
  1. Staphylokinase/streptokinase [54329] (2)
    1. Staphylokinase [54330]
      1. Staphylococcus aureus [TaxId: 1280] [54331] (7)
        phage-borne; Bacteriophage 42D
    2. Streptokinase [54332]
      duplication: consists of three similar domains
      1. Streptococcus equisimilis [TaxId: 119602] [54333] (5)
7. Doublecortin (DC) [89837] (1)
  possibly related to the ubiquitin-like superfamily
  uperfamily
  1. Doublecortin (DC) [89838] (2)
    1. Doublecortin-like kinase Dclk [89839]
      KIAA0369; duplication: contains tandem repeat of two DC domains
      1. Human (Homo sapiens) [TaxId: 9606] [89840] (3)
    2. Doublecortin [89841]
      duplication: contains tandem repeat of two DC domains
      1. Human (Homo sapiens) [TaxId: 9606] [89842] (1)
8. Superantigen toxins, C-terminal domain [54334] (1)
  uperfamily
  1. Superantigen toxins, C-terminal domain [54335] (15)
    1. Staphylococcal enterotoxin A, SEA [54336]
      1. Staphylococcus aureus [TaxId: 1280] [54337] (6)
    2. Staphylococcal enterotoxin C2, SEC2 [54338]
      1. Staphylococcus aureus [TaxId: 1280] [54339] (8)
    3. Toxic shock syndrome toxin-1 (TSST-1) [54340]
      1. Staphylococcus aureus [TaxId: 1280] [54341] (13)
    4. Staphylococcal enterotoxin B, SEB [54342]
      1. Staphylococcus aureus [TaxId: 1280] [54343] (12)
    5. Staphylococcal enterotoxin C3, SEC3 [54344]
      1. Staphylococcus aureus [TaxId: 1280] [54345] (11)
        SQ P23313
    6. Staphylococcal enterotoxin H, SEH [54346]
      1. Staphylococcus aureus [TaxId: 1280] [54347] (4)
    7. Superantigen-like protein SET3 [75370]
      1. Staphylococcus aureus [TaxId: 1280] [75371] (3)
    8. Streptococcal superantigen Spe-C [54348]
      1. Streptococcus pyogenes [TaxId: 1314] [54349] (3)
    9. Streptococcal superantigen Spe-H [54350]
      1. Streptococcus pyogenes [TaxId: 1314] [54351] (2)
    10. Streptococcal superantigen Smez-2 [54352]
      1. Streptococcus pyogenes [TaxId: 1314] [54353] (2)
    11. Streptococcal superantigen SSA [54354]
      1. Streptococcus pyogenes [TaxId: 1314] [54355] (10)
    12. Streptococcal pyrogenic exotoxin A1 [54356]
      1. Streptococcus pyogenes [TaxId: 1314] [54357] (8)
        SQ P08095
    13. Exotoxin 1 (SET1, Superantigen-like protein 7) [110810]
      1. Staphylococcus aureus [TaxId: 1280] [110811] (2)
        SQ Q9ZFS5 36-231
    14. Streptococcal pyrogenic exotoxin Spe-J [110812]
      1. Streptococcus pyogenes [TaxId: 1314] [110813] (2)
        SQ Q7BAE3
    15. Enterotoxin type I [159934]
      1. Staphylococcus aureus [TaxId: 1280] [159935] (1)
        SQ Q52T95 87-216
9. Immunoglobulin-binding domains [54358] (1)
  uperfamily
  1. Immunoglobulin-binding domains [54359] (2)
    1. Immunoglobulin-binding protein G, different constituent domains [54360]
      1. Streptococcus sp., group G [TaxId: 1306] [54361] (30)
    2. Immunoglobulin light chain-binding domain of protein L [54362]
      1. Peptostreptococcus magnus [TaxId: 1260] [54363] (12)
10. Translation initiation factor IF3, N-terminal domain [54364] (1)
  uperfamily
  1. Translation initiation factor IF3, N-terminal domain [54365] (1)
    1. Translation initiation factor IF3, N-terminal domain [54366]
      1. Bacillus stearothermophilus [TaxId: 1422] [54367] (1)
11. Glutamine synthetase, N-terminal domain [54368] (1)
  uperfamily
  1. Glutamine synthetase, N-terminal domain [54369] (2)
    1. Glutamine synthetase, N-terminal domain [54370]
      1. Salmonella typhimurium [TaxId: 90371] [54371] (18)
      2. Mycobacterium tuberculosis [TaxId: 1773] [75372] (8)
12. TmoB-like [110814] (1)
  possibly related to the ubiquitin-like and/or 2Fe-2S ferredoxin-like superfamilies
  uperfamily
  1. TmoB-like [110815] (1)
    Pfam 06234
    1. Toluene, o-xylene monooxygenase oxygenase subunit TouB [110816]
      1. Pseudomonas stutzeri [TaxId: 316] [110817] (6)
        SQ O87799
13. Nqo1 middle domain-like [142984] (1)
  possibly evolved from 2Fe-2S ferredoxins; contains no iron-sulfur cluster
  uperfamily
  1. Nqo1 middle domain-like [142985] (1)
    C-terminal part of Pfam 01512
    1. NADH-quinone oxidoreductase chain 1, Nqo1 [142986]
      1. Thermus thermophilus [TaxId: 274] [142987] (4)
        SQ Q56222 250-333
14. NSP3A-like [159936] (1)
  short helical inserions in the common fold
  1. NSP3A-like [159937] (1)
    1. Nsp3 [159938]
      1. SARS coronavirus [TaxId: 227859] [159939] (2)
        SQ P59641 819-930
MM3350-like [159940] (1)
beta(2)-alpha-beta(4); antiparallel beta-sheet; order: 216534; similar to a ubiquitin-like fold with the extra C-terminal strand inserted in the middle of the beta-sheet
1. MM3350-like [159941] (1)
  1. MM3350-like [159942] (1)
    Pfam07929; plasmid pRiA4b ORF-3-like protein
    1. Hypothetical protein MM3350 [159943]
      1. Methanosarcina mazei [TaxId: 2209] [159944] (2)
        SQ Q8PRU3 4-188
WWE domain [117838] (1)
beta(2)-alpha-beta(4); antiparallel folded beta-sheet (half-barrel), order 216543
1. WWE domain [117839] (1)
  uperfamily
  1. WWE domain [117840] (2)
    Pfam 02825
    1. RING finger protein 146 (Dactylidin) [117841]
      1. Mouse (Mus musculus) [TaxId: 10090] [117842] (1)
        SQ Q9CZW6 83-179
    2. Deltex (Dx) [159945]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [159946] (2)
        SQ Q23985 132-211! SQ Q23985 43-131
FAD-linked reductases, C-terminal domain [54372] (1)
alpha+beta sandwich
1. FAD-linked reductases, C-terminal domain [54373] (7)
  N-terminal domain is beta/beta/alpha common fold
  uperfamily
  1. GMC oxidoreductases [54374] (8)
    1. Cholesterol oxidase [54375]
      1. Brevibacterium sterolicum [TaxId: 1702] [54376] (2)
      2. Streptomyces sp. [TaxId: 1931] [54377] (13)
      3. Streptomyces sp. (strain SA-COO) (Streptomyces sp. SA-COO) [TaxId: 74576] [159947] (1)
    2. Glucose oxidase [54391]
      1. Aspergillus niger [TaxId: 5061] [54392] (2)
      2. Penicillium amagasakiense [TaxId: 63559] [54393] (1)
    3. Hydroxynitrile lyase [82588]
      1. Almond (Prunus dulcis) [TaxId: 3755] [82589] (1)
    4. Flavoprotein domain of flavocytochrome cellobiose dehydrogenase (CDH), substrate-binding domain [82590]
      1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [82591] (2)
    5. Pyranose 2-oxidase [117843]
      1. White-rot fungus (Peniophora sp. SG) [TaxId: 204723] [117844] (19)
        SQ Q8J136 43-619
  2. PHBH-like [54378] (5)
    1. p-Hydroxybenzoate hydroxylase (PHBH) [54379]
      1. Pseudomonas fluorescens [TaxId: 294] [54380] (17)
      2. Pseudomonas aeruginosa [TaxId: 287] [54381] (19)
    2. Phenol hydroxylase [54382]
      structurally very similar to PHBH, but contains additional C-terminal domain of the thioredoxin-like fold
      1. Soil-living yeast (Trichosporon cutaneum) [TaxId: 5554] [54383] (2)
    3. Monooxygenase PhzS [159948]
      1. Pseudomonas aeruginosa [TaxId: 287] [159949] (1)
        SQ Q9HWG9 183-293
    4. Dihydroxypyridine hydroxylase DhpH [159950]
      1. Arthrobacter nicotinovorans [TaxId: 29320] [159951] (3)
        SQ Q93NG3 164-201
  3. D-aminoacid oxidase-like [54384] (4)
    1. D-aminoacid oxidase [54385]
      1. Pig (Sus scrofa) [TaxId: 9823] [54386] (6)
      2. Rhodotorula gracilis [TaxId: 5286] [54387] (4)
    2. Sarcosine oxidase [54388]
      1. Bacillus sp., strain b0618 [TaxId: 1409] [54389] (18)
    3. Glycine oxidase ThiO [89843]
      1. Bacillus sp. [TaxId: 1409] [89844] (6)
  4. UDP-galactopyranose mutase [69670] (2)
    1. UDP-galactopyranose mutase [69671]
      1. Escherichia coli [TaxId: 562] [69672] (1)
      2. Klebsiella pneumoniae [TaxId: 573] [117845] (3)
        SQ Q48485
  5. L-aminoacid/polyamine oxidase [54394] (9)
    1. Polyamine oxidase [54395]
      1. Maize (Zea mays) [TaxId: 4577] [54396] (7)
    2. L-aminoacid oxidase [54397]
      1. Malayan pit viper (Calloselasma rhodostoma) [TaxId: 8717] [54398] (6)
      2. Halys viper (Agkistrodon halys) [TaxId: 8714] [102800] (4)
        SQ Q90W54 21-504
    3. Monoamine oxidase B [69673]
      1. Human (Homo sapiens) [TaxId: 9606] [69674] (20)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [102801] (27)
    4. N,N-dimethylglycine oxidase [102802]
      1. Arthrobacter globiformis [TaxId: 1665] [102803] (3)
    5. Protoporphyrinogen oxidase [102804]
      1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [102805] (1)
      2. Myxococcus xanthus [TaxId: 34] [159952] (4)
        SQ P56601 307-414
    6. Lysine-specific histone demethylase 1, LSD1 [159953]
      1. Human (Homo sapiens) [TaxId: 9606] [159954] (8)
        SQ O60341 655-763
  6. GDI-like [54399] (3)
    Similar to FAD-linked reductases in both domains but does not bind FAD
    1. Guanine nucleotide dissociation inhibitor, GDI [54400]
      1. Cow (Bos taurus) [TaxId: 9913] [54401] (3)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110818] (7)
        SQ P39958 5-446
    2. Rab escort protein 1 [89845]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89846] (3)
        SQ P37727
  7. Electron transfer flavoprotein-ubiquinone oxidoreductase-like [142988] (1)
    1. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [142989]
      1. Pig (Sus scrofa) [TaxId: 9823] [142990] (4)
        SQ P55931 260-358
Cystatin-like [54402] (7)
Core: alpha-beta(4); helix packs against coiled antiparallel beta-sheet
1. Cystatin/monellin [54403] (6)
  has a additional strand at the N-terminus
  uperfamily
  1. Monellin [54404] (1)
    1. Monellin, B & A chains together [54405]
      1. Serendipity berry (Dioscoreophyllum cumminsii) [TaxId: 3457] [54406] (12)
  2. Cystatins [54407] (6)
    1. Phytocystatin [54408]
      1. Japanese rice (Oryza sativa), subsp. japonica, oryzacystatin-I [TaxId: 4530] [54409] (1)
    2. Cystatin [54410]
      1. Chicken (Gallus gallus) [TaxId: 9031] [54411] (4)
    3. Cystatin A (stefin A) [54412]
      1. Human (Homo sapiens) [TaxId: 9606] [54413] (9)
    4. Cystatin B (stefin B) [54414]
      1. Human (Homo sapiens) [TaxId: 9606] [54415] (1)
    5. Cystatin C [64231]
      1. Human (Homo sapiens) [TaxId: 9606] [64232] (4)
        SQ P01034 37-146
    6. Cystatin D [110819]
      1. Human (Homo sapiens) [TaxId: 9606] [110820] (2)
        SQ P28325 31-142
  3. Cathelicidin motif [82592] (1)
    cathelin-like domain
    1. Cathelicidin motif of protegrin-3 [82593]
      antimicrobial protein
      1. Pig (Sus scrofa) [TaxId: 9823] [82594] (5)
  4. Staphopain B, prodomain [117846] (1)
    1. Staphopain B, prodomain [117847]
      includes additional beta-sheet subdomain, connecting the N-terminal cystatin-like domain to the catalytic domain/mature enzyme
      1. Staphylococcus aureus [TaxId: 1280] [117848] (1)
        SQ Q70UQ9 41-393
  5. Latexin-like [142991] (1)
    Pfam 06907; duplication: consits of two domains of this fold
    1. Latexin [142992]
      1. Human (Homo sapiens) [TaxId: 9606] [142993] (4)
        SQ Q9BS40 1-98! SQ Q9BS40 99-217
  6. PepSY-like [159955] (1)
    Pfam 03413; Peptidase propeptide and YPEB domain
    1. Uncharacterized protein YpmB [159956]
      duplication; consist of two similar domains
      1. Bacillus subtilis [TaxId: 1423] [159957] (2)
        SQ P54396 34-98! SQ P54396 99-161
2. Amine oxidase N-terminal region [54416] (1)
  uperfamily
  1. Amine oxidase N-terminal region [54417] (5)
    duplication: contains two domains of this fold
    1. Copper amine oxidase, domains 1 and 2 [54418]
      1. Escherichia coli [TaxId: 562] [54419] (11)
      2. Pea seedling (Pisum sativum) [TaxId: 3888] [54420] (2)
        SQ Q43077
      3. Arthrobacter globiformis [TaxId: 1665] [54421] (91)
        SQ P46881 9-628
      4. Yeast (Hansenula polymorpha) [TaxId: 4905] [54422] (26)
    2. Lysyl oxidase PplO, domains 1 and 2 [102806]
      1. Yeast (Pichia pastoris) [TaxId: 4922] [102807] (4)
        SQ Q96X16 43-777
3. DsbC/DsbG N-terminal domain-like [54423] (1)
  uperfamily
  1. DsbC/DsbG N-terminal domain-like [54424] (3)
    1. Disulfide bond isomerase, DsbC, N-terminal domain [54425]
      1. Escherichia coli [TaxId: 562] [54426] (7)
        SQ P21892
      2. Haemophilus influenzae [TaxId: 727] [110821] (1)
        SQ P45111 20-228
    2. Thiol:disulfide interchange protein DsbG, N-terminal domain [110822]
      1. Escherichia coli [TaxId: 562] [110823] (10)
        SQ P77202
4. NTF2-like [54427] (30)
  has a beta-alpha(2)-beta insertion after the main helix
  uperfamily
  1. Scytalone dehydratase [54428] (1)
    1. Scytalone dehydratase [54429]
      1. Fungus (Magnaporthe grisea) [TaxId: 148305] [54430] (8)
  2. NTF2-like [54431] (11)
    1. Nuclear transport factor-2 (NTF2) [54432]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [54433] (10)
        SQ P61972
      2. Human (Homo sapiens) [TaxId: 9606] [75373] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75374] (2)
      4. Cryptosporidium parvum [TaxId: 5807] [159958] (2)
        SQ Q5CQI4 4-127
    2. NTF2-related export protein 1 (p15) [69675]
      1. Human (Homo sapiens) [TaxId: 9606] [69676] (2)
    3. NTF2-like domain of Tip associating protein, TAP [69677]
      1. Human (Homo sapiens) [TaxId: 9606] [69678] (2)
    4. NTF2-like domain of mRNA export factor MEX67 [89847]
      similar to the TAP domain; forms complex with MTR2 similar to the TAP-p15 complex
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89848] (1)
        Ypl169C
      2. Yeast (Candida albicans) [TaxId: 5476] [102808] (1)
    5. mRNA transport regulator MTR2 [89849]
      similar to p15; forms complex with MEX67 similar to the TAP-p15 complex
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89850] (1)
        Ykl186C
      2. Yeast (Candida albicans) [TaxId: 5476] [102809] (2)
    6. UBP3-associated protein BRE5 [159959]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159960] (4)
        SQ P53741 1-141
  3. Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A [89851] (3)
    1. Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A [89852]
      1. Mouse (Mus musculus) [TaxId: 10090] [89853] (1)
      2. Caenorhabditis elegans [TaxId: 6239] [159961] (7)
        SQ Q9U6Q0 343-471
      3. Human (Homo sapiens) [TaxId: 9606] [159962] (6)
        SQ Q8N4I3 387-521
  4. Limonene-1,2-epoxide hydrolase-like [89854] (2)
    1. Limonene-1,2-epoxide hydrolase [89855]
      1. Rhodococcus erythropolis [TaxId: 1833] [89856] (2)
    2. Uncharacterized protein Mb2760 [159963]
      1. Mycobacterium tuberculosis [TaxId: 1773] [159964] (3)
        SQ Q7TY00 13-144
  5. SnoaL-like polyketide cyclase [102810] (5)
    1. Nogalonic acid methyl ester cyclase SnoaL [102811]
      1. Streptomyces nogalater [TaxId: 38314] [102812] (1)
    2. Aklanonic acid methyl ester cyclase, AknH [159965]
      1. Streptomyces galilaeus [TaxId: 33899] [159966] (8)
        SQ O52646 2-141
    3. Nogalamycin biosynthesis protein SnoL [159967]
      1. Streptomyces nogalater [TaxId: 38314] [159968] (2)
        SQ Q9RN64 2-139
    4. Putative hydroxylase AclR [159969]
      1. Streptomyces galilaeus [TaxId: 33899] [159970] (2)
        SQ Q1XDX7 2-145
    5. Uncharacterized protein BPSS0132 [159971]
      1. Burkholderia pseudomallei [TaxId: 28450] [159972] (1)
        SQ Q63P16 1-131
  6. PhzA/PhzB-like [102813] (4)
    1. Hypothetical protein YesE [102814]
      1. Bacillus subtilis [TaxId: 1423] [102815] (1)
    2. Uncharacterized protein BTHI0051 [159973]
      1. Burkholderia thailandensis [TaxId: 57975] [159974] (2)
        SQ Q2T2I4 10-139
    3. Uncharacterized protein Ava2261 [159975]
      1. Anabaena variabilis [TaxId: 1172] [159976] (2)
        SQ Q3MAV7 1-133
    4. Uncharacterized protein PA3332 [159977]
      1. Pseudomonas aeruginosa [TaxId: 287] [159978] (1)
        SQ Q9HYR3 1-129
  7. Ketosteroid isomerase-like [54434] (4)
    1. Delta-5-3-ketosteroid isomerase, steroid delta-isomerase, KSI [54435]
      1. Comamonas testosteroni, also known as Pseudomonas testosteroni [TaxId: 285] [54436] (14)
      2. Pseudomonas putida [TaxId: 303] [54437] (23)
        SQ P07445
    2. Hypothetical protein Rv0760c [142994]
      1. Mycobacterium tuberculosis [TaxId: 1773] [142995] (1)
        SQ P71817 5-136
      2. Mycobacterium tuberculosis H37Rv [TaxId: 83332] [159979] (10)
  8. Ring hydroxylating beta subunit [54438] (7)
    Pfam 00866
    1. Naphthalene 1,2-dioxygenase beta subunit [54439]
      1. Pseudomonas putida [TaxId: 303] [54440] (16)
      2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [142996] (6)
        SQ Q7BSK6 6-172
    2. Biphenyl dioxygenase small subunit BphA2 [110824]
      1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [110825] (2)
        SQ Q53123 11-187
    3. Small subunit of cumene dioxygenase CumA2 [142997]
      1. Pseudomonas fluorescens [TaxId: 294] [142998] (1)
        SQ Q51744 6-186
    4. Nitrobenzene dioxygenase beta subunit, NBDO-beta [142999]
      1. Comamonas sp. JS765 [TaxId: 58226] [143000] (3)
        SQ Q8RTL3 1-194
    5. Putative hydroxylase subunit Saro3860 [159980]
      1. Novosphingobium aromaticivorans [TaxId: 48935] [159981] (1)
        SQ A4XDU4 6-162
    6. Benzoate 1,2-dioxygenase beta subunit BenB [159982]
      1. Burkholderia mallei [TaxId: 13373] [159983] (1)
        SQ Q62E64 1-163
  9. Penicillin binding protein 2a (PBP2A), N-terminal domain [82595] (1)
    some sequence similarity to KSI
    1. Penicillin binding protein 2a (PBP2A), N-terminal domain [82596]
      1. Staphylococcus aureus [TaxId: 1280] [82597] (5)
        SQ O54286 27-668
  10. Orange carotenoid protein, C-terminal domain [82598] (1)
    1. Orange carotenoid protein, C-terminal domain [82599]
      1. Cyanobacteria (Arthrospira maxima) [TaxId: 129910] [82600] (1)
  11. Hypothetical protein egc068 from a soil-derived mobile gene cassette [110826] (1)
    1. Hypothetical protein egc068 from a soil-derived mobile gene cassette [110827]
      1. uncultured organism [TaxId: 155900] [110828] (1)
        SQ Q99IU3
  12. PA1314-like [110829] (1)
    COG4460
    1. Hypothetical protein PA1314 [110830]
      1. Pseudomonas aeruginosa [TaxId: 287] [110831] (1)
        SQ Q9I430
  13. TIM44-like [143001] (2)
    contains extra N-terminal helices but lacks the beta-hairpin in the superfamily-specific insertion
    1. Translocase of inner mitochondrial membrane TIMM44 (TIM44), C-terminal domain [143002]
      1. Human (Homo sapiens) [TaxId: 9606] [143003] (1)
        SQ O43615 270-451
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159984] (1)
        SQ Q01852 234-425
  14. Sbal0622-like [159985] (1)
    PfamB 002762
    1. Uncharacterized protein Sbal0622 [159986]
      1. Shewanella baltica [TaxId: 62322] [159987] (12)
        SQ A3D088 3-126
  15. CHU142-like [159988] (1)
    single domain covered by PfamB 000743 in the N-terminal part and PfamB 000860 in the C-terminal part
    1. Uncharacterized protein CHU142 [159989]
      1. Cytophaga hutchinsonii [TaxId: 985] [159990] (4)
        SQ Q11V67 1-122
  16. SO0125-like [159991] (2)
    PfamB 003666
    1. Uncharacterized protein Sfri1973 [159992]
      1. Shewanella frigidimarina [TaxId: 56812] [159993] (6)
        SQ Q082J6 23-147
    2. Uncharacterized protein SO0125 [159994]
      1. Shewanella oneidensis [TaxId: 70863] [159995] (1)
        SQ Q8EKG8 1-121
  17. SAV4671-like [159996] (1)
    PfamB 000442; uncertain annotation of some members as 3-dehydroquinate dehydratase
    1. Uncharacterized protein SAV4671 [159997]
      1. Streptomyces avermitilis [TaxId: 33903] [159998] (3)
        SQ Q82EE4 5-157
  18. BxeB1374-like [159999] (2)
    similar dimer to KSI
    1. Uncharacterized protein ECA3500 [160000]
      1. Pectobacterium atrosepticum [TaxId: 29471] [160001] (4)
        SQ Q6D1E8 1-127
    2. Hypothetical protein BxeB1374 [160002]
      1. Burkholderia xenovorans [TaxId: 36873] [160003] (2)
        SQ Q13MU9 1-128
  19. Atu0744-like [160004] (1)
    PfamB 003773
    1. Uncharacterized protein Atu0744 [160005]
      1. Agrobacterium tumefaciens [TaxId: 358] [160006] (2)
        SQ Q7D0S4 1-117
  20. Rpa4348-like [160007] (2)
    PfamB 000085
    1. Uncharacterized protein BxeB2092 [160008]
      1. Burkholderia xenovorans [TaxId: 36873] [160009] (1)
        SQ Q13PU4 1-127
    2. Uncharacterized protein Rpa4348 [160010]
      1. Rhodopseudomonas palustris [TaxId: 1076] [160011] (1)
        SQ Q6N1Q6 1-135
  21. Ava4193-like [160012] (1)
    PfamB 183524
    1. Uncharacterized protein Ava4193 [160013]
      1. Anabaena variabilis [TaxId: 1172] [160014] (4)
        SQ Q3M5E4 2-129
  22. YybH-like [160015] (1)
    PfamB 052627
    1. Hypothetical protein YybH [160016]
      1. Bacillus subtilis [TaxId: 1423] [160017] (4)
        SQ P37496 1-128
  23. PFL3262-like [160018] (1)
    Pfam 07080; DUF1348
    1. Hypothetical protein PFL3262 [160019]
      1. Pseudomonas fluorescens [TaxId: 294] [160020] (4)
        SQ Q4KBL6 5-159
  24. Exig0174-like [160021] (1)
    PfamB 092483
    1. Uncharacterized protein Exig0174 [160022]
      1. Exiguobacterium sibiricum 255-15 [TaxId: 262543] [160023] (2)
        SQ B1YHC8 5-122
  25. Rv3472-like [160024] (2)
    similar trimer to Scytalone dehydratase
    1. Uncharacterized protein NpunR3134 [160025]
      1. Nostoc punctiforme [TaxId: 272131] [160026] (3)
        SQ B2IXS6 1-133
    2. Uncharacterized protein Rv3472 [160027]
      1. Mycobacterium tuberculosis [TaxId: 1773] [160028] (3)
        SQ O06337 1-167
  26. VirB8-like [160029] (2)
    Pfam 04335
    1. Type IV secretion system protein VirB8 [160030]
      1. Agrobacterium tumefaciens [TaxId: 358] [160031] (2)
        SQ P17798 92-231
      2. Brucella melitensis [TaxId: 29459] [160032] (5)
        SQ Q7CEG3 97-235
  27. ECA1476-like [160033] (1)
    single domain covered by PfamB 006272 in the N-terminal part and PfamB 005262 in the C-terminal part
    1. Uncharacterized protein ECA1476 [160034]
      1. Pectobacterium atrosepticum [TaxId: 29471] [160035] (4)
        SQ Q6D750 3-134
  28. BaiE/LinA-like [160036] (5)
    PfamB 000019; includes sequences of characterized enzymes BaiE and LinA
    1. Uncharacterized protein Saro2766 [160037]
      1. Novosphingobium aromaticivorans [TaxId: 48935] [160038] (1)
        SQ Q2G4M1 2-160
    2. Uncharacterized protein Saro3722 [160039]
      1. Novosphingobium aromaticivorans [TaxId: 48935] [160040] (1)
        SQ A4XF70 13-165
    3. Uncharacterized protein Saro1465 [160041]
      1. Novosphingobium aromaticivorans [TaxId: 48935] [160042] (2)
        SQ Q2G8B5 1-149
    4. Uncharacterized protein NpunR1993 [160043]
      1. Nostoc punctiforme [TaxId: 272131] [160044] (1)
        SQ B2J4W9 9-170
    5. Uncharacterized protein Saro3538 [160045]
      1. Novosphingobium aromaticivorans [TaxId: 48935] [160046] (6)
        SQ A4XEN7 1-144
  29. Atu0742-like [160047] (1)
    PfamB 017405
    1. Uncharacterized protein Atu0742 [160048]
      1. Agrobacterium tumefaciens [TaxId: 358] [160049] (1)
        SQ A9CJY7 1-123
  30. SEC-C associated NTF2-like domain [160050] (1)
    there is a C-terminal SEC-C motif, also there can be an additional SEC-C like motif at the N-terminus (there is only C-terminal motif in the new entry 2JQ5)
    1. Hypothetical protein Psyc2064 [160051]
      1. Psychrobacter arcticus [TaxId: 334543] [160052] (1)
        SQ Q4FPZ7 46-158
5. Uracil-DNA glycosylase inhibitor protein [54441] (1)
  has an additional strand at the C-terminus and a helix inserted after the first strand
  uperfamily
  1. Uracil-DNA glycosylase inhibitor protein [54442] (2)
    1. Uracil-DNA glycosylase inhibitor protein [54443]
      1. Bacteriophage pbs1 [TaxId: 10683] [54444] (1)
      2. Bacteriophage pbs2 [TaxId: 10684] [54445] (17)
6. Putative dsDNA mimic [102816] (1)
  elaborated with additional structures; some similarity to Uracil-DNA glycosylase (UGI) and Nuclease A (NuiA) inhibitors
  uperfamily
  1. Putative dsDNA mimic [102817] (1)
    Pfam 04269, DUF440
    1. Hypothetical protein HI1450 [102818]
      putative dsDNA mimic
      1. Haemophilus influenzae [TaxId: 727] [102819] (1)
7. Pre-PUA domain [88802] (5)
  this domain is found in association with the PUA domain in the C-terminal region of Archaeosine tRNA-guanine transglycosylase and related stand-alone proteins
  uperfamily
  1. Archaeosine tRNA-guanine transglycosylase, C2 domain [88803] (1)
    1. Archaeosine tRNA-guanine transglycosylase, C2 domain [88804]
      the second of the 3 additional C-terminal domains to the TGT-like domain, also includes "linker" C1 domain
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [88805] (4)
  2. Hypothetical protein Ta1423, N-terminal domain [102820] (1)
    1. Hypothetical protein Ta1423, N-terminal domain [102821]
      this protein is related to the C-terminal part (domains C2 and C3) of Archaeosine tRNA-guanine transglycosylase
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102822] (1)
  3. Nip7p homolog, N-terminal domain [110832] (1)
    1. Nip7p homolog, N-terminal domain [110833]
      1. Human (Homo sapiens) [TaxId: 9606] [110834] (2)
        SQ Q9Y221
  4. Hypothetical protein APE0525, N-terminal domain [143004] (1)
    1. Hypothetical protein APE0525, N-terminal domain [143005]
      1. Archaeon Aeropyrum pernix [TaxId: 56636] [143006] (3)
        SQ Q9YEQ6 1-90
  5. AF0587 pre C-terminal domain-like [160053] (1)
    PfamB 006016
    1. Uncharacterized protein AF0587 [160054]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160055] (1)
        SQ O29668 394-459
Nuclease A inhibitor (NuiA) [82601] (1)
alpha-beta-alpha-beta-alpha(2)-beta(3); antiparallel beta-sheet; order: 15432
1. Nuclease A inhibitor (NuiA) [82602] (1)
  some structural similarity to Uracil-DNA glycosylase inhibitor and putative dsDNA mimic HI1450 of the cystatin-like fold
  uperfamily
  1. Nuclease A inhibitor (NuiA) [82603] (1)
    1. Nuclease A inhibitor (NuiA) [82604]
      1. Anabaena sp., pcc 7120 [TaxId: 1167] [82605] (3)
Colicin D/E5 nuclease domain [102823] (1)
alpha(2)-beta(4)-alpha, 2 layers: alpha/beta, antiparallel beta sheet, meander
1. Colicin D/E5 nuclease domain [102824] (2)
  uperfamily
  1. Colicin D nuclease domain [102825] (1)
    1. Colicin D nuclease domain [102826]
      tRNA-specific ribonuclease
      1. Escherichia coli [TaxId: 562] [102827] (2)
  2. Colicin E5 nuclease domain [143007] (1)
    1. Colicin E5 [143008]
      1. Escherichia coli [TaxId: 562] [143009] (7)
        SQ P18000 84-177
RelE-like [143010] (1)
beta-alpha(2)-beta(4), 2 layers; a/b, antiparallel beta-sheet; order 15432
1. RelE-like [143011] (2)
  Toxin component of plasmid stabilisation system
  uperfamily
  1. YoeB/Txe-like [143012] (1)
    Pfam 06769
    1. Toxin YoeB [143013]
      1. Escherichia coli [TaxId: 562] [143014] (12)
        SQ P69348 1-84
  2. RelE-like [143015] (2)
    Pfam 05016
    1. Hypothetical protein PHS013 [143016]
      1. Pyrococcus horikoshii [TaxId: 53953] [143017] (2)
        SQ O73966 1-88
    2. Hypothetical protein HP0894 [143018]
      1. Helicobacter pylori [TaxId: 210] [143019] (1)
        SQ O25554 1-88
Hypothetical protein SAV1430 [110835] (1)
beta(3)-alpha-beta(2)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet, order: 12543
1. Hypothetical protein SAV1430 [110836] (1)
  uperfamily
  1. Hypothetical protein SAV1430 [110837] (1)
    1. Hypothetical protein SAV1430 [110838]
      1. Staphylococcus aureus [TaxId: 1280] [110839] (2)
        SQ Q99U58
Ns1 effector domain-like [143020] (1)
beta-X-beta(5)-alpha-beta-alpha; 2 layers: a/b; bifurcated beta-sheet; order 23654[1,7]
1. Ns1 effector domain-like [143021] (1)
  uperfamily
  1. Ns1 effector domain-like [143022] (1)
    C-terminal part of Pfam 00600
    1. Non-structural protein NS1 C-terminal domain [143023]
      1. Influenza A virus [TaxId: 11320] [143024] (2)
        SQ Q71QT3 79-205
YbaB-like [82606] (1)
core: alpha-beta(3)-alpha, 2 layers:alpha/beta, three-stranded antiparallel beta sheet, strand order 123
1. YbaB-like [82607] (1)
  forms tight dimer of a 3-layer structure: beta/alpha/beta
  uperfamily
  1. YbaB-like [82608] (2)
    Pfam 02575; DUF149; function unknown
    1. Hypothetical upf0133 protein YbaB [89857]
      1. Escherichia coli [TaxId: 562] [89858] (1)
    2. Hypothetical protein HI0442 [82609]
      1. Haemophilus influenzae [TaxId: 727] [82610] (1)
Kinetochore globular domain-like [143025] (1)
core: alpha-beta(3)-alpha; variant: alpha-beta(4)-alpha(2)
1. Kinetochore globular domain [143026] (2)
  swapped heterodimer with the N-terminal helices; Spc24-like subunits have the core fold, whereas Spc25-like subunits have a variant fold
  uperfamily
  1. Spc25-like [143027] (1)
    Pfam 08234
    1. Kinetochore protein Spc25 [143028]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143029] (2)
        SQ P40014 133-221
  2. Spc24-like [143030] (1)
    Pfam 08286
    1. Kinetochore protein Spc24 [143031]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143032] (2)
        SQ Q04477 155-213! SQ Q04477 156-213
L35p-like [143033] (1)
core: alpha-beta(3)-alpha; 2layers a/b
1. L35p-like [143034] (1)
  uperfamily
  1. Ribosomal protein L35p [143035] (3)
    Pfam 01632
    1. Ribosomal protein L35p [143036]
      1. Escherichia coli [TaxId: 562] [143037] (27)
        SQ P0A7Q1 1-64
      2. Deinococcus radiodurans [TaxId: 1299] [160056] (10)
        SQ Q9RSW6 2-64
      3. Thermus thermophilus [TaxId: 274] [160057] (5)
        SQ P80341 1-64
Cell division protein ZapA-like [102828] (1)
core: beta(2)-alpha(2), 2 layers: alpha/beta; long C-terminal helix forms dimeric parallel and tetrameric antiparallel coiled coils
1. Cell division protein ZapA-like [102829] (1)
  uperfamily
  1. Cell division protein ZapA-like [102830] (1)
    Pfam 05164; ZapA is a Z-ring associated protein first discovered in B. subtilis (formerly hypothetical protein YshA);
    1. ZapA homologue PA5227 [102831]
      1. Pseudomonas aeruginosa [TaxId: 287] [102832] (2)
        SQ Q9HTW3
ssDNA-binding transcriptional regulator domain [54446] (1)
helix-swapped dimer of beta(4)-alpha motifs
1. ssDNA-binding transcriptional regulator domain [54447] (4)
  uperfamily
  1. Transcriptional coactivator PC4 C-terminal domain [54448] (1)
    dimer of two separate motifs
    1. Transcriptional coactivator PC4 C-terminal domain [54449]
      1. Human (Homo sapiens) [TaxId: 9606] [54450] (5)
  2. Plant transcriptional regulator PBF-2 [75375] (1)
    single-chain domain formed by a tandem repeat of two motifs
    1. Plant transcriptional regulator PBF-2 [75376]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [75377] (1)
  3. PMN2A0962/syc2379c-like [143038] (2)
    Pfam 08848; DUF1818; specific to cyanobacteria; single-chain domain made of two repeats of this structural motif
    1. Hypothetical protein PMN2A_0962 [143039]
      1. Prochlorococcus marinus [TaxId: 1219] [143040] (4)
        SQ Q46J75 1-122
    2. Hypothetical protein syc2379_c [143041]
      1. Synechococcus sp. pcc 7942 [TaxId: 1140] [143042] (1)
        SQ Q5MZF1 1-121
  4. Guide RNA binding protein gBP [143043] (2)
    includes PfamB 080318 and PB073991; forms heterooligomers; similar subunit and oligomeric structures to the Plant transcriptional regulator family
    1. GBP21 [143044]
      Mitochondrial RNA binding protein 1, MRP1
      1. Trypanosoma brucei [TaxId: 5691] [143045] (7)
        SQ P90629 28-173
    2. Guide RNA binding protein gBP25 [143046]
      Mitochondrial RNA-binding protein 2, MRP2
      1. Trypanosoma brucei [TaxId: 5691] [143047] (6)
        SQ Q952G2 56-221
Photosystem I subunit PsaD [64233] (1)
beta-BETA(2)-beta-alpha-beta(2); antiparallel sheet: order 2134 packed against helix and BETA-hairpin on the same side; irregular C-terminal tail
1. Photosystem I subunit PsaD [64234] (1)
  uperfamily
  1. Photosystem I subunit PsaD [64235] (1)
    1. Photosystem I subunit PsaD [64236]
      1. Synechococcus elongatus [TaxId: 32046] [64237] (1)
GINS/PriA/YqbF domain [160058] (1)
beta(4)-alpha-beta; 3-stranded antiparallel beta-sheet (strands 4,1 and 5) are covered on the same side by the helix and beta hairpin of strands 2 and 3; similarity to the L9 N-domain-like fold (scop_cf 55657) and the PsaD fold (scop_sf 64243)
1. PriA/YqbF domain [160059] (4)
  associated with known or presumed DNA-binding domains; this superfamily also includes the C-terminal domain of PriA (PDB entry 1zt2)
  1. YqbF N-terminal domain-like [160060] (2)
    1. Hypothetical protein YqbF [160061]
      1. Bacillus subtilis [TaxId: 1423] [160062] (1)
        SQ P45922 1-49
    2. Mu-like prophage FluMu protein gp35, HI1506 [160063]
      1. Haemophilus influenzae [TaxId: 727] [160064] (1)
        SQ P44228 1-67
  2. PSF2 N-terminal domain-like [160065] (1)
    N-terminal part of Pfam 04128
    1. DNA replication complex GINS protein PSF2 [160066]
      1. Human (Homo sapiens) [TaxId: 9606] [160067] (7)
        SQ Q9Y248 1-61
  3. SLD5 C-terminal domain-like [160068] (1)
    C-terminal part of Pfam 05916
    1. GINS complex subunit 4, SLD5 [160069]
      1. Human (Homo sapiens) [TaxId: 9606] [160070] (4)
        SQ Q9BRT9 166-223
  4. PSF3 N-terminal domain-like [160071] (1)
    N-terminal part of Pfam 06425
    1. GINS complex subunit 3, PSF3 [160072]
      1. Human (Homo sapiens) [TaxId: 9606] [160073] (7)
        SQ Q9BRX5 1-87
MHC antigen-recognition domain [54451] (1)
dimeric
1. MHC antigen-recognition domain [54452] (1)
  uperfamily
  1. MHC antigen-recognition domain [54453] (73)
    1. Class II MHC alpha chain, N-terminal domain [88806]
      1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88807] (1)
      2. Human (Homo sapiens), HLA-DR1 [TaxId: 9606] [88808] (15)
        SQ P01903 28-207
      3. Human (Homo sapiens), HLA-DR2 [TaxId: 9606] [88809] (8)
      4. Human (Homo sapiens), HLA-DR3 [TaxId: 9606] [88810] (1)
      5. Human (Homo sapiens), HLA-DR4 [TaxId: 9606] [88811] (5)
      6. Human (Homo sapiens), HLA-DQ2 [TaxId: 9606] [102833] (1)
      7. Human (Homo sapiens), HLA-DQ6 [TaxId: 9606] [102834] (1)
      8. Human (Homo sapiens), HLA-DQ8 [TaxId: 9606] [88812] (1)
      9. Mouse (Mus musculus), I-AK [TaxId: 10090] [88813] (3)
      10. Mouse (Mus musculus), I-AU [TaxId: 10090] [89859] (30)
      11. Mouse (Mus musculus), I-EK [TaxId: 10090] [88814] (9)
      12. Mouse (Mus musculus), I-AB [TaxId: 10090] [88815] (2)
      13. Mouse (Mus musculus), I-AD [TaxId: 10090] [88816] (2)
      14. Mouse (Mus musculus), I-A(G7) [TaxId: 10090] [88817] (2)
      15. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88818] (1)
    2. Class II MHC beta chain, N-terminal domain [88819]
      1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88820] (1)
      2. Human (Homo sapiens), HLA-DR1 [TaxId: 9606] [88821] (13)
      3. Human (Homo sapiens), HLA-DR2 [TaxId: 9606] [88822] (16)
        SQ P04229 30-219
      4. Human (Homo sapiens), HLA-DR3 [TaxId: 9606] [88823] (1)
      5. Human (Homo sapiens), HLA-DR4 [TaxId: 9606] [88824] (18)
      6. Human (Homo sapiens), HLA-DQ2 [TaxId: 9606] [102835] (1)
      7. Human (Homo sapiens), HLA-DQ6 [TaxId: 9606] [102836] (1)
      8. Human (Homo sapiens), HLA-DQ8 [TaxId: 9606] [88825] (1)
      9. Mouse (Mus musculus), I-AK [TaxId: 10090] [88826] (3)
      10. Mouse (Mus musculus), I-AU [TaxId: 10090] [89860] (1)
      11. Mouse (Mus musculus), I-EK [TaxId: 10090] [88827] (9)
      12. Mouse (Mus musculus), I-AB [TaxId: 10090] [88828] (8)
      13. Mouse (Mus musculus), I-AD [TaxId: 10090] [88829] (2)
      14. Mouse (Mus musculus), I-A(G7) [TaxId: 10090] [88830] (6)
      15. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88831] (1)
    3. Class I MHC, alpha-1 and alpha-2 domains [54468]
      1. Human (Homo sapiens), HLA-A2 [TaxId: 9606] [54469] (1)
      2. Human (Homo sapiens), HLA-A2.1 [TaxId: 9606] [54470] (95)
        SQ P01892 25-298
      3. Human (Homo sapiens), HLA-AW68 [TaxId: 9606] [54472] (3)
      4. Human (Homo sapiens), HLA-B08 [TaxId: 9606] [54473] (7)
      5. Human (Homo sapiens), HLA-B27 [TaxId: 9606] [54471] (8)
        SQ P03989 25-300
      6. Human (Homo sapiens), HLA-BW44 [TaxId: 9606] [102837] (12)
        SQ P30481 25-300
      7. Human (Homo sapiens), HLA-B53 [TaxId: 9606] [54474] (31)
      8. Human (Homo sapiens), HLA-B35 [TaxId: 9606] [54475] (5)
        SQ P30685 25-300
      9. Human (Homo sapiens), HLA-B51 [TaxId: 9606] [54476] (2)
      10. Human (Homo sapiens), HLA-CW3 [TaxId: 9606] [54477] (1)
      11. Human (Homo sapiens), HLA-CW4 [TaxId: 9606] [54478] (2)
      12. Human (Homo sapiens), HLA-E [TaxId: 9606] [54479] (14)
      13. Mouse (Mus musculus), H-2KB [TaxId: 10090] [54481] (40)
        SQ P01901 22-299
      14. Mouse (Mus musculus), H-2DB [TaxId: 10090] [54482] (18)
      15. Mouse (Mus musculus), H-2M3 [TaxId: 10090] [54483] (1)
      16. Mouse (Mus musculus), H-2LD [TaxId: 10090] [54484] (2)
      17. Mouse (Mus musculus), H-2DD [TaxId: 10090] [54485] (36)
      18. Mouse (Mus musculus), tla(c), H-2 class [TaxId: 10090] [89861] (1)
      19. Mouse (Mus musculus), IB QA-2 [TaxId: 10090] [69680] (1)
      20. Rat (Rattus norvegicus), RT1-AA [TaxId: 10116] [54486] (3)
      21. Human (Homo sapiens), HLA-A11 [TaxId: 9606] [110840] (4)
        SQ P13746 25-299 # 1A11_HUMAN HLA class I histocompatibility antigen, A-11 alpha chain precursor
      22. Human (Homo sapiens), HLA-A1 [TaxId: 9606] [117849] (1)
        SQ P30443 25-298 # 1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain precursor
      23. Rhesus monkey (Macaca mulatta) [TaxId: 9544] [160074] (2)
      24. Mouse (Mus musculus), H-2KK [TaxId: 10090] [160075] (3)
        SQ P04223 22-197
      25. Human (Homo sapiens), HLA-G [TaxId: 9606] [160076] (4)
        SQ P17693 25-205! SQ P17693 26-205
      26. Mouse (Mus musculus), H-2M10 [TaxId: 10090] [160077] (5)
      27. Mouse (Mus musculus), H-2KD [TaxId: 10090] [160078] (2)
        SQ P01902 22-202
    4. Hemochromatosis protein Hfe, alpha-1 and alpha-2 domains [88832]
      1. Human (Homo sapiens) [TaxId: 9606] [54480] (2)
    5. Fc (IgG) receptor, alpha-1 and alpha-2 domains [54454]
      class I MHC-related
      1. Rat (Rattus norvegicus) [TaxId: 10116] [54455] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [54493] (1)
    6. CD1, alpha-1 and alpha-2 domains [54456]
      Class I MHC-related
      1. Mouse (Mus musculus) [TaxId: 10090] [54457] (10)
      2. Human (Homo sapiens), CD1b [TaxId: 9606] [75378] (3)
      3. Human (Homo sapiens), CD1a [TaxId: 9606] [102838] (4)
      4. Human (Homo sapiens), CD1d [TaxId: 9606] [160079] (4)
        SQ P15813 24-201
    7. Zinc-alpha-2-glycoprotein, ZAG [54487]
      fat depleting factor related to class I MHC
      1. Human (Homo sapiens) [TaxId: 9606] [54488] (7)
        SQ P25311 22-294
    8. Class I MHC homolog [54489]
      gamma, delta T-cell ligand
      1. Human (Homo sapiens), Mic-a [TaxId: 9606] [54490] (2)
      2. Human (Homo sapiens), Mic-b [TaxId: 9606] [75380] (1)
      3. Mouse (Mus musculus), t22 [TaxId: 10090] [54491] (3)
      4. Mouse (Mus musculus), t10 [TaxId: 10090] [102839] (1)
    9. Class I MHC-related molecule Ulbp3 [69681]
      1. Human (Homo sapiens) [TaxId: 9606] [69682] (1)
    10. NK cell ligand RAE-1 beta [69683]
      1. Mouse (Mus musculus) [TaxId: 10090] [69684] (2)
    11. Endothelial protein C receptor [75381]
      phospholipid-binding protein
      1. Human (Homo sapiens) [TaxId: 9606] [75382] (2)
    12. Immunomodulatory protein m144, alpha-1 and alpha-2 domains [110841]
      1. Murine cytomegalovirus [TaxId: 10366] [110842] (2)
        SQ Q69G19 27-263 # 95% sequence identity
UBC-like [54494] (1)
alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2
1. UBC-like [54495] (4)
  uperfamily
  1. UBC-related [54496] (38)
    1. Ubiquitin conjugating enzyme, UBC [54497]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [54498] (1)
      2. Baker's yeast (Saccharomyces cerevisiae), ubc1 [TaxId: 4932] [69685] (3)
        SQ P21734
      3. Baker's yeast (Saccharomyces cerevisiae), ubc2 (RAD6) [TaxId: 4932] [54499] (1)
      4. Baker's yeast (Saccharomyces cerevisiae), ubc4 [TaxId: 4932] [54500] (1)
      5. Baker's yeast (Saccharomyces cerevisiae), ubc7 [TaxId: 4932] [54501] (1)
      6. Baker's yeast (Saccharomyces cerevisiae), ubc13 [TaxId: 4932] [64239] (3)
      7. Baker's yeast (Saccharomyces cerevisiae), mms2 [TaxId: 4932] [64241] (2)
      8. Human (Homo sapiens), ubc13 [TaxId: 9606] [64240] (5)
      9. Human (Homo sapiens), mms2 [TaxId: 9606] [64242] (3)
      10. Human (Homo sapiens), ubch7 [TaxId: 9606] [54502] (2)
      11. Human (Homo sapiens), ubc9 [TaxId: 9606] [54503] (12)
        identical sequence in many other species
      12. Human (Homo sapiens), ubch10 [TaxId: 9606] [64243] (1)
      13. Human (Homo sapiens), ubc2b [TaxId: 9606] [102840] (1)
        E2-17 kDa
      14. Human (Homo sapiens), ubch5b [TaxId: 9606] [102841] (14)
        SQ P62837
        E2-17 kDa 2
      15. Clam (Spisula solidissima), E-2C [TaxId: 6584] [54504] (1)
      16. Nematode (Caenorhabditis elegans), E2-19 kDa [TaxId: 6239] [89862] (1)
      17. Nematode (Caenorhabditis elegans), E2-21.5 kDa [TaxId: 6239] [102842] (2)
      18. Human (Homo sapiens), ubch8 [TaxId: 9606] [117850] (1)
        SQ Q96LR5 54-201
      19. Human(Homo sapiens), E2 S [TaxId: 9606] [143048] (2)
        SQ Q16763 6-156
      20. Leishmania major [TaxId: 5664] [143049] (3)
        SQ Q4Q5L3 9-166
        Ubiquitin carrier protein 4, putative
      21. Human (Homo sapiens), E2 J2 [TaxId: 9606] [143050] (2)
        SQ Q5T7L1 12-168
        ubc6 homologue
      22. Human (Homo sapiens), E2 variant 1 [TaxId: 9606] [143051] (5)
        SQ Q13404 80-221! SQ Q13404 82-220
      23. Human (Homo sapiens), E2 L6 [TaxId: 9606] [143052] (3)
        SQ O14933 2-151
      24. Human (Homo sapiens), E2 U [TaxId: 9606] [143053] (1)
        SQ Q5VVX9 1-148
      25. Human (Homo sapiens), E2 D3 [TaxId: 9606] [143054] (5)
        SQ P61077 1-147
      26. Human (Homo sapiens), E2 H [TaxId: 9606] [143055] (2)
        SQ P62256 4-155
      27. Human (Homo sapiens), E2 G1 [TaxId: 9606] [143056] (1)
        SQ P62253 7-131
      28. Human (Homo sapiens), E2 T [TaxId: 9606] [143057] (1)
        SQ Q9NPD8 1-154
        Hspc150
      29. Human (Homo sapiens), E2 M [TaxId: 9606] [143058] (2)
        SQ P61081 27-183
        the extra N-terminal peptide, bound to the heterodimeric E1 enzyme for NEDD8, can be seen in the PDB entry 1tt5, chains E and F
      30. Toxoplasma gondii [TaxId: 5811] [143059] (1)
      31. Caenorhabditis elegans, E2 2 [TaxId: 6239] [143060] (1)
        SQ P35129 1-147
      32. Xenopus laevis [TaxId: 8355] [160080] (1)
    2. Ubiquitin-protein ligase W (E2 W) [143061]
      forms segment-swapped dimer
      1. Human (Homo sapiens) [TaxId: 9606] [143062] (2)
        SQ Q96B02 1-117
    3. Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain [143063]
      ubc1 homologue; also contains the C-terminal UBA domain
      1. Human (Homo sapiens) [TaxId: 9606] [143064] (5)
        SQ P61086 1-156
      2. Cow (Bos taurus) [TaxId: 9913] [143065] (2)
        SQ P61085 1-154
    4. Hypothetical protein Tgtwinscan_2721, E2 domain [143066]
      1. Toxoplasma gondii [TaxId: 5811] [143067] (2)
    5. Ubiquitin-conjugating enzyme E2 Q2, C-terminal domain [143068]
      this proteins contains the N-terminal RWD domain
      1. Human (Homo sapiens) [TaxId: 9606] [143069] (1)
        SQ Q8WVN8 201-362
    6. Putative ubiquitin-conjugating enzyme, E2 domain [143070]
      1. Plasmodium chabaudi [TaxId: 5825] [143071] (1)
        SQ Q4Y037 88-196
  2. UEV domain [75383] (2)
    1. Tumor susceptibility gene 101 (TSG101) [75384]
      1. Human (Homo sapiens) [TaxId: 9606] [75385] (7)
    2. Vacuolar protein sorting-associated [102843]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102844] (1)
  3. RWD domain [110843] (4)
    Pfam 05773
    1. EIF2-alpha kinase 4 (GCN2-like protein) [110844]
      1. Mouse (Mus musculus) [TaxId: 10090] [110845] (1)
        SQ Q9QZ05 17-139
    2. E3 ubiquitin-protein ligase RNF25 [160081]
      RING finger protein 25
      1. Human (Homo sapiens) [TaxId: 9606] [160082] (2)
        SQ Q96BH1 10-125! SQ Q96BH1 10-134
    3. Uncharacterized protein C21orf6 [160083]
      1. Human (Homo sapiens) [TaxId: 9606] [160084] (1)
        SQ P57060 34-173
    4. RWD domain-containing protein 2 [160085]
      1. Human (Homo sapiens) [TaxId: 9606] [160086] (1)
        SQ Q9UIY3 1-141
  4. UFC1-like [143072] (1)
    1. Ufm1-conjugating enzyme 1, UFC1 [143073]
      aka cgi-126
      1. Human (Homo sapiens) [TaxId: 9606] [143074] (3)
        SQ Q9Y3C8 1-167
SAND domain-like [63762] (1)
core: three short helices packed against a barrel-like beta-sheet; some similarity to the SH3-like fold
1. SAND domain-like [63763] (2)
  uperfamily
  1. SAND domain [63764] (3)
    1. Nuclear autoantigen Sp100b [63765]
      1. Human (Homo sapiens) [TaxId: 9606] [63766] (1)
    2. Glucocorticoid modulatory element binding protein-1 (Gmeb1) [102845]
      1. Human (Homo sapiens) [TaxId: 9606] [102846] (1)
    3. Putative nuclear protein homolog 5830484a20rik [110846]
      1. Mouse (Mus musculus) [TaxId: 10090] [110847] (1)
        SQ Q8BVK9 353-433
  2. SMAD4-binding domain of oncoprotein Ski [82611] (1)
    1. SMAD4-binding domain of oncoprotein Ski [82612]
      1. Human (Homo sapiens) [TaxId: 9606] [82613] (1)
NRDP1 C-terminal domain-like [160087] (1)
alpha-beta-alpha(3)-beta(3); a pseudo barrel beta-sheet of an SH3-like topology, surrounded by helices
1. NRDP1 C-terminal domain-like [160088] (1)
  1. USP8 interacting domain [160089] (1)
    Pfam 08941
    1. E3 ubiquitin-protein ligase NRDP1 [160090]
      RING finger protein 41
      1. Human (Homo sapiens) [TaxId: 9606] [160091] (6)
        SQ Q9H4P4 193-317! SQ Q9H4P4 197-317
Coronavirus NSP8-like [143075] (1)
core: alpha-beta(2)-alpha-beta(4)-alpha-beta; bifurcated barrel-like beta-sheet
1. Coronavirus NSP8-like [143076] (1)
  uperfamily
  1. Coronavirus NSP8-like [143077] (1)
    1. Nonstructural protein 8, NSP8 [143078]
      contains extra N-terminal helical regions involved in heterooligomerisation with NSP7
      1. SARS coronavirus [TaxId: 227859] [143079] (3)
        SQ P59641 3961-4111
ParB/Sulfiredoxin [110848] (1)
beta*-alpha-beta(2)-alpha-beta-alpha; mixed beta sheet forms a partly open barrel: (n*=4, S*=8)
1. ParB/Sulfiredoxin [110849] (4)
  uperfamily
  1. ParB-like nuclease domain [110850] (1)
    Pfam 02195
    1. Putative partitioning protein ParB/Spo0J [110851]
      1. Thermus thermophilus [TaxId: 274] [110852] (1)
        SQ Q9LCY0 # Fragment
  2. Hypothetical protein PF0380 [110853] (1)
    contains insert domain (101-200) of an unusual alpha+beta fold beta-alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order 516342; possibly related to Pfam 06245
    1. Hypothetical protein PF0380 [110854]
      1. Pyrococcus furiosus [TaxId: 2261] [110855] (1)
        SQ Q8U3S5
  3. Atu1540-like [160092] (1)
    Pfam 08857; ParBc_2; contains extra C-terminal all-alpha subdomain
    1. Hypothetical protein Atu1540 [160093]
      1. Agrobacterium tumefaciens [TaxId: 358] [160094] (6)
        SQ Q8UF59 4-204
  4. Sulfiredoxin-like [160095] (1)
    PfamB 015736
    1. Sulfiredoxin [160096]
      1. Human (Homo sapiens) [TaxId: 9606] [160097] (4)
        SQ Q9BYN0 17-137! SQ Q9BYN0 28-137! SQ Q9BYN0 30-137
Gamma-glutamyl cyclotransferase-like [110856] (1)
beta-alpha-beta(4)-alpha-beta(2); contains beta-sheet barrel (n=5, S=8)
1. Gamma-glutamyl cyclotransferase-like [110857] (1)
  uperfamily
  1. Gamma-glutamyl cyclotransferase-like [110858] (3)
    Pfam 03674
    1. Hypothetical protein LOC223267 [110859]
      1. Mouse (Mus musculus) [TaxId: 10090] [110860] (1)
        SQ Q923B0
    2. Hypothetical protein PH0828 [117851]
      1. Pyrococcus horikoshii [TaxId: 53953] [117852] (1)
        SQ O58558
    3. Hypothetical protein YtfP [117853]
      1. Escherichia coli [TaxId: 562] [117854] (1)
        SQ P0AE48
BB1717-like [143080] (1)
complex fold with a bifurcated beta-sheet structure surrounded by helices; contains beta-sheet barrel, closed (n=5, S=8)
1. BB1717-like [143081] (1)
  uperfamily
  1. BB1717-like [143082] (4)
    Pfam 02586; DUF159, COG2135
    1. Hypothetical protein Atu5096 [143083]
      1. Agrobacterium tumefaciens [TaxId: 358] [143084] (3)
        SQ Q8UKK6 2-244
    2. Phage-related hypothetical protein BB1717 [143085]
      1. Bordetella bronchiseptica [TaxId: 518] [143086] (1)
        SQ Q7WLM8 2-219
    3. Phage-related hypothetical protein BB2244 [143087]
      1. Bordetella bronchiseptica [TaxId: 518] [143088] (1)
        SQ Q7WK92 2-218
    4. Hypothetical protein BT1218 [143089]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143090] (2)
        SQ Q8A8E9 2-232
SARS Nsp1-like [160098] (1)
complex alpha+beta fold; contains mixed beta-sheet barrel, n=6, S=10
1. SARS Nsp1-like [160099] (1)
  1. SARS Nsp1-like [160100] (1)
    1. Nsp1 [160101]
      1. SARS coronavirus [TaxId: 227859] [160102] (2)
        SQ P59641 13-127
Acetoacetate decarboxylase-like [160103] (1)
complex fold: contains a 3-layer beta-sheet structure, which is folded in two conjoint barrels capped by helices; one rounded barrel has 7 strands, the other flattened barrel has 9 strands
1. Acetoacetate decarboxylase-like [160104] (1)
  1. Acetoacetate decarboxylase-like [160105] (2)
    Pfam 06314
    1. Acetoacetate decarboxylase [160106]
      1. Legionella pneumophila [TaxId: 446] [160107] (4)
        SQ Q5ZXQ9 5-254
      2. Methanoculleus marisnigri [TaxId: 2198] [160108] (4)
        SQ A3CUL0 1-264
AF0104/ALDC/Ptd012-like [117855] (1)
duplication: consists of two similar beta-alpha-beta(4) motifs
1. AF0104/ALDC/Ptd012-like [117856] (3)
  characteristic metal ion (zinc)-binding motif in the putative active site
  uperfamily
  1. Alpha-acetolactate decarboxylase-like [117857] (1)
    Pfam 03306
    1. Hypothetical protein SA2394 [117858]
      1. Staphylococcus aureus [TaxId: 1280] [117859] (1)
        SQ Q7A3A7
  2. PTD012-like [143091] (1)
    1. Hypothetical protein PTD012 [143092]
      Ester hydrolase C11orf54
      1. Human (Homo sapiens) [TaxId: 9606] [143093] (2)
        SQ Q9H0W9 3-315
  3. AF0104-like [143094] (2)
    Pfam 03479; DUF296; PD1 domain; plant- and prokaryote conserved (PPC; see new PDB 2DT4)
    1. Hypothetical protein AF0104 [143095]
      1. Archaeoglobus fulgidus [TaxId: 2234] [143096] (3)
        SQ O30132 1-138
    2. Hypothetical protein STM3071 [143097]
      1. Salmonella typhimurium [TaxId: 90371] [143098] (2)
        SQ Q8ZM67 6-141
NSFL1 (p97 ATPase) cofactor p47, SEP domain [102847] (1)
beta(3)-alpha(2)-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other
1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102848] (1)
  uperfamily
  1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102849] (2)
    1. NSFL1 (p97 ATPase) cofactor p47, SEP domain [102850]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [102851] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [117860] (1)
        SQ Q9UNZ2 171-270
TTHA1013/TTHA0281-like [143099] (1)
beta(3)-alpha-beta; 2 layers; mixed beta-sheet, order 4123, strands 1 and 4 are parallel to each other; topological similarity to the SEP domain fold (scop_cf 102847); dimerises via the long C-terminal strand with the formation of a single beta-sheet
1. TTHA1013/TTHA0281-like [143100] (2)
  uperfamily
  1. TTHA1013-like [143101] (1)
    1. Hypothetical protein TTHA1013 [143102]
      1. Thermus thermophilus [TaxId: 274] [143103] (1)
        SQ Q5SJJ5 2-72
  2. TTHA0281-like [160109] (1)
    Pfam 03681; UPF0150; alpha-beta(3)-alpha-X
    1. Hypothetical protein TTHA0281 [160110]
      1. Thermus thermophilus [TaxId: 274] [160111] (4)
        SQ Q5SLL2 3-82
YegP-like [160112] (1)
comprises two subunits or tandem repeats of beta(3)-alpha-beta motifs; these assemble with the formation of a single beta-sheet and swapping of the C-terminal strands
1. YegP-like [160113] (1)
  1. YegP-like [160114] (4)
    Pfam 07411; DUF1508
    1. Uncharacterized protein Atu0232 [160115]
      homodimer
      1. Agrobacterium tumefaciens [TaxId: 358] [160116] (2)
        SQ Q8UIR1 1-62
    2. Uncharacterized protein SO3888 [160117]
      duplication: consists of two repeats
      1. Shewanella oneidensis [TaxId: 70863] [160118] (2)
        SQ Q8EAL4 1-58! SQ Q8EAL4 59-110
    3. Uncharacterized protein YegP [160119]
      duplication: consists of two repeats
      1. Escherichia coli [TaxId: 562] [160120] (2)
        SQ P76402 1-58! SQ P76402 59-110
    4. Uncharacterized protein NMB1088 [160121]
      homodimer
      1. Neisseria meningitidis [TaxId: 487] [160122] (8)
        SQ Q7DDI1 1-56
Diaminopimelate epimerase-like [54505] (1)
mixed beta-sheet folds into a barrel (n=8, S=14) around the central helix
1. Diaminopimelate epimerase-like [54506] (4)
  duplication: consists of two similar domain swapped with C-terminal strands
  uperfamily
  1. Diaminopimelate epimerase [54507] (1)
    1. Diaminopimelate epimerase [54508]
      1. Haemophilus influenzae [TaxId: 727] [54509] (10)
  2. PhzC/PhzF-like [89863] (4)
    Pfam 02567
    1. Hypothetical protein YddE [89864]
      1. Escherichia coli [TaxId: 562] [89865] (3)
        SQ P37757
        structural genomics; NESG target ET25
    2. Hypothetical protein EF0119 [102852]
      1. Enterococcus faecalis [TaxId: 1351] [102853] (1)
    3. Hypothetical protein PA4716 [110861]
      1. Pseudomonas aeruginosa [TaxId: 287] [110862] (1)
        SQ Q9HV82
    4. Phenazine biosynthesis protein PhzF [117861]
      1. Pseudomonas fluorescens [TaxId: 294] [117862] (6)
        SQ Q51792
  3. Proline racemase [110863] (1)
    Pfam 05544
    1. Proline racemase [110864]
      1. Brucella melitensis [TaxId: 29459] [110865] (1)
        SQ Q8YFD6
  4. PA0793-like [160123] (1)
    Pfam 04303; DUF453
    1. Hypothetical protein PA0793 [160124]
      1. Pseudomonas aeruginosa [TaxId: 287] [160125] (2)
        SQ Q9I5E5 1-182! SQ Q9I5E5 187-395
GFP-like [54510] (1)
beta-sheet folds into a barrel (n=11, S=14) around the central helix
1. GFP-like [54511] (2)
  uperfamily
  1. Fluorescent proteins [54512] (6)
    1. Green fluorescent protein, GFP [54513]
      1. Jellyfish (Aequorea victoria) [TaxId: 6100] [54514] (53)
        SQ P42212
      2. Renilla reniformis [TaxId: 6136] [160126] (4)
        SQ Q963I9 7-226
    2. Red fluorescent protein (fp583 or dsred(clontech)) [54515]
      1. Coral (Discosoma sp.) [TaxId: 86600] [54516] (2)
    3. Red fluorescent protein fp61 [102854]
      1. Sea anemone (Entacmaea quadricolor) [TaxId: 6118] [102855] (1)
    4. Pocilloporin pigment Rtms5 [89866]
      1. Coral (Montipora efflorescens) [TaxId: 105610] [89867] (2)
    5. GFP-like non-fluorescent chromoprotein FP595 [117863]
      1. Anemonia sulcata [TaxId: 6108] [117864] (1)
        SQ Q9GZ28 # 95% sequence identity
  2. Domain G2 of nidogen-1 [64244] (1)
    1. Domain G2 of nidogen-1 [64245]
      1. Mouse (Mus musculus) [TaxId: 10090] [64246] (2)
Tubby C-terminal domain-like [54517] (1)
beta-sheet folds into a barrel (n=12, S=12) around the central helix
1. Tubby C-terminal domain-like [54518] (2)
  uperfamily
  1. Transcriptional factor tubby, C-terminal domain [54519] (1)
    1. Transcriptional factor tubby, C-terminal domain [54520]
      1. Mouse (Mus musculus) [TaxId: 10090] [54521] (2)
  2. At5g01750-like [143104] (1)
    Pfam 04525; DUF567
    1. Hypothetical protein At5g01750 [143105]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143106] (2)
        SQ Q9LZX1 24-212
Pili subunits [54522] (1)
contains very long N-terminal helix, which end is packed against beta-sheet
1. Pili subunits [54523] (7)
  bacterial filament proteins
  uperfamily
  1. Pilin [54524] (4)
    1. Pilin Gc [109618]
      1. Neisseria gonorrhoeae [TaxId: 485] [54526] (2)
    2. Pilin P1 [109619]
      1. Pseudomonas aeruginosa [TaxId: 287] [64247] (3)
        SQ P17838 36-147
    3. Type IV Pilin Pak [109620]
      1. Pseudomonas aeruginosa [TaxId: 287] [54527] (8)
    4. Type IVb pilin PilS [110866]
      1. Salmonella typhi [TaxId: 90370] [110867] (1)
        SQ Q9ZIU9 51-206
  2. TcpA-like pilin [89868] (1)
    common fold is decorated with additional structures
    1. Toxin-coregulated pilus subunit TcpA [89869]
      1. Vibrio cholerae [TaxId: 666] [89870] (1)
  3. Pseudopilin [117865] (1)
    1. Pullulanase secretion protein PulG [117866]
      1. Klebsiella pneumoniae [TaxId: 573] [117867] (1)
        SQ P15746 32-138
  4. YadA C-terminal domain-like [143107] (1)
    Pfam 03895; trimerizes with the formation of closed beta-barrel (n=12, S=12), wrapped around triple parallel coiled coil
    1. Adhesin Hia [143108]
      1. Haemophilus influenzae [TaxId: 727] [143109] (12)
        SQ Q48152 1022-1098! SQ Q48152 998-1098
  5. EpsJ-like [160127] (2)
    1. Type II secretory pathway component EpsJ [160128]
      1. Vibrio vulnificus [TaxId: 672] [160129] (4)
        SQ Q7MPZ0 48-213
    2. Pseudopilin GspJ [160130]
      1. Escherichia coli [TaxId: 562] [160131] (1)
        SQ Q8VRM4 34-187
  6. GspK pilin-like domain [160132] (1)
    N-terminal and C-terminal regions of Pfam 03934
    1. Pseudopilin GspK [160133]
      1. Escherichia coli [TaxId: 562] [160134] (1)
        SQ A7ZRI8 38-102,284-324
  7. GSPII I/J protein-like [160135] (2)
    Pfam 02501
    1. Pseudopilin EpsI [160136]
      1. Vibrio vulnificus [TaxId: 672] [160137] (4)
        SQ Q7MPZ1 63-143
    2. Pseudopilin GspI [160138]
      1. Escherichia coli [TaxId: 562] [160139] (1)
        SQ Q8VPC3 35-118
Mitochondrial glycoprotein MAM33-like [54528] (1)
core: beta(7)-alpha(2); N- and C-terminal extensions form a coiled coil subdomain
1. Mitochondrial glycoprotein MAM33-like [54529] (1)
  uperfamily
  1. Mitochondrial glycoprotein MAM33-like [54530] (2)
    1. Acidic mitochondrial matrix protein p32 [54531]
      1. Human (Homo sapiens) [TaxId: 9606] [54532] (1)
    2. Hypothetical protein Lmaj011689 [143110]
      1. Leishmania major [TaxId: 5664] [143111] (6)
        SQ Q4Q7K6 14-195
NAP-like [143112] (1)
core: central meander 4-stranded beta-sheet (order: 1234) transversed by a C-terminal helix
1. NAP-like [143113] (1)
  uperfamily
  1. NAP-like [143114] (2)
    Pfam 00956
    1. Nucleosome assembly protein, NAP [143115]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143116] (3)
        SQ P25293 70-370
    2. Protein SET [160140]
      Phosphatase 2A inhibitor I2PP2A
      1. Human (Homo sapiens) [TaxId: 9606] [160141] (2)
        SQ Q01105 1-235
Polo-box domain [82614] (1)
beta(6)-alpha; antiparallel beta-sheet, meander
1. Polo-box domain [82615] (2)
  Serine/threonine protein kinase-associated motif embedded in two distinct folds
  uperfamily
  1. Polo-box duplicated region [102856] (1)
    duplication: consists of two polo-box domains; binds phosphothreonine peptide
    1. Serine/threonine-protein kinase plk C-terminal domain [102857]
      1. Human (Homo sapiens) [TaxId: 9606] [102858] (9)
  2. Swapped Polo-box domain [82616] (1)
    beta(5)-alpha-beta; forms swapped dimer with two 6-stranded antiparallel beta sheets; order [6]123[4][5]
    1. Serine/threonine-protein kinase Sak C-terminal domain [82617]
      1. Mouse (Mus musculus) [TaxId: 10090] [82618] (1)
mRNA decapping enzyme DcpS N-terminal domain [102859] (1)
beta(3)-alpha-beta(3)-alpha; 3 layers a/b/a
1. mRNA decapping enzyme DcpS N-terminal domain [102860] (1)
  forms swapped dimer with two 6-stranded antiparallel beta sheets; order 1236[5][4]
  uperfamily
  1. mRNA decapping enzyme DcpS N-terminal domain [102861] (2)
    1. mRNA decapping enzyme DcpS N-terminal domain [102862]
      1. Human (Homo sapiens) [TaxId: 9606] [102863] (14)
      2. Mouse (Mus musculus) [TaxId: 10090] [110868] (1)
        SQ Q9DAR7
Inhibitor of vertebrate lysozyme, Ivy [89871] (1)
alpha(2)-beta(5)-alpha(2); 3 layers a/b/a; meander beta-sheet
1. Inhibitor of vertebrate lysozyme, Ivy [89872] (1)
  uperfamily
  1. Inhibitor of vertebrate lysozyme, Ivy [89873] (2)
    1. Inhibitor of vertebrate lysozyme, Ivy [89874]
      formerly hypothetical protein YkfE
      1. Escherichia coli [TaxId: 562] [89875] (2)
        SQ P45502 31-157
      2. Pseudomonas aeruginosa [TaxId: 287] [89876] (1)
FKBP-like [54533] (3)
core: beta(2)-alpha-beta(2); antiparallel beta-sheet
1. FKBP-like [54534] (3)
  uperfamily
  1. FKBP immunophilin/proline isomerase [54535] (24)
    1. FK-506 binding protein (FKBP12), an immunophilin [54536]
      cis-trans prolyl-isomerase
      1. Human (Homo sapiens) [TaxId: 9606] [54537] (33)
      2. Cow (Bos taurus) [TaxId: 9913] [54538] (2)
    2. Calcineurin (FKBP12.6) [54539]
      1. Human (Homo sapiens) [TaxId: 9606] [54540] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [54541] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54542] (1)
    3. FKBP25 [54543]
      1. Human (Homo sapiens) [TaxId: 9606] [54544] (1)
    4. FKB-6, N-terminal domain [102864]
      1. Caenorhabditis elegans [TaxId: 6239] [102865] (1)
    5. FKBP59-I, N-terminal domain [54545]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [54546] (2)
    6. FKBP52, N-terminal domains [82619]
      1. Human (Homo sapiens) [TaxId: 9606] [82620] (4)
        SQ Q02790 21-427; contains tandem repeat of two FKPB domains
    7. FKBP51, N-terminal domains [82621]
      duplication: tandem repeat of two FKBP domains
      1. Human (Homo sapiens) [TaxId: 9606] [82622] (1)
      2. Monkey (Saimiri boliviensis) [TaxId: 27679] [82623] (1)
    8. Mitotic rotamase PIN1, domain 2 [54547]
      Domain 1 is a WW-domain
      1. Human (Homo sapiens) [TaxId: 9606] [54548] (7)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [75386] (1)
    9. Parvulin [64248]
      1. Human (Homo sapiens), hpar14 [TaxId: 9606] [64249] (2)
    10. Parvulin 10 (rotamase C) [89877]
      1. Escherichia coli [TaxId: 562] [89878] (2)
    11. Archaeal FKBP [89879]
      contains insert all-beta subdomain; dual function: PPI and chaperone-like activities
      1. Archaeon Methanococcus thermolithotrophicus [TaxId: 2186] [89880] (1)
    12. Macrophage infectivity potentiator protein (MIP) [64250]
      contains all-alpha dimerisation subdomain in the N-terminal extension
      1. Legionella pneumophila [TaxId: 446] [64251] (1)
      2. Trypanosoma cruzi [TaxId: 5693] [75387] (1)
    13. Peptidyl-prolyl cis-trans isomerase FkpA [102866]
      similar to MIP; contains all-alpha dimerisation subdomain in the N-terminal extension
      1. Escherichia coli [TaxId: 562] [102867] (3)
    14. Trigger factor PPIase domain [75388]
      1. Mycoplasma genitalium [TaxId: 2097] [75389] (1)
      2. Escherichia coli [TaxId: 562] [89881] (3)
        SQ P22257
      3. Vibrio cholerae [TaxId: 666] [110869] (1)
        SQ Q9KQS5
    15. Porin chaperone SurA, PPIase domains [82624]
      1. Escherichia coli [TaxId: 562] [82625] (8)
    16. FKBP13 [110870]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [110871] (6)
        SQ Q9SCY2 84-208
  2. GreA transcript cleavage factor, C-terminal domain [54549] (3)
    1. GreA transcript cleavage factor, C-terminal domain [54550]
      N-terminal domain is a long alpha-hairpin
      1. Escherichia coli [TaxId: 562] [54551] (1)
      2. Thermus aquaticus [TaxId: 271] [143117] (3)
        SQ Q8VQD7 78-156
      3. Thermus thermophilus [TaxId: 274] [143118] (6)
        SQ Q5SJG6 78-156! SQ Q72JT8 78-156
  3. 3-mercaptopyruvate sulfurtransferase, C-terminal domain [102868] (1)
    1. 3-mercaptopyruvate sulfurtransferase, C-terminal domain [102869]
      1. Leishmania major [TaxId: 5664] [102870] (1)
2. Colicin E3 immunity protein [54552] (1)
  uperfamily
  1. Colicin E3 immunity protein [54553] (1)
    1. Colicin E3 immunity protein [54554]
      1. Escherichia coli [TaxId: 562] [54555] (5)
3. Chitinase insertion domain [54556] (1)
  uperfamily
  1. Chitinase insertion domain [54557] (15)
    1. Chitinase A [54558]
      1. Serratia marcescens [TaxId: 615] [54559] (11)
        SQ P07254 24-563
    2. Chitinase B [54560]
      1. Serratia marcescens [TaxId: 615] [54561] (14)
    3. Psychrophilic chitinase B [82626]
      1. Arthrobacter sp., tad20 [TaxId: 1667] [82627] (1)
    4. Chitinase A1 [75390]
      1. Bacillus circulans [TaxId: 1397] [75391] (1)
    5. Chitinase 1 [54562]
      1. Fungus (Coccidioides immitis) [TaxId: 5501] [54563] (4)
      2. Aspergillus fumigatus [TaxId: 5085] [117868] (26)
        SQ Q873X9
    6. Chitotriosidase [82628]
      1. Human (Homo sapiens) [TaxId: 9606] [82629] (10)
    7. Signal processing protein (SPC-40, MGP-40) [89882]
      secreted during involution
      1. Goat (Capra hircus) [TaxId: 9925] [89883] (14)
      2. Cow (Bos taurus) [TaxId: 9913] [110872] (1)
        SQ P30922
      3. Sheep (Ovis aries) [TaxId: 9940] [109621] (12)
        SQ Q6TMG6
      4. Buffalo (Bubalus bubalis) [TaxId: 89462] [110873] (3)
        SQ Q7YS85
      5. Pig (Sus scrofa) [TaxId: 9823] [117869] (4)
        SQ Q5UC99
    8. Chitinase-3 like protein 1 (GP-39, YKL-40) [89884]
      1. Human (Homo sapiens) [TaxId: 9606] [89885] (7)
    9. Chitinase-like lectin ym1 [64252]
      1. Mouse (Mus musculus) [TaxId: 10090] [64253] (2)
    10. Imaginal disc growth factor-2 [75392]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75393] (2)
Ribosomal protein S16 [54564] (1)
beta(4)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet, order: 51234
1. Ribosomal protein S16 [54565] (1)
  uperfamily
  1. Ribosomal protein S16 [54566] (3)
    1. Ribosomal protein S16 [54567]
      1. Thermus thermophilus [TaxId: 274] [54568] (37)
        SQ P80379
      2. Aquifex aeolicus [TaxId: 63363] [160142] (1)
        SQ O66523 2-102
      3. Escherichia coli [TaxId: 562] [160143] (26)
        SQ P0A7T3 1-82
Ribosomal protein S19 [54569] (1)
alpha-beta-X-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 123
1. Ribosomal protein S19 [54570] (1)
  uperfamily
  1. Ribosomal protein S19 [54571] (2)
    1. Ribosomal protein S19 [54572]
      1. Thermus thermophilus [TaxId: 274] [54573] (38)
        SQ P80381
      2. Escherichia coli [TaxId: 562] [160144] (26)
        SQ P0A7U3 2-80
YefM-like [143119] (1)
core: beta-alpha(2)-beta(2)-alpha; mixed beta-sheet, order:123, strands 1 and 2 are parallel; forms compact dimer with a single beta-sheet;
1. YefM-like [143120] (1)
  uperfamily
  1. YefM-like [143121] (2)
    antitoxin component of the YefM/YoeB-like system; binds to the toxin component wia extra C-terminal tail, unstructured in the free state, but adopting a RelB-like conformation in the bound state
    1. Antitoxin YefM [143122]
      1. Escherichia coli [TaxId: 562] [143123] (4)
        SQ P69346 1-55! SQ P69346 1-83
    2. Hypothetical protein NE2111 [143124]
      1. Nitrosomonas europaea [TaxId: 915] [143125] (4)
        SQ Q82T22 1-51
Ribosomal protein L31e [54574] (1)
beta-alpha-beta-(alpha)-beta(2); 2 layers: alpha/beta; mixed beta-sheet, order: 1342
1. Ribosomal protein L31e [54575] (1)
  uperfamily
  1. Ribosomal protein L31e [54576] (1)
    1. Ribosomal protein L31e [54577]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [54578] (40)
        SQ P18138
Allophycocyanin linker chain (domain) [54579] (1)
beta(2)-alpha-beta; 2 layers: alpha/beta
1. Allophycocyanin linker chain (domain) [54580] (1)
  uperfamily
  1. Allophycocyanin linker chain (domain) [54581] (1)
    1. Allophycocyanin linker chain (domain) [54582]
      1. Mastigocladus laminosus [TaxId: 83541] [54583] (1)
Cdc48 domain 2-like [54584] (1)
beta-alpha-beta(3); 2 layers: alpha/beta
1. Cdc48 domain 2-like [54585] (1)
  uperfamily
  1. Cdc48 domain 2-like [54586] (5)
    1. C-terminal domain of NSF-N, NSF-Nc [54587]
      NSF-N, the N-terminal 'functional' domain of the N-ethylmaleimide sensitive fusion protein, consists of two structural domains
      1. Hamster (Cricetulus griseus) [TaxId: 10029] [54588] (2)
      2. Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932] [54589] (1)
    2. C-terminal domain of VAT-N, VAT-Nc [54590]
      VAT-N is the N-terminal 'functional' domain of the VCP-like ATPase
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [54591] (2)
    3. Membrane fusion atpase p97 domain 2, P97-Nc [64254]
      1. Mouse (Mus musculus) [TaxId: 10090] [64255] (5)
    4. Peroxisome biogenesis factor 1 (PEX-1), domain 2 [110874]
      1. Mouse (Mus musculus) [TaxId: 10090] [110875] (1)
        SQ Q5BL07 13-179
Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54592] (1)
beta-alpha-beta(3); 2 layers: alpha/beta
1. Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase [54593] (10)
  uperfamily
  1. Glyoxalase I (lactoylglutathione lyase) [54594] (3)
    duplication: consists of two clear structural repeats each having this fold
    1. Glyoxalase I (lactoylglutathione lyase) [54595]
      1. Human (Homo sapiens) [TaxId: 9606] [54596] (4)
      2. Escherichia coli [TaxId: 562] [54597] (5)
      3. Leishmania major [TaxId: 5664] [143126] (6)
        SQ Q68RJ8 3-141
        Trypanothione-dependent glyoxalase i
  2. Antibiotic resistance proteins [54598] (10)
    duplication: consists of two clear structural repeats each having this fold
    subunit fold and dimeric assembly are similar to those of glyoxalase
    1. Bleomycin resistance protein, BRP [54599]
      Active as dimer
      1. Streptomyces verticillus [TaxId: 29309] [54600] (3)
      2. Streptoalloteichus hindustanus [TaxId: 2017] [54601] (2)
        SQ P17493
      3. Klebsiella pneumoniae [TaxId: 573] [64256] (4)
        the transposon tn5-encoding bleomycin-binding protein, BlmT
    2. Mitomycin resistance protein D, MRD [75394]
      1. Streptomyces lavendulae [TaxId: 1914] [75395] (6)
    3. Fosfomycin resistance protein A (FosA) [82630]
      1. Pseudomonas aeruginosa [TaxId: 287] [82631] (5)
      2. Serratia marcescens [TaxId: 615] [102871] (1)
        gene from transposon tn2921
    4. Fosfomycin resistance protein FosX [102872]
      1. Mesorhizobium loti [TaxId: 381] [102873] (1)
    5. Hypothetical protein BC3580 [117870]
      1. Bacillus cereus [TaxId: 1396] [117871] (1)
        SQ Q81AI8
    6. Hypotheical protein SP0731 [143127]
      1. Streptococcus pneumoniae [TaxId: 1313] [143128] (2)
        SQ Q97RR3 1-115
    7. Uncharacterized protein Atu1953 [160145]
      1. Agrobacterium tumefaciens [TaxId: 358] [160146] (2)
        SQ Q8UE11 2-115
  3. Methylmalonyl-CoA epimerase [64257] (1)
    Different association of repeats but a similar dimeric structure to the glyoxalase dimer
    1. Methylmalonyl-CoA epimerase [64258]
      1. Propionibacterium shermanii [TaxId: 1752] [64259] (2)
  4. Hypothetical protein YecM (EC4020) [75396] (1)
    Similar subunit fold is to methylmalonyl-CoA epimerase
    1. Hypothetical protein YecM (EC4020) [75397]
      1. Escherichia coli [TaxId: 562] [75398] (1)
  5. Extradiol dioxygenases [54602] (10)
    duplication: consists of 2 similar domains with 2 repeats in each
    Similar to the Methylmalonyl-CoA epimerase dimer
    1. 2,3-Dihydroxybiphenyl dioxygenase (DHBD, BPHC enzyme) [54603]
      1. Pseudomonas sp. [TaxId: 306] [54604] (10)
      2. Burkholderia cepacia, formerly Pseudomonas cepacia [TaxId: 292] [54605] (6)
    2. Catechol 2,3-dioxygenase (metapyrocatechase) [54606]
      1. Pseudomonas putida, mt2 [TaxId: 303] [54607] (1)
    3. Homoprotocatechuate 2,3-dioxygenase [89886]
      1. Arthrobacter globiformis [TaxId: 1665] [89887] (3)
      2. Brevibacterium fuscum [TaxId: 47914] [89888] (43)
    4. 4-hydroxyphenylpyruvate dioxygenase, HppD [54608]
      1. Pseudomonas fluorescens [TaxId: 294] [54609] (1)
      2. Streptomyces avermitilis [TaxId: 33903] [110876] (1)
        SQ Q53586
      3. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [110877] (4)
        SQ P93836 33-428 ! SQ P93836 63-459
      4. Human (Homo sapiens) [TaxId: 9606] [110878] (1)
        SQ P32755
      5. Corn (Zea mays) [TaxId: 4577] [110879] (1)
        SQ O48604 29-423 # 85% sequence identity
  6. Hypothetical protein BC1747 [110880] (1)
    subunit fold and dimeric assembly are similar to those of glyoxalase
    1. Hypothetical protein BC1747 [110881]
      1. Bacillus cereus (strain ATCC 14579 / DSM 31) [TaxId: 226900] [110882] (1)
        SQ Q81F54
  7. 3-demethylubiquinone-9 3-methyltransferase [110883] (4)
    Pfam 06983; both variants of dimeric assembly are observed in the family (domain swapping)
    1. Hypothetical protein PA1358 [110884]
      1. Pseudomonas aeruginosa [TaxId: 287] [110885] (1)
        SQ Q9I3Y6
    2. Hypothetical protein PA2721 [110886]
      1. Pseudomonas aeruginosa [TaxId: 287] [110887] (1)
        SQ Q9I0C1
    3. Hypothetical protein MW1090 [117872]
      1. Staphylococcus aureus [TaxId: 1280] [117873] (1)
        SQ Q8NX24
    4. Hypothetical protein PA1353 [117874]
      Family assignment by BLAST; HMM assignment is the Glyoxalase family (Pfam 00903)
      1. Pseudomonas aeruginosa [TaxId: 287] [117875] (1)
        SQ Q9I3Z1
  8. Hypothetical protein YycE [110888] (1)
    subunit fold and dimeric assembly are similar to those of glyoxalase
    1. Hypothetical protein YycE [110889]
      1. Bacillus subtilis [TaxId: 1423] [110890] (1)
        SQ P37479
  9. Hypothetical protein At5g48480 [117876] (1)
    subunit fold and dimeric assembly are similar to those of glyoxalase
    1. Hypothetical protein At5g48480 [117877]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117878] (3)
        SQ Q9LV66 20-154
  10. BC1024-like [143129] (1)
    duplication: consists of 2 similar domains with 2 repeats in each; similar to the glyoxalase dimer
    1. Hypothetical protein BC1024 [143130]
      1. Bacillus cereus [TaxId: 1396] [143131] (2)
        SQ Q81H03 1-144! SQ Q81H03 145-314
Chromosomal protein MC1 [102874] (1)
beta(2)-alpha-beta(3); 2 layers: alpha/beta
1. Chromosomal protein MC1 [102875] (1)
  uperfamily
  1. Chromosomal protein MC1 [102876] (1)
    1. Chromosomal protein MC1 [102877]
      1. Archaeon Methanosarcina thermophila [TaxId: 2210] [102878] (1)
        SQ P12770
CPE0013-like [160147] (1)
beta(2)-alpha-beta(3); mixed, mostly antiparallel beta-sheet, folded in a half-barrel; order:31254; strand 3 is parallel to strand 1 and is shorter than the rest
1. CPE0013-like [160148] (1)
  1. CPE0013-like [160149] (1)
    Pfam 07892; DUF1667; the founding protein lacks the predicted metal-binding motif, found at the N-termini of other members of the Pfam family
    1. Hypothetical protein CPE0013 [160150]
      1. Clostridium perfringens [TaxId: 1502] [160151] (1)
        SQ Q8XPF0 1-77
beta-hairpin-alpha-hairpin repeat [74651] (2)
multiple repeats of beta(2)-alpha(2) motif
1. Ankyrin repeat [48403] (1)
  repeats organized in elongated structures
  uperfamily
  1. Ankyrin repeat [48404] (20)
    1. Ankyrin-R [82632]
      1. Human (Homo sapiens) [TaxId: 9606] [82633] (1)
    2. 53BP2 [48405]
      1. Human (Homo sapiens) [TaxId: 9606] [48406] (1)
    3. GA bindinig protein (GABP) beta 1 [48407]
      1. Mouse (Mus musculus) [TaxId: 10090] [48408] (1)
    4. Cell cycle inhibitor p19ink4D [48409]
      1. Human (Homo sapiens) [TaxId: 9606] [48410] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [48411] (1)
    5. p18ink4C(ink6) [48412]
      1. Human (Homo sapiens) [TaxId: 9606] [48413] (6)
    6. Cell cycle inhibitor p16ink4A [48414]
      1. Human (Homo sapiens) [TaxId: 9606] [48415] (4)
      2. Mouse (Mus musculus) [TaxId: 10090] [48416] (1)
    7. I-kappa-B-alpha [48417]
      1. Human (Homo sapiens) [TaxId: 9606] [48418] (2)
    8. bcl-3 [69091]
      a member of the I-kappa-B family
      1. Human (Homo sapiens) [TaxId: 9606] [69092] (2)
    9. Transcription factor inhibitor I-kappa-B-beta, IKBB [82634]
      1. Mouse (Mus musculus) [TaxId: 10090] [82635] (2)
    10. Myotrophin [48419]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [48420] (2)
    11. Swi6 ankyrin-repeat fragment [48421]
      interrupted by an insertion
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [48422] (1)
    12. Pyk2-associated protein beta [48423]
      1. Mouse (Mus musculus) [TaxId: 10090] [48424] (1)
    13. Neurogenic locus notch receptor domain [102879]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102880] (1)
    14. 26S proteasome non-ATPase regulatory subunit 10, gankyrin [102881]
      1. Human (Homo sapiens) [TaxId: 9606] [102882] (3)
        SQ O75832
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102883] (7)
    15. Myosin phosphatase targeting subunit 1, MYPT1 [110891]
      1. Chicken (Gallus gallus) [TaxId: 9031] [110892] (1)
        SQ Q90623 1-299
    16. RNase L, 2-5a-dependent ribonuclease [117879]
      1. Human (Homo sapiens) [TaxId: 9606] [117880] (1)
        SQ Q05823 21-305
    17. Lin-12 [160152]
      1. Caenorhabditis elegans [TaxId: 6239] [160153] (1)
        SQ P14585 1021-1297
2. Plakin repeat [75399] (1)
  repeats associate forming globular subdomains
  uperfamily
  1. Plakin repeat [75400] (1)
    1. Desmoplakin intermediate filament-binding domains [75401]
      1. Human (Homo sapiens) [TaxId: 9606] [75402] (2)
Proguanylin [89889] (1)
beta(2)-alpha(3)-beta; two layers: alpha/beta; antiparallel sheet: order 213
1. Proguanylin [89890] (1)
  uperfamily
  1. Proguanylin [89891] (1)
    1. Proguanylin [89892]
      processing of this protein releases peptide hormone guanylin, structure of which structure is known: see 1gna
      1. Human (Homo sapiens) [TaxId: 9606] [89893] (1)
SecB-like [54610] (1)
beta(4)-alpha(2); two layers: alpha/beta; antiparallel sheet: order 1432
1. SecB-like [54611] (2)
  uperfamily
  1. Bacterial protein-export protein SecB [54612] (2)
    1. Bacterial protein-export protein SecB [54613]
      1. Haemophilus influenzae [TaxId: 727] [54614] (2)
      2. Escherichia coli [TaxId: 562] [102884] (1)
  2. SP1558-like [160154] (2)
    Pfam 06619; DUF1149
    1. Hypothetical protein SP1558 [160155]
      1. Streptococcus pneumoniae [TaxId: 1313] [160156] (1)
        SQ Q97PP5 5-128
    2. Hypothetical protein gbs1413 [160157]
      1. Streptococcus agalactiae [TaxId: 1311] [160158] (4)
        SQ Q8E4I8 1-124
MesJ substrate recognition domain-like [82828] (1)
beta-alpha(2)-beta(3); 2 layers: a/b; antiparallel beta-sheet, order:1432
1. MesJ substrate recognition domain-like [82829] (1)
  uperfamily
  1. MesJ substrate recognition domain-like [82830] (2)
    1. tRNA-Ile-lysidine synthetase, TilS, substrate-binding domain [82831]
      formerly putative cell cycle protein MesJ
      1. Escherichia coli [TaxId: 562] [82832] (1)
    2. TilS-like protein Aq_1887 [143132]
      lacks the C-terminal domain of the E. coli homologue
      1. Aquifex aeolicus [TaxId: 63363] [143133] (10)
        SQ O67728 217-311
FYSH domain [89894] (1)
beta(2)-alpha(2)-beta(2)-alpha-beta; two layers: alpha/beta; antiparallel sheet: order 51234
1. FYSH domain [89895] (2)
  uperfamily
  1. Hypothetical protein Yhr087W [89896] (1)
    1. Hypothetical protein Yhr087W [89897]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89898] (1)
  2. Hypothetical protein AF0491, N-terminal domain [110893] (1)
    1. Hypothetical protein AF0491, N-terminal domain [110894]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110895] (2)
        SQ O29759
VSV matrix protein [75403] (1)
beta-alpha(2)-beta(4)-alpha-beta(2); two layers: alpha/beta; bifurcated coiled beta-sheet: order of the first 5 strands: 23154
1. VSV matrix protein [75404] (1)
  uperfamily
  1. VSV matrix protein [75405] (1)
    1. VSV matrix protein [75406]
      1. Vesicular stomatitis virus, VSV [TaxId: 11276] [75407] (1)
DNA-binding domain of Mlu1-box binding protein MBP1 [54615] (1)
beta(4)-alpha(2)-beta(2)-alpha; antiparallel sheet: order 123465
1. DNA-binding domain of Mlu1-box binding protein MBP1 [54616] (1)
  has some topological similarity to the "winged helix" DNA-binding domain, to B1 and B5 domains of PheRS-beta (1PYS CH B) and to methyl-CpG-binding domain
  uperfamily
  1. DNA-binding domain of Mlu1-box binding protein MBP1 [54617] (1)
    1. DNA-binding domain of Mlu1-box binding protein MBP1 [54618]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54619] (3)
Heme-binding protein A (HasA) [54620] (1)
beta-alpha-beta(6)-alpha(2); antiparallel sheet: order 165432
1. Heme-binding protein A (HasA) [54621] (1)
  uperfamily
  1. Heme-binding protein A (HasA) [54622] (1)
    1. Heme-binding protein A (HasA) [54623]
      1. Serratia marcescens [TaxId: 615] [54624] (6)
Chalcone isomerase [54625] (1)
beta(3)-alpha(2)-beta-alpha(2)-beta3; 2 layers alpha/beta; antiparallel sheet: order 1234567
1. Chalcone isomerase [54626] (1)
  uperfamily
  1. Chalcone isomerase [54627] (1)
    1. Chalcone isomerase [54628]
      1. Alfalfa (Medicago sativa) [TaxId: 3879] [54629] (7)
Coproporphyrinogen III oxidase [102885] (1)
alpha-beta(6)-alpha(2)-beta-alpha(n); 3 layers alpha/beta/alpha; antiparallel sheet: order 1234567
1. Coproporphyrinogen III oxidase [102886] (1)
  uperfamily
  1. Coproporphyrinogen III oxidase [102887] (2)
    Pfam 01218
    1. Hypothetical protein Lmaj006828 [102888]
      1. Leishmania major [TaxId: 5664] [102889] (7)
    2. Coproporphyrinogen III oxidase [110896]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110897] (4)
        SQ P11353
Hypothetical protein Ta1206 [102890] (1)
beta(4)-alpha-beta(2)-alpha(2); mixed, predominately antiparallel beta-sheet, order: 123465, strands 4 and 5 are parallel to each other
1. Hypothetical protein Ta1206 [102891] (1)
  can be divided into an N-terminal, tetramerisation all-beta subdomain and a C-terminal alpha+beta subdomain related by a circular permutation to the Y-family DNA-polymerase 'fingers' subdomain
  uperfamily
  1. Hypothetical protein Ta1206 [102892] (1)
    1. Hypothetical protein Ta1206 [102893]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102894] (1)
CBS-domain pair [54630] (1)
duplication: tandem repeat of two beta-X-beta-alpha-beta(2)-alpha motifs of similar sequences; 4 layers: a/b/b/a
1. CBS-domain pair [54631] (1)
  uperfamily
  1. CBS-domain pair [54632] (24)
    Pfam 00571; pairs of CBS domains dimerize to form a stable globular domain, a.k.a. Bateman domain
    1. Hypothetical protein TM0935 [102895]
      1. Thermotoga maritima [TaxId: 2336] [102896] (1)
    2. Hypothetical protein MTH1622 [102897]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [102898] (1)
    3. Hypothetical protein Ta0289 [102899]
      contains extra C-terminal zinc-finger domain
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102900] (3)
    4. Type II inosine monophosphate dehydrogenase CBS domains [54633]
      contains tandem repeat of two CBS domains inserted into the catalytic TIM-barrel domain; may be disordered in the crystals
      1. Human (Homo sapiens), type I [TaxId: 9606] [89899] (1)
      2. Human (Homo sapiens), type II [TaxId: 9606] [54634] (3)
      3. Chinese hamster (Cricetulus griseus) [TaxId: 10029] [64260] (1)
      4. Streptococcus pyogenes [TaxId: 1314] [54635] (1)
    5. Hypothetical protein YkuL [117881]
      1. Bacillus subtilis [TaxId: 1423] [117882] (1)
        SQ O31698 9-142
    6. Nuclear protein SNF4 [143134]
      duplication: comprises four CBS repeats
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143135] (3)
        SQ P12904 181-265
    7. Hypothetical protein TM0892, CBS tandem [143136]
      1. Thermotoga maritima [TaxId: 2336] [143137] (2)
        SQ Q9WZZ4 1-60! SQ Q9WZZ4 61-121
    8. Chloride channel protein, CBS tandem [143138]
      contains additional structures between the two CBS repeats
      1. Marbled electric ray (Torpedo marmorata) [TaxId: 7788] [143139] (2)
        SQ P21564 527-606! SQ P21564 691-770
    9. Hypothetical protein VC0737 [143140]
      Putative acetoin utilization protein AcuB
      1. Vibrio cholerae [TaxId: 666] [143141] (2)
        SQ Q9KTZ3 21-83! SQ Q9KTZ3 93-159
    10. Hypothetical protein Rv2626c [143142]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143143] (4)
        SQ O06186 2-124
    11. Uncharacterized protein PH1780 [160159]
      duplication: comprises four CBS repeats
      1. Pyrococcus horikoshii [TaxId: 53953] [160160] (2)
        SQ O59416 125-281! SQ O59416 126-281
    12. Uncharacterized protein ST2348 [160161]
      1. Sulfolobus tokodaii [TaxId: 111955] [160162] (2)
        SQ Q96Y20 1-127
    13. Magnesium transporter MgtE [160163]
      1. Thermus thermophilus [TaxId: 274] [160164] (4)
        SQ Q5SMG8 132-275
      2. Enterococcus faecalis [TaxId: 1351] [160165] (1)
        SQ Q830V1 136-262
    14. Uncharacterized protein C1556.08c [160166]
      consists of 4 CBS units
      1. Schizosaccharomyces pombe [TaxId: 4896] [160167] (2)
        SQ Q10343 182-334! SQ Q10343 3-181
    15. Uncharacterized protein PH0107 [160168]
      1. Pyrococcus horikoshii [TaxId: 53953] [160169] (2)
        SQ O57847 4-135
    16. Uncharacterized protein SSO3205 [160170]
      duplication: comprises four CBS repeats
      1. Sulfolobus solfataricus [TaxId: 2287] [160171] (2)
        SQ Q97U20 1-135! SQ Q97U20 136-276
    17. Uncharacterized protein NE2398 [160172]
      1. Nitrosomonas europaea [TaxId: 915] [160173] (4)
        SQ Q82SE2 1-127
    18. Chloride channel protein 5, ClC-5 [160174]
      1. Human (Homo sapiens) [TaxId: 9606] [160175] (1)
        SQ P51795 578-746
    19. 5'-AMP-activated protein kinase subunit gamma-1, AMPKg [160176]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [160177] (6)
        SQ P80385 182-326! SQ P80385 23-181
    20. Uncharacterized protein PAE2072 [160178]
      2 CBS domains = 1 Bateman domain; binds two adenosine nucleotides per subunit (one per one CBS repeat)
      1. Pyrobaculum aerophilum [TaxId: 13773] [160179] (6)
        SQ Q8ZVX8 2-132
Thioesterase/thiol ester dehydrase-isomerase [54636] (1)
core: beta-alpha-beta(4); 2 layers: alpha/beta
1. Thioesterase/thiol ester dehydrase-isomerase [54637] (8)
  uperfamily
  1. 4HBT-like [54638] (18)
    Pfam 03061
    1. 4-hydroxybenzoyl-CoA thioesterase [54639]
      1. Pseudomonas sp., CBS-3 [TaxId: 306] [54640] (4)
    2. Hypothetical protein YbaW [89900]
      1. Escherichia coli [TaxId: 562] [89901] (1)
    3. Hypothetical protein YbgC [102901]
      1. Escherichia coli [TaxId: 562] [102902] (1)
    4. Putative acyl-coa thioester hydrolase HI0827 [102903]
      1. Haemophilus influenzae [TaxId: 727] [102904] (2)
    5. Acyl-CoA hydrolase BH0798 [117883]
      1. Bacillus halodurans [TaxId: 86665] [117884] (1)
        SQ Q9KEQ1
    6. Hypothetical protein PP0301 [143144]
      1. Pseudomonas putida [TaxId: 303] [143145] (1)
        SQ Q88R33 1-156
    7. Hypothetical protein XCC1147 [143146]
      1. Xanthomonas campestris pv. campestris [TaxId: 340] [143147] (1)
        SQ Q8PBH4 5-122
    8. Probable acyl-CoA hydrolase AGR_L_2016 [143148]
      1. Agrobacterium tumefaciens [TaxId: 358] [143149] (6)
        SQ Q7CTE6 147-262! SQ Q7CTE6 9-143
    9. Probable thioesterase TTHA1846 [143150]
      1. Thermus thermophilus [TaxId: 274] [143151] (4)
        SQ Q5SH84 1-132
    10. Probable thioesterase TTHA0908 [143152]
      1. Thermus thermophilus [TaxId: 274] [143153] (4)
        SQ Q5SJV0 1-132
    11. Hypothetical protein Jann_1972 [143154]
      1. Jannaschia sp. CCS1 [TaxId: 290400] [143155] (2)
        SQ Q28QX3 3-161
    12. Hypothetical protein SSO2295 [143156]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [143157] (4)
        SQ Q97WD2 1-134
    13. Hypothetical thioesterase PA5185 [143158]
      1. Pseudomonas aeruginosa [TaxId: 287] [143159] (25)
        SQ Q9HU04 5-146
    14. Hypothetical protein PMT2055 [143160]
      1. Prochlorococcus marinus [TaxId: 1219] [143161] (1)
        SQ Q7V4A7 1-144
    15. Hypothetical protein PA2801 [143162]
      1. Pseudomonas aeruginosa [TaxId: 287] [143163] (1)
        SQ Q9I042 5-134
    16. Acyl-coa hydrolase BC2038 [143164]
      1. Bacillus cereus [TaxId: 1396] [143165] (3)
        SQ Q81EE4 8-171
    17. Hypothetical protein Jann0674 [160180]
      1. Jannaschia sp. ccs1 [TaxId: 290400] [160181] (2)
        SQ Q28UM1 1-143
    18. GK1870 orthologue [160182]
      Predicted 4-hydroxybenzoyl-CoA thioesterase
      1. Bacillus stearothermophilus [TaxId: 1422] [160183] (4)
        SQ Q5KYT1 1-131
  2. beta-Hydroxydecanol thiol ester dehydrase [54641] (1)
    contains two additional beta-strands in the N-terminal extension
    1. beta-Hydroxydecanol thiol ester dehydrase [54642]
      1. Escherichia coli [TaxId: 562] [54643] (4)
  3. Acyl-CoA thioesterase [54644] (2)
    duplication: consists of two domains of this fold
    1. Thioesterase II (TesB) [54645]
      1. Escherichia coli [TaxId: 562] [54646] (1)
    2. Peroxisomal long-chain acyl-CoA thioesterase 1, TES1 [143166]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143167] (4)
        SQ P41903 13-116
  4. MaoC-like [82636] (7)
    1. (R)-specific enoyl-CoA hydratase [82637]
      involved in polyhydroxyalkanoate (PHA) biosynthesis
      1. Aeromonas caviae [TaxId: 648] [82638] (1)
    2. Monoamine oxidase regulatory protein [102905]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102906] (1)
    3. 2-enoyl-coa hydratase domain of multifunctional peroxisomal hydratase-dehydrogenase-epimerase [102907]
      duplication: consists of two MaoC-like domains; there is a greater structural divergence in the N-terminal domain
      1. Yeast (Candida tropicalis) [TaxId: 5482] [102908] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [143168] (24)
        SQ P51659 326-479! SQ P51659 480-605
        the structure of N-terminal, SDR domain is also known, PDB entry 1ZBQ
    4. Hypothetical protein Rv0216/MT0226 [143169]
      duplication: consists of two MaoC-like domains
      1. Mycobacterium tuberculosis [TaxId: 1773] [143170] (2)
        SQ P96398 186-337! SQ P96398 8-185
    5. Hypothetical protein AF1124 [143171]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143172] (3)
        SQ O29141 6-159
    6. Hypothetical protein Rv0130 [143173]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143174] (2)
        SQ P96807 2-150
  5. PaaI/YdiI-like [89902] (16)
    1. Phenylacetic acid degradation protein PaaI [89903]
      1. Escherichia coli [TaxId: 562] [89904] (3)
      2. Thermus thermophilus [TaxId: 274] [102909] (26)
    2. Hypothetical protein HI1161 [89905]
      1. Haemophilus influenzae [TaxId: 727] [89906] (10)
    3. Hypothetical protein YdiI [102910]
      1. Escherichia coli [TaxId: 562] [102911] (3)
    4. Hypothetical protein YbdB [102912]
      1. Escherichia coli [TaxId: 562] [102913] (1)
    5. 4-hydroxybenzoyl CoA thioesterase [102914]
      1. Arthrobacter sp., strain su [TaxId: 1667] [102915] (3)
    6. Hypothetical protein PH1136 [102916]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102917] (1)
    7. Putative thioesterase SO4397 [110898]
      1. Shewanella oneidensis [TaxId: 70863] [110899] (1)
        SQ Q8E989
    8. Hypothetical protein PA5026 [110900]
      1. Pseudomonas aeruginosa [TaxId: 287] [110901] (1)
        SQ Q9HUE3
    9. Hypothetical protein PA5202 [143175]
      1. Pseudomonas aeruginosa [TaxId: 287] [143176] (2)
        SQ Q9HTY7 4-129
    10. Hypothetical protein CC3309 [143177]
      1. Caulobacter crescentus [TaxId: 155892] [143178] (1)
        SQ Q9A395 12-153
    11. Hypothetical protein Them2 [143179]
      1. Mouse (Mus musculus) [TaxId: 10090] [143180] (2)
        SQ Q9CQR4 13-139
      2. Human (Homo sapiens) [TaxId: 9606] [143181] (12)
        SQ Q9NPJ3 19-139! SQ Q9NPJ3 3-138
    12. Hypothetical protein PA1835 [143182]
      1. Pseudomonas aeruginosa [TaxId: 287] [143183] (2)
        SQ Q9I2R0 1-145
    13. Transcription factor FapR, C-terminal domain [143184]
      1. Bacillus subtilis [TaxId: 1423] [143185] (6)
        SQ O34835 66-186! SQ O34835 73-183
    14. Hypothetical protein RHA1_ro05818 [160184]
      includes two extra N-terminal helices forming an interlocking four-helical bundle in the dimer
      1. Rhodococcus sp. RHA1 [TaxId: 101510] [160185] (3)
        SQ Q0S4E1 7-209
  6. FabZ-like [110902] (2)
    1. (3R)-hydroxymyristoyl ACP dehydrase FabZ [110903]
      1. Pseudomonas aeruginosa [TaxId: 287] [110904] (1)
        SQ Q9HXY7
      2. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [143186] (8)
        SQ Q965D7 84-229! SQ Q965D7 94-229
  7. TTHA0967-like [143187] (2)
    contains extra C-terminal helix
    1. Hypothetical protein TTHA0967 [143188]
      1. Thermus thermophilus [TaxId: 274] [143189] (4)
        SQ Q5SJP1 1-138
    2. Uncharacterized protein TM0581 [160186]
      1. Thermotoga maritima [TaxId: 2336] [160187] (8)
        SQ Q9WZ50 1-130
  8. Acyl-ACP thioesterase-like [143190] (2)
    Pfam 01643; duplication: consists of two 4HBT-like domains
    1. Acyl-ACP thioesterase [143191]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143192] (2)
        SQ Q8A611 1-149! SQ Q8A611 150-257
    2. Putative oleoyl-ACP thioesterase LP0708 [160188]
      1. Lactobacillus plantarum [TaxId: 1590] [160189] (4)
        SQ Q88YP1 150-258! SQ Q88YP1 3-149
DLC [54647] (1)
core: beta-alpha(2)-beta-X-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 1342
1. DLC [54648] (1)
  uperfamily
  1. DLC [54649] (4)
    8 kDa dynein light chain, DLC8
    1. Dynein light chain 1 (DLC1) [54650]
      synonym: PIN, a protein inhibitor of neuronal nitric oxide synthase
      1. Human (Homo sapiens) [TaxId: 9606] [54651] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [54652] (5)
      3. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102918] (7)
    2. Dynein light chain 2 (DLC2) [102919]
      1. Mouse (Mus musculus) [TaxId: 10090] [102920] (1)
CI-2 family of serine protease inhibitors [54653] (1)
alpha+beta sandwich; loop across free side of beta-sheet
1. CI-2 family of serine protease inhibitors [54654] (1)
  uperfamily
  1. CI-2 family of serine protease inhibitors [54655] (4)
    1. Eglin C [54656]
      1. Leech (Hirudo medicinalis) [TaxId: 6421] [54657] (11)
    2. Chymotrypsin inhibitor CI-2 [54658]
      1. Barley (Hordeum vulgare) [TaxId: 4513] [54659] (29)
        SQ Q40059 22-84
    3. Trypsin inhibitor V [54660]
      1. Pumpkin (Cucurbita maxima) [TaxId: 3661] [54661] (3)
    4. Trypsin inhibitor LUTI [54662]
      1. Flax (Linum usitatissimum) [TaxId: 4006] [54663] (1)
Integrin beta tail domain [69686] (1)
alpha-beta-loop-beta(3); loop across free side of beta-sheet
1. Integrin beta tail domain [69687] (1)
  uperfamily
  1. Integrin beta tail domain [69688] (1)
    1. Integrin beta tail domain [69689]
      1. Human (Homo sapiens) [TaxId: 9606] [69690] (4)
        SQ P05106 27-716
YcgL-like [160190] (1)
beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet, order:3124
1. YcgL-like [160191] (1)
  1. YcgL-like [160192] (1)
    Pfam 05166
    1. Hypothetical protein YcgL [160193]
      1. Escherichia coli [TaxId: 562] [160194] (1)
        SQ Q2LD68 1-108
alpha/beta-Hammerhead [54664] (5)
core: beta-BETA-alpha-beta-BETA-beta-alpha; contains a beta-hammerhead motif similar to that in barrel-sandwich hybrids
1. CO dehydrogenase molybdoprotein N-domain-like [54665] (1)
  uperfamily
  1. CO dehydrogenase molybdoprotein N-domain-like [54666] (8)
    1. Aldehyde oxidoreductase, domain 3 [54667]
      1. Desulfovibrio gigas [TaxId: 879] [54668] (3)
        SQ Q46509
      2. Desulfovibrio desulfuricans [TaxId: 876] [54669] (1)
    2. Xanthine oxidase, domain 5 (?) [54670]
      1. Cow (Bos taurus) [TaxId: 9913] [54671] (6)
        SQ P80457
    3. Xanthine dehydrogenase chain B, N-terminal domain [69691]
      1. Rhodobacter capsulatus [TaxId: 1061] [69692] (2)
    4. Carbon monoxide (CO) dehydrogenase molybdoprotein, N-domain [54672]
      1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [54673] (6)
      2. Hydrogenophaga pseudoflava [TaxId: 47421] [54674] (2)
    5. Quinoline 2-oxidoreductase large subunit QorL, N-domain [110905]
      1. Pseudomonas putida [TaxId: 303] [110906] (1)
        SQ P72224
    6. 4-hydroxybenzoyl-CoA reductase alpha subunit HrcA, N-terminal domain [117885]
      1. Thauera aromatica [TaxId: 59405] [117886] (2)
        SQ O33819
2. Nicotinate/Quinolinate PRTase N-terminal domain-like [54675] (2)
  uperfamily
  1. NadC N-terminal domain-like [54676] (6)
    1. Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), N-terminal domain [54677]
      1. Salmonella typhimurium [TaxId: 90371] [54678] (1)
      2. Mycobacterium tuberculosis [TaxId: 1773] [54679] (4)
      3. Thermotoga maritima [TaxId: 2336] [89907] (1)
        TM1645
    2. Nicotinate phosphoribosyltransferase Ta1145 [143193]
      1. Thermoplasma acidophilum [TaxId: 2303] [143194] (1)
        SQ Q9HJ28 1-119
    3. Nicotinate-nucleotide pyrophosphorylase PF1904 [143195]
      1. Pyrococcus furiosus [TaxId: 2261] [143196] (6)
        SQ Q8TZS9 1-110
    4. Putative nicotinate phosphoribosyltransferase EF2626 [143197]
      1. Enterococcus faecalis [TaxId: 1351] [143198] (1)
        SQ Q830Y8 4-140
  2. Monomeric nicotinate phosphoribosyltransferase N-terminal domain-like [110907] (3)
    1. Nicotinate phosphoribosyltransferase, N-terminal domain [110908]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110909] (1)
        SQ P39683
      2. Agrobacterium tumefaciens [TaxId: 358] [117887] (1)
        SQ Q8UIS9
      3. Pseudomonas aeruginosa [TaxId: 287] [143199] (4)
        SQ Q9HW26 2-142
        NAPRTase 2
3. Pyrimidine nucleoside phosphorylase C-terminal domain [54680] (1)
  uperfamily
  1. Pyrimidine nucleoside phosphorylase C-terminal domain [54681] (3)
    1. Thymidine phosphorylase [54682]
      1. Escherichia coli [TaxId: 562] [54683] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [102921] (1)
    2. Pyrimidine nucleoside phosphorylase [54684]
      1. Bacillus stearothermophilus [TaxId: 1422] [54685] (1)
4. Ribosomal protein L16p/L10e [54686] (2)
  uperfamily
  1. Ribosomal protein L10e [54687] (2)
    1. Ribosomal protein L10e [54688]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [54689] (58)
        SQ P60617
      2. Human (Homo sapiens) [TaxId: 9606] [160195] (2)
        SQ P27635 40-176
  2. Ribosomal protein L16p [117888] (4)
    Pfam 00252
    1. Ribosomal protein L16p [117889]
      1. Thermotoga maritima [TaxId: 2336] [117890] (1)
        SQ P60489
      2. Escherichia coli [TaxId: 562] [143200] (29)
        SQ P0ADY7 1-136
      3. Deinococcus radiodurans [TaxId: 1299] [160196] (6)
        SQ Q9RXJ5 5-140
      4. Thermus thermophilus [TaxId: 274] [160197] (5)
5. Molybdopterin synthase subunit MoaE [54690] (1)
  uperfamily
  1. Molybdopterin synthase subunit MoaE [54691] (1)
    1. Molybdopterin synthase subunit MoaE [54692]
      1. Escherichia coli [TaxId: 562] [54693] (5)
POZ domain [54694] (1)
core: beta(2)-alpha(2)-beta(2)-alpha(2); 2 layers a/b; mixed sheet: 2143
1. POZ domain [54695] (2)
  uperfamily
  1. BTB/POZ domain [54696] (6)
    1. Promyelocytic leukaemia zinc finger (PLZF) protein BTB domain [54697]
      1. Human (Homo sapiens) [TaxId: 9606] [54698] (2)
    2. B-cell lymphoma 6 (Bcl6) protein BTB domain [102922]
      1. Human (Homo sapiens) [TaxId: 9606] [102923] (11)
    3. Elongin C [54699]
      1. Human (Homo sapiens) [TaxId: 9606] [54700] (9)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64261] (1)
    4. Cyclin A/CDK2-associated p45, Skp1 [54710]
      1. Human (Homo sapiens) [TaxId: 9606] [54711] (8)
    5. Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D [82639]
      Suppressor of kinetochore protein 1,Scskp1
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82640] (1)
  2. Tetramerization domain of potassium channels [54701] (6)
    1. Shaker potassium channel [54702]
      1. California sea hare (Aplysia californica) [TaxId: 6500] [54703] (5)
    2. akv3.1 voltage-gated potassium channel [54704]
      1. California sea hare (Aplysia californica) [TaxId: 6500] [54705] (1)
    3. KV1.1 [54706]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [54707] (1)
    4. Kv1.2 [54708]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [54709] (3)
    5. Potassium channel kv4.2 [89908]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89909] (1)
    6. Potassium channel kv4.3 [102924]
      1. Human (Homo sapiens) [TaxId: 9606] [102925] (1)
EF-Ts domain-like [54712] (2)
beta(2)-alpha(n)-beta; 2 layers a/b; antiparallel sheet: 123
1. Elongation factor Ts (EF-Ts), dimerisation domain [54713] (1)
  comprises two structural repeats of this fold
  uperfamily
  1. Elongation factor Ts (EF-Ts), dimerisation domain [54714] (3)
    1. Elongation factor Ts (EF-Ts), dimerisation domain [63422]
      1. Escherichia coli [TaxId: 562] [54716] (1)
        duplication: consists of two subdomains of this fold
      2. Thermus thermophilus [TaxId: 274] [54717] (2)
      3. Cow (Bos taurus), mitochondrial [TaxId: 9913] [117891] (1)
        SQ P43896 56-331
2. Band 7/SPFH domain [117892] (1)
  beta(2)-alpha(3)-beta
  uperfamily
  1. Band 7/SPFH domain [117893] (1)
    Pfam 01145
    1. Flotillin-2 [117894]
      1. Mouse (Mus musculus) [TaxId: 10090] [117895] (1)
        SQ Q60634 1-123
Fe,Mn superoxide dismutase (SOD), C-terminal domain [54718] (1)
alpha-beta(2)-alpha-beta-alpha(2); 3 strands of antiparallel sheet: 213
1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54719] (1)
  uperfamily
  1. Fe,Mn superoxide dismutase (SOD), C-terminal domain [54720] (19)
    1. Mn superoxide dismutase (MnSOD) [54721]
      1. Escherichia coli [TaxId: 562] [54722] (12)
      2. Thermus thermophilus [TaxId: 274] [54723] (2)
      3. Bacillus halodenitrificans [TaxId: 1482] [75408] (1)
      4. Anabaena sp. [TaxId: 1167] [75409] (1)
      5. Human (Homo sapiens) [TaxId: 9606] [54724] (44)
      6. Aspergillus fumigatus [TaxId: 5085] [69693] (1)
      7. Deinococcus radiodurans [TaxId: 1299] [117896] (3)
        SQ Q9RUV2
    2. Fe superoxide dismutase (FeSOD) [54725]
      1. Pseudomonas ovalis [TaxId: 303] [54726] (2)
      2. Escherichia coli [TaxId: 562] [54727] (13)
      3. Mycobacterium tuberculosis [TaxId: 1773] [54728] (5)
      4. Thermosynechococcus elongatus [TaxId: 146786] [89910] (1)
      5. Aquifex pyrophilus [TaxId: 2714] [54729] (1)
      6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [54730] (2)
        SQ P80857
      7. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [54731] (1)
      8. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75410] (1)
      9. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [102926] (1)
      10. Cowpea (Vigna unguiculata) [TaxId: 3917] [117897] (1)
        SQ Q9M7R2 21-245
    3. Cambialistic superoxide dismutase [54732]
      active with either fe or mn
      1. Propionibacterium shermanii [TaxId: 1752] [54733] (6)
      2. Porphyromonas gingivalis [TaxId: 837] [54734] (3)
        SQ P19665
ClpS-like [54735] (1)
beta-alpha(2)-beta-alpha-beta; 2 layers, alpha/beta
1. ClpS-like [54736] (2)
  uperfamily
  1. Ribosomal protein L7/12, C-terminal domain [54737] (3)
    1. Ribosomal protein L7/12, C-terminal domain [54738]
      1. Escherichia coli [TaxId: 562] [54739] (9)
      2. Thermotoga maritima [TaxId: 2336] [54740] (4)
      3. Deinococcus radiodurans [TaxId: 1299] [160198] (1)
        SQ Q9RST0 52-122
  2. Adaptor protein ClpS (YljA) [82641] (1)
    1. Adaptor protein ClpS (YljA) [82642]
      1. Escherichia coli [TaxId: 562] [82643] (9)
Hypothetical protein MTH1880 [75411] (1)
beta-alpha-beta(2)-alpha(2); 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
1. Hypothetical protein MTH1880 [75412] (1)
  uperfamily
  1. Hypothetical protein MTH1880 [75413] (1)
    1. Hypothetical protein MTH1880 [75414]
      1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75415] (2)
Ribosomal L11/L12e N-terminal domain [54746] (1)
beta-alpha(2)-beta(2); 2 layers, alpha/beta; antiparallel beta-sheet: order 123
1. Ribosomal L11/L12e N-terminal domain [54747] (1)
  uperfamily
  1. Ribosomal L11/L12e N-terminal domain [54748] (5)
    Pfam 03946
    1. Ribosomal protein L11, N-terminal domain [54749]
      1. Thermotoga maritima [TaxId: 2336] [54750] (6)
      2. Deinococcus radiodurans [TaxId: 1299] [160199] (4)
        SQ Q9RSS7 1-71
      3. Thermus thermophilus [TaxId: 274] [160200] (19)
        SQ P36238 1-70! SQ P36238 2-68! SQ P36238 2-70
      4. Escherichia coli [TaxId: 562] [160201] (29)
        SQ P0A7J7 1-72
    2. 60S ribosomal protein L12 [117898]
      1. Mouse (Mus musculus) [TaxId: 10090] [117899] (1)
        SQ P35979 2-80
Anti-LPS factor/recA domain [54751] (2)
alpha-beta(3)-alpha(2); 2 layers, alpha/beta
1. RecA protein, C-terminal domain [54752] (1)
  uperfamily
  1. RecA protein, C-terminal domain [54753] (4)
    1. RecA protein, C-terminal domain [54754]
      1. Escherichia coli [TaxId: 562] [54755] (8)
        SQ P0A7G6 P03017
      2. Mycobacterium tuberculosis [TaxId: 1773] [54756] (6)
      3. Mycobacterium smegmatis [TaxId: 1772] [89911] (4)
      4. Deinococcus radiodurans [TaxId: 1299] [117900] (1)
        SQ P42443 15-341
2. Anti-lipopolysaccharide factor [54757] (1)
  uperfamily
  1. Anti-lipopolysaccharide factor [54758] (1)
    1. Endotoxin-neutralizing protein [54759]
      1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [54760] (1)
        SQ P07086 # ALPS_LIMPO
Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54761] (1)
(beta)-alpha-beta(3)-alpha; 2 layers, alpha/beta
1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54762] (1)
  uperfamily
  1. Signal recognition particle alu RNA binding heterodimer, SRP9/14 [54763] (4)
    1. Signal recognition particle 9KDa protein, SRP9 [88845]
      1. Human (Homo sapiens) [TaxId: 9606] [88846] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [88847] (1)
    2. Signal recognition particle 14KDa protein, SRP14 [88848]
      1. Human (Homo sapiens) [TaxId: 9606] [88849] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [88850] (1)
dsRBD-like [54767] (5)
alpha-beta(3)-alpha; 2 layers: alpha/beta
1. dsRNA-binding domain-like [54768] (3)
  uperfamily
  1. Double-stranded RNA-binding domain (dsRBD) [54769] (15)
    Pfam 00035
    1. Double-stranded RNA-binding protein A, second dsRBD [54770]
      1. Xenopus laevis [TaxId: 8355] [54771] (1)
    2. Staufen, domain III [54772]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [54773] (2)
    3. dsRNA-dependent protein kinase pkr [54774]
      contains tandem repeat of two dsRBD
      1. Human (Homo sapiens) [TaxId: 9606] [54775] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [143201] (2)
        SQ Q03963 1-85! SQ Q03963 96-181
    4. RNase III, C-terminal domain [54776]
      1. Thermotoga maritima [TaxId: 2336] [82644] (1)
      2. Aquifex aeolicus [TaxId: 63363] [102927] (19)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110913] (3)
        SQ Q02555 364-447 ! SQ Q02555 366-453 ! SQ Q02555 363-443
    5. staufen homolog 2 [110914]
      1. Mouse (Mus musculus) [TaxId: 10090] [110915] (1)
        SQ Q9D5N7 3-78
    6. ATP-dependent RNA helicase A, Dhx9 [117901]
      formerly hypothetical protein bab28848
      1. Mouse (Mus musculus) [TaxId: 10090] [117902] (2)
        SQ O70133 4-89, 168-262
    7. tRNA-dihydrouridine synthase 2-like, Dus2l (2310016k04Rik) [117903]
      1. Mouse (Mus musculus) [TaxId: 10090] [117904] (1)
        SQ Q9D7B1 350-464
    8. dsRNA-specific editase 1 [143202]
      duplication: contains two dsRBD domains
      1. Rat (Rattus norvegicus) [TaxId: 10116] [143203] (2)
        SQ P51400 231-301! SQ P51400 74-146
    9. Interferon-inducible double stranded RNA-dependent protein kinase activator A [143204]
      1. Human (Homo sapiens) [TaxId: 9606] [143205] (1)
        SQ O75569 32-104
    10. Dgcr8 protein [143206]
      1. Human (Homo sapiens) [TaxId: 9606] [143207] (1)
        SQ Q8WYQ5 502-586
    11. TAR RNA-binding protein 2 [143208]
      duplication: contains three dsRBD
      1. Human (Homo sapiens) [TaxId: 9606] [143209] (1)
        SQ Q15633 150-225
    12. Spermatid perinuclear RNA-binding protein [143210]
      1. Human (Homo sapiens) [TaxId: 9606] [143211] (1)
        SQ Q96SI9 378-461
  2. The homologous-pairing domain of Rad52 recombinase [82645] (1)
    contains N- and C-terminal extensions to the common fold involved in the oligomerization
    1. The homologous-pairing domain of Rad52 recombinase [82646]
      forms an undecameric ring structure; binds to ssDNA and dsDNA
      1. Human (Homo sapiens) [TaxId: 9606] [82647] (2)
  3. Ribosomal S5 protein, N-terminal domain [54778] (3)
    1. Ribosomal S5 protein, N-terminal domain [54779]
      lacks the N-terminal helix
      1. Bacillus stearothermophilus [TaxId: 1422] [54780] (1)
      2. Thermus thermophilus [TaxId: 274] [54781] (36)
        SQ P27152
      3. Escherichia coli [TaxId: 562] [160202] (24)
        SQ P0A7W1 9-77
2. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54782] (1)
  uperfamily
  1. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54783] (1)
    1. Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain [54784]
      1. Escherichia coli [TaxId: 562] [54785] (5)
3. YcfA/nrd intein domain [54786] (3)
  uperfamily
  1. PI-Pfui intein middle domain [54787] (1)
    1. PI-Pfui intein middle domain [54788]
      contains additional C-terminal helix
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [54789] (1)
  2. YcfA-like [117905] (1)
    Pfam 07927
    1. Hypothetical protein TTHA1913 [117906]
      1. Thermus thermophilus [TaxId: 274] [117907] (1)
        SQ Q5SH17
  3. YkfF-like [160203] (1)
    Pfam 06006; DUF905
    1. Hypothetical protein YkfF [160204]
      1. Escherichia coli [TaxId: 562] [160205] (1)
        SQ P75677 10-75
4. Peptidyl-tRNA hydrolase domain-like [110916] (1)
  uperfamily
  1. Peptidyl-tRNA hydrolase domain [110917] (1)
    Pfam 00472; related to domain 3 of the Polypeptide chain release factors RF1 and RF2 (scop_fa 75621)
    1. Ict1 protein [110918]
      1. Mouse (Mus musculus) [TaxId: 10090] [110919] (1)
        SQ Q8R035 63-162
5. Rv2632c-like [143212] (1)
  lacks the N-terminal helix; dimerises via the N-terminal strand and the C-terminal helix with the formation of a single beta-sheet wrapped around an antiparallel coiled coil
  uperfamily
  1. Rv2632c-like [143213] (1)
    1. Hypothetical protein Rv2632c/MT2708 [143214]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143215] (1)
        SQ P65033 4-87
2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110920] (1)
duplication: consists of two beta(3)-alpha repeats; 3 layers, beta/alpha/beta
1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110921] (1)
  uperfamily
  1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110922] (1)
    1. 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain [110923]
      1. Mycobacterium tuberculosis [TaxId: 1773] [110924] (1)
        SQ P96420
NMB0488-like [160206] (1)
duplication: two beta(3)-alpha motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456, shaped into a half-barrel; helical linker region
1. NMB0488-like [160207] (1)
  1. NMB0488-like [160208] (1)
    Pfam 07262; DUF1436
    1. Hypothetical protein NMB0488 [160209]
      1. Neisseria meningitidis [TaxId: 487] [160210] (1)
        SQ Q9K0T5 1-164
SRP19 [69694] (1)
beta-alpha-beta(2)-alpha; 2 layers: alpha/beta
1. SRP19 [69695] (1)
  uperfamily
  1. SRP19 [69696] (3)
    1. SRP19 [69697]
      1. Human (Homo sapiens) [TaxId: 9606] [69698] (4)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75416] (2)
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [75417] (4)
SufE/NifU [82648] (1)
alpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
1. SufE/NifU [82649] (3)
  iron-sulfur cluster assembly proteins
  uperfamily
  1. SufE-like [82650] (2)
    Fe-S metabolism associated domain
    1. SufE (YhnA) [82651]
      unknown function; probably involved in Fe-S center assembly
      1. Escherichia coli [TaxId: 562] [82652] (1)
    2. Hypothetical protein YgdK [89912]
      1. Escherichia coli [TaxId: 562] [89913] (1)
  2. NifU/IscU domain [102928] (4)
    1. NifU-like protein HI0377 [102929]
      1. Haemophilus influenzae [TaxId: 727] [102930] (2)
        SQ Q57074
    2. IscU homolog SPy0289 [110925]
      1. Streptococcus pyogenes [TaxId: 1314] [110926] (1)
        SQ Q9A1G2
    3. Iron-sulfur cluster protein U (IscU) [117908]
      1. Mouse (Mus musculus), mitochondrial [TaxId: 10090] [117909] (1)
        SQ Q9D7P6 45-161
    4. NifU [117910]
      1. Bacillus subtilis [TaxId: 1423] [117911] (1)
        SQ O32163
  3. SP1160 C-terminal domain-like [143216] (2)
    1. LplA-like protein SP1160, C-terminal domain [143217]
      1. Streptococcus pneumoniae [TaxId: 1313] [143218] (1)
        SQ Q97QP1 242-329
    2. Two-domain LplA, C-terminal domain [160211]
      1. Escherichia coli [TaxId: 562] [160212] (6)
        SQ P32099 247-337
FlaG-like [160213] (1)
alpha(2)-beta(3)-alpha; 2 layers: a/b; antiparallel beta-sheet, order: 123; partial similatity to the dsRBD-like fold(sop_cf 54767)
1. FlaG-like [160214] (1)
  1. FlaG-like [160215] (1)
    Pfam 03646
    1. Hypothetical protein YvyC [160216]
      1. Bacillus subtilis [TaxId: 1423] [160217] (1)
        SQ P39737 1-109
AMPKBI-like [160218] (1)
comprises 3 short helices and 3-stranded meander beta-sheet; makes extensive intermolecular interactions
1. AMPKBI-like [160219] (1)
  1. AMPKBI-like [160220] (3)
    Pfam 04739; 5'-AMP-activated protein kinase, beta subunit, complex-interacting region
    1. SIP2 [160221]
      1. Saccharomyces cerevisiae [TaxId: 4932] [160222] (2)
        SQ P34164 306-412
    2. 5'-AMP-activated protein kinase subunit beta-2 [160223]
      1. Human (Homo sapiens) [TaxId: 9606] [160224] (3)
        SQ O43741 190-272
    3. AMP-activated protein kinase beta subunit [160225]
      1. Schizosaccharomyces pombe [TaxId: 4896] [160226] (12)
        SQ P78789 205-297
        Spcc1919.03c
DNA-binding protein Tfx [89914] (1)
alpha(3)-beta-alpha(2)-beta(2); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123
1. DNA-binding protein Tfx [89915] (1)
  uperfamily
  1. DNA-binding protein Tfx [89916] (1)
    1. DNA-binding protein Tfx [89917]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89918] (1)
        MTH916
Eukaryotic type KH-domain (KH-domain type I) [54790] (1)
beta-alpha(2)-beta(2)-alpha; 2 layers: alpha/beta
1. Eukaryotic type KH-domain (KH-domain type I) [54791] (1)
  Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
  uperfamily
  1. Eukaryotic type KH-domain (KH-domain type I) [54792] (20)
    an RNA-binding domain
    1. Neuro-oncological ventral antigen 1, nova-1, KH3 [54793]
      1. Human (Homo sapiens) [TaxId: 9606] [54794] (1)
    2. Neuro-oncological ventral antigen 2, nova-2, KH3 [54795]
      1. Human (Homo sapiens) [TaxId: 9606] [54796] (2)
    3. Vigilin [54797]
      1. Human (Homo sapiens) [TaxId: 9606] [54798] (8)
    4. Fragile X protein, KH1 [54799]
      1. Human (Homo sapiens) [TaxId: 9606] [54800] (1)
    5. HnRNP K, KH3 [54801]
      1. Human (Homo sapiens) [TaxId: 9606] [54802] (8)
    6. RNA splicing factor 1 [69699]
      1. Human (Homo sapiens) [TaxId: 9606] [69700] (1)
    7. Far upstream binding element, FBP [75418]
      1. Human (Homo sapiens) [TaxId: 9606] [75419] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [143219] (2)
        SQ Q91WJ8 175-255! SQ Q91WJ8 89-168
    8. Hypothetical protein APE0754 [110927]
      duplication: tandem repeat of two KH-1 domains
      1. Aeropyrum pernix [TaxId: 56636] [110928] (1)
        SQ Q9YE16
    9. Tudor and KH domain containing protein, Tdrkh [117912]
      1. Mouse (Mus musculus) [TaxId: 10090] [117913] (1)
        SQ Q80VL1 118-208
    10. Poly(RC)-binding protein 2 [143220]
      contains three KH domains
      1. Human (Homo sapiens) [TaxId: 9606] [143221] (12)
        SQ Q15366 11-81
    11. Fragile X mental retardation syndrome related protein 1, FXR1 [143222]
      1. Human (Homo sapiens) [TaxId: 9606] [143223] (1)
        SQ P51114 212-289
    12. Poly(RC)-binding protein 1 [143224]
      1. Human (Homo sapiens) [TaxId: 9606] [143225] (1)
        SQ Q15365 279-348
    13. Quaking protein A (Xqua) [143226]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [143227] (1)
        SQ Q32NN2 82-215
    14. Ribosomal RNA-processing protein 4, RRP4 [160227]
      1. Human (Homo sapiens) [TaxId: 9606] [160228] (1)
        SQ Q13868 168-293
    15. Exosome complex RNA-binding protein 1, ECR1 [160229]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160230] (3)
        SQ O29758 136-219
      2. Aeropyrum pernix [TaxId: 56636] [160231] (1)
        SQ Q9YC02 148-234
      3. Sulfolobus solfataricus [TaxId: 2287] [160232] (2)
        SQ Q9UXC4 153-221
    16. Ribosomal RNA-processing protein 40, RRP40 [160233]
      1. Saccharomyces cerevisiae [TaxId: 4932] [160234] (1)
        SQ Q08285 152-236
      2. Human (Homo sapiens) [TaxId: 9606] [160235] (1)
        SQ Q9NQT5 196-275
Alpha-lytic protease prodomain-like [54805] (10)
core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta
1. Alpha-lytic protease prodomain [54806] (1)
  uperfamily
  1. Alpha-lytic protease prodomain [54807] (1)
    1. Alpha-lytic protease prodomain [54808]
      duplication: consists of two domains of this fold
      1. Lysobacter enzymogenes [TaxId: 69] [54809] (3)
2. GMP synthetase C-terminal dimerisation domain [54810] (1)
  uperfamily
  1. GMP synthetase C-terminal dimerisation domain [54811] (1)
    1. GMP synthetase C-terminal dimerisation domain [54812]
      1. Escherichia coli [TaxId: 562] [54813] (1)
3. Prokaryotic type KH domain (KH-domain type II) [54814] (1)
  Prokaryotic and eukaryotic domains share a KH-motif but have different topologies
  uperfamily
  1. Prokaryotic type KH domain (KH-domain type II) [54815] (9)
    1. Ribosomal protein S3 N-terminal domain [54816]
      1. Thermus thermophilus [TaxId: 274] [54817] (36)
        SQ P80372
      2. Mouse (Mus musculus) [TaxId: 10090] [117914] (1)
        SQ P23396 17-95
      3. Escherichia coli [TaxId: 562] [160236] (24)
        SQ P0A7V3 1-105
      4. Canis lupus familiaris [TaxId: 9615] [160237] (1)
    2. GTPase Era C-terminal domain [54818]
      1. Escherichia coli [TaxId: 562] [54819] (3)
      2. Thermus thermophilus [TaxId: 274] [117915] (1)
        SQ Q5SM23
    3. Transcription factor NusA, C-terminal domains [69701]
      duplication: tandem repeat of two type II KH-domains
      1. Thermotoga maritima [TaxId: 2336] [69702] (2)
      2. Mycobacterium tuberculosis [TaxId: 1773] [69703] (7)
    4. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6 [54803]
      the type of KH-domain fold (II or I) adopted by this domain is not ascertained yet
      1. Streptomyces antibioticus [TaxId: 1890] [54804] (2)
4. Probable GTPase Der, C-terminal domain [82653] (1)
  possible distant relative of the Era C-terminal domain lacking the KH motif
  uperfamily
  1. Probable GTPase Der, C-terminal domain [82654] (1)
    1. Probable GTPase Der, C-terminal domain [82655]
      1. Thermotoga maritima [TaxId: 2336] [82656] (1)
5. Ribosome-binding factor A, RbfA [89919] (1)
  possible distant homologue of the type I KH domain lacking the KH motif
  uperfamily
  1. Ribosome-binding factor A, RbfA [89920] (5)
    1. Ribosome-binding factor A, RbfA [89921]
      1. Escherichia coli [TaxId: 562] [89922] (1)
      2. Haemophilus influenzae [TaxId: 727] [89923] (1)
        HI1288
      3. Mycoplasma pneumoniae [TaxId: 2104] [102931] (1)
      4. Human (Homo sapiens) [TaxId: 9606] [160238] (1)
        SQ Q8N0V3 86-201
      5. Thermus thermophilus [TaxId: 274] [160239] (3)
        SQ Q5SJV1 4-94
6. YhbC-like, N-terminal domain [75420] (1)
  uperfamily
  1. YhbC-like, N-terminal domain [75421] (1)
    1. Hypothetical protein SP14.3 (SP0552) [75422]
      1. Streptococcus pneumoniae [TaxId: 1313] [75423] (1)
7. BolA-like [82657] (1)
  uperfamily
  1. BolA-like [82658] (2)
    Pfam 01722
    1. BolA-like protein [82659]
      1. Mouse (Mus musculus) [TaxId: 10090] [82660] (1)
    2. Hypothetical protein YrbA [110929]
      1. Escherichia coli [TaxId: 562] [110930] (1)
        SQ P43781
8. Fe-S cluster assembly (FSCA) domain-like [117916] (2)
  similar putative active site with a conserved cysteine residue
  uperfamily
  1. NifU C-terminal domain-like [117917] (3)
    Pfam 01106
    1. HIRA-interacting protein 5, HIRIP5 [117918]
      1. Mouse (Mus musculus) [TaxId: 10090] [117919] (1)
        SQ Q9QZ23 106-185
    2. Nitrogen fixation protein NifU homolog SE0630 [117920]
      1. Staphylococcus epidermidis [TaxId: 1282] [117921] (1)
        SQ Q8CPV7
    3. NifU-like protein 1, NIFUL1 [143228]
      1. Rice (Oryza sativa) [TaxId: 4530] [143229] (1)
        SQ Q84LK7 154-226
  2. PaaD-like [117922] (2)
    Pfam 01883; DUF59
    1. Hypothetical protein TM0487 [117923]
      1. Thermotoga maritima [TaxId: 2336] [117924] (2)
        SQ Q9WYV7
    2. Hypothetical protein TTHB138 [143230]
      1. Thermus thermophilus [TaxId: 274] [143231] (2)
        SQ Q53W28 6-96
9. Cation efflux protein cytoplasmic domain-like [160240] (1)
  1. Cation efflux protein cytoplasmic domain-like [160241] (2)
    C=terminal part of Pfam 01545
    1. Putative Zinc transporter CzrB [160242]
      1. Thermus thermophilus [TaxId: 274] [160243] (3)
        SQ Q8VLX7 203-284
    2. Ferrous-iron efflux pump FieF (YiiP) [160244]
      Also able to transport Zn(2+)
      1. Escherichia coli [TaxId: 562] [160245] (2)
        SQ P69380 209-290
10. EspE N-terminal domain-like [160246] (1)
  contains extra C-terminal helix that packs against shorter N-terminal helix
  1. GSPII protein E N-terminal domain-like [160247] (2)
    Pfam 05157 (also includes PfamB 000210)
    1. Type II secretion ATPase XpsE [160248]
      contains extra N-terminal alpha-helical subdomain, that can form swapped dimers
      1. Xanthomonas campestris [TaxId: 339] [160249] (2)
        SQ P31742 1-148! SQ P31742 1-149
    2. General secretion pathway protein E, EpsE [160250]
      1. Vibrio cholerae [TaxId: 666] [160251] (2)
        SQ P37093 14-81
Nucleotidyltransferase [81302] (1)
core: alpha-beta-turn-beta-X-beta-(alpha); mixed beta-sheet, order of core strands: 123
1. Nucleotidyltransferase [81301] (14)
  uperfamily
  1. Catalytic subunit of bi-partite nucleotidyltransferase [102932] (3)
    insert X in the core is an alpha-helix; minimal nucleotidyltransferase fold
    1. Hypothetical protein HI0073 [102933]
      nucleotide binding subunit of the HI0073/HI0074 nucleotidyltransferase (see 1jog)
      1. Haemophilus influenzae [TaxId: 727] [102934] (1)
    2. Unnamed putative nucleotidyltransferase [102935]
      1. Thermus thermophilus [TaxId: 274] [102936] (1)
        SQ P83814 # 100% identical to SQ Q72I47 (TTC1285)
    3. Putative nucleotidyltransferase AF0614 [143232]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143233] (2)
        SQ O29641 1-90
  2. Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [56708] (1)
    insert X in the core is a beta-strand ; mixed 4-stranded sheet, order: 1243
    1. Kanamycin nucleotidyltransferase (KNTase), N-terminal domain [56709]
      1. Staphylococcus aureus [TaxId: 1280] [56710] (2)
  3. Poly(A) polymerase, PAP, N-terminal domain [81589] (2)
    insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543
    1. Poly(A) polymerase, PAP, N-terminal domain [81588]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81586] (7)
      2. Cow (Bos taurus) [TaxId: 9913] [81587] (3)
        SQ P25500 18-497
  4. 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [102937] (1)
    similar overall structure to the first two domains of poly(A) polymerase, PAP
    1. 2'-5'-oligoadenylate synthetase 1, OAS1, N-terminal domain [102938]
      1. Pig (Sus scrofa) [TaxId: 9823] [102939] (1)
  5. Archaeal tRNA CCA-adding enzyme catalytic domain [102940] (1)
    similar overall structure to poly(A) polymerase, PAP
    1. tRNA nucleotidyltransferase, N-terminal domain [102941]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102942] (28)
        SQ O28126
  6. DNA polymerase beta-like [81300] (5)
    insert X in the core is an alpha-beta(2) unit; mixed 5-stranded sheet, order: 12543; contains extra C-terminal alpha+beta subdomain
    1. DNA polymerase beta, catalytic (31 kD) fragment [81578]
      1. Human (Homo sapiens) [TaxId: 9606] [81574] (107)
        SQ P06746
      2. Rat (Rattus norvegicus) [TaxId: 10116] [81576] (18)
    2. Terminal deoxynucleotidyl transferase [81581]
      1. Mouse (Mus musculus) [TaxId: 10090] [81580] (3)
    3. DNA polymerase lambda [102943]
      1. Human (Homo sapiens) [TaxId: 9606] [102944] (24)
    4. DNA polymerase X [69885]
      1. African swine fever virus [TaxId: 10497] [69886] (2)
  7. Poly A polymerase head domain-like [82661] (3)
    overlaps with the N-terminal part of Pfam 01743; this family is distinct from eukaryotic PAPs
    insert X in the core is an alpha-beta(2) unit; contains two extra C-terminal strands; mixed 7-stranded sheet, order: 7612543
    1. tRNA CCA-adding enzyme, head domain [82662]
      1. Bacillus stearothermophilus [TaxId: 1422] [82663] (3)
      2. Human (Homo sapiens), mitochondrial [TaxId: 9606] [89924] (1)
    2. Poly A polymerase PcnB [110931]
      1. Aquifex aeolicus [TaxId: 63363] [110932] (1)
        SQ O66728 443-824
  8. RelA/SpoT domain [102945] (2)
    Pfam 04607; ppGpp-synthetase
    1. Stringent response-like protein RelA domain 2 [102946]
      1. Streptococcus equisimilis [TaxId: 119602] [102947] (1)
    2. Putative GTP pyrophosphokinase SP1097 [143234]
      1. Streptococcus pneumoniae [TaxId: 1313] [143235] (2)
        SQ Q97QV1 1-203
  9. GlnE-like domain [110933] (1)
    Pfam 03710; Pfam coverage excludes the extra N-terminal subdomain but includes a short segment of the next domain 2
    1. Glutamine synthase adenylyltransferase GlnE, N-terminal domain [110934]
      includes extra N-terminal all-alpha subdomain (2-61) structurally similar to the PABP domain (scop_fa 63571)
      1. Escherichia coli [TaxId: 562] [110935] (1)
        SQ P30870 1-437
  10. RNA editing terminal uridyl transferase 2, RET2, catalytic domain [143236] (1)
    contains insert domain of a ferredoxin-like fold
    1. RNA editing terminal uridyl transferase 2, TUTase 2, RET2 [143237]
      1. Trypanosoma brucei [TaxId: 5691] [143238] (1)
        SQ Q86MV5 30-288
  11. TM1012-like [143239] (1)
    insert X in the core is an alpha-beta(2) unit; contains extra C-terminal structures; mixed 7-stranded sheet, order: 6712543;
    1. Hypothetical protein TM1012 [143240]
      1. Thermotoga maritima [TaxId: 2336] [143241] (2)
        SQ Q9X0A5 1-157! SQ Q9X0A5 2-157
  12. Iojap/YbeB-like [160252] (2)
    Pfam 02410, probably has evolved a different function; closer relationship to the GrpB-like family
    1. Hypothetical protein CV0518 [160253]
      1. Chromobacterium violaceum [TaxId: 536] [160254] (2)
        SQ Q7P0P8 1-120
    2. Uncharacterized protein BH1328 [160255]
      1. Bacillus halodurans [TaxId: 86665] [160256] (2)
        SQ Q9KD89 2-114
  13. AadK N-terminal domain-like [160257] (1)
    N-terminal part of Pfam 04439; Streptomycin adenylyltransferase; insert X is alpha-beta(2) unit; overall domain architecture is similar to Kanamycin nucleotidyltransferase
    1. Aminoglycoside 6-adenylyltransferase AadK [160258]
      1. Bacillus subtilis [TaxId: 1423] [160259] (1)
        SQ P17585 1-135
  14. GrpB-like [160260] (1)
    Pfam 04229, different set of active-site residues
    1. Hypothetical protein GrpB [160261]
      1. Enterococcus faecalis [TaxId: 1351] [160262] (1)
        SQ Q837C3 4-170
Nqo5-like [143242] (1)
core: alpha-beta(2)-alpha-beta(3); 2 layers, a/b; mixed beta-sheet, order 12534, strands 2 and 5 are parallel
1. Nqo5-like [143243] (1)
  uperfamily
  1. Nqo5-like [143244] (1)
    Globular region is covered by PfamB 121908 from N-end and then by PfamB 000646; contains extra C-terminal unstructured region, corresponding to Pfam 00329
    1. NADH-quinone oxidoreductase chain 5, Nqo5 [143245]
      1. Thermus thermophilus [TaxId: 274] [143246] (4)
        SQ Q56219 1-196
Ribosomal protein S3 C-terminal domain [54820] (1)
alpha(2)-beta(4); 2 layers: alpha/beta; antiparallel beta-sheet: order 2143
1. Ribosomal protein S3 C-terminal domain [54821] (1)
  uperfamily
  1. Ribosomal protein S3 C-terminal domain [54822] (2)
    1. Ribosomal protein S3 C-terminal domain [54823]
      1. Thermus thermophilus [TaxId: 274] [54824] (36)
        SQ P80372
      2. Escherichia coli [TaxId: 562] [160263] (24)
        SQ P0A7V3 106-206
Transcription factor NusA, N-terminal domain [69704] (1)
alpha-beta(3)-alpha-beta-alpha; bifurcated coiled beta-sheet
1. Transcription factor NusA, N-terminal domain [69705] (1)
  uperfamily
  1. Transcription factor NusA, N-terminal domain [69706] (2)
    1. Transcription factor NusA, N-terminal domain [69707]
      1. Thermotoga maritima [TaxId: 2336] [69708] (2)
      2. Mycobacterium tuberculosis [TaxId: 1773] [69709] (1)
Enolase N-terminal domain-like [54825] (1)
beta(3)-alpha(3); meander and up-and-down bundle
1. Enolase N-terminal domain-like [54826] (1)
  uperfamily
  1. Enolase N-terminal domain-like [54827] (28)
    C-terminal domain is beta/alpha-barrel
    1. Enolase [54828]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54829] (18)
      2. European lobster (Homarus vulgaris) [TaxId: 6707] [54830] (2)
      3. Trypanosoma brucei brucei [TaxId: 5702] [89925] (1)
      4. Enterococcus hirae [TaxId: 1354] [89926] (1)
      5. Escherichia coli [TaxId: 562] [69710] (5)
      6. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110936] (5)
        SQ P09104
      7. Streptococcus pneumoniae [TaxId: 1313] [143247] (2)
        SQ Q8DPS0 1-137
      8. Trypanosoma brucei [TaxId: 5691] [160264] (6)
    2. D-glucarate dehydratase [54831]
      1. Pseudomonas putida [TaxId: 303] [54832] (1)
      2. Escherichia coli [TaxId: 562] [54833] (6)
    3. O-succinylbenzoate synthase [54834]
      1. Escherichia coli [TaxId: 562] [54835] (7)
    4. Muconate-lactonizing enzyme (cis muconate cycloisomerase) [54836]
      1. Pseudomonas putida [TaxId: 303] [54837] (5)
    5. Mandelate racemase [54838]
      1. Pseudomonas putida [TaxId: 303] [54839] (6)
    6. Chlormuconate cycloisomerase [54840]
      1. Alcaligenes eutrophus [TaxId: 106590] [54841] (2)
      2. Pseudomonas sp. p51 [TaxId: 65067] [102948] (1)
    7. L-Ala-D/L-Glu epimerase [69711]
      1. Escherichia coli [TaxId: 562] [69712] (1)
      2. Bacillus subtilis [TaxId: 1423] [69713] (2)
        SQ O34508
    8. beta-Methylaspartase [69714]
      1. Clostridium tetanomorphum [TaxId: 1553] [69715] (2)
      2. Citrobacter amalonaticus [TaxId: 35703] [69716] (2)
    9. Hypothetical protein Atu3453 [102949]
      1. Agrobacterium tumefaciens [TaxId: 358] [102950] (1)
    10. N-acylamino acid racemase [110937]
      1. Amycolatopsis sp. [TaxId: 37632] [110938] (4)
        SQ Q44244; similar activity to a remotely related O-succinylbenzoate synthase from E. coli
      2. Deinococcus radiodurans [TaxId: 1299] [110939] (4)
        SQ Q9RYA6
      3. Enterococcus faecalis [TaxId: 1351] [117925] (1)
        SQ Q838J7; EF0450; protein assignment by sequence similarity
      4. Listeria innocua [TaxId: 1642] [117926] (1)
        SQ Q927X3; Lin2664; protein assignment by sequence similarity
    11. Hypothetical protein Bll6730 [117927]
      1. Bradyrhizobium japonicum [TaxId: 375] [117928] (21)
        SQ Q89FH0
    12. RTS beta protein [117929]
      1. Xanthomonas campestris pv. campestris [TaxId: 340] [117930] (1)
        SQ Q8P3K2; extended, mainly helical linker between the domains
    13. Hypothetical protein YitF [143248]
      1. Bacillus subtilis [TaxId: 1423] [143249] (10)
        SQ O06741 1-114
    14. Putative dehydratase protein STM2273 [143250]
      1. Salmonella typhimurium [TaxId: 90371] [143251] (2)
        SQ Q8ZNH1 1-122
Ribosomal protein L22 [54842] (1)
beta-alpha(3)-beta(2); 2 layers: alpha/beta; related to the enolase/MLE N-domain fold by a circular permutation
1. Ribosomal protein L22 [54843] (1)
  some topological similarity to prokaryotic ribosomal protein L17
  uperfamily
  1. Ribosomal protein L22 [54844] (5)
    1. Ribosomal protein L22 [54845]
      1. Thermus aquaticus, subsp. Thermus thermophilus [TaxId: 271] [54846] (6)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [54847] (58)
        SQ P10970
      3. Deinococcus radiodurans [TaxId: 1299] [160265] (6)
        SQ Q9RXJ7 8-134
      4. Escherichia coli [TaxId: 562] [160266] (29)
        SQ P61175 1-110
      5. Thermus thermophilus [TaxId: 274] [160267] (6)
Prokaryotic ribosomal protein L17 [64262] (1)
alpha-beta-alpha(3)-beta(2); 2 layers: alpha/beta;
1. Prokaryotic ribosomal protein L17 [64263] (1)
  some topological similarity to ribosomal protein L22
  uperfamily
  1. Prokaryotic ribosomal protein L17 [64264] (4)
    1. Prokaryotic ribosomal protein L17 [64265]
      1. Thermus thermophilus [TaxId: 274] [64266] (11)
      2. Deinococcus radiodurans [TaxId: 1299] [160268] (6)
        SQ Q9RSJ5 3-115
      3. Human (Homo sapiens) [TaxId: 9606] [160269] (1)
        SQ Q9NRX2 28-136
      4. Escherichia coli [TaxId: 562] [160270] (27)
        SQ P02416 1-127
GroEL-intermediate domain like [54848] (1)
3-helical bundle packed against 3-stranded mixed beta-sheet
1. GroEL-intermediate domain like [54849] (2)
  uperfamily
  1. GroEL-like chaperone, intermediate domain [54850] (4)
    1. GroEL, I domain [54851]
      1. Escherichia coli [TaxId: 562] [54852] (15)
      2. Paracoccus denitrificans [TaxId: 266] [69717] (1)
      3. Thermus thermophilus [TaxId: 274] [110940] (2)
        SQ P61491
      4. Mycobacterium tuberculosis, GroEL2 [TaxId: 1773] [117931] (1)
        SQ P0A520 60-514
  2. Group II chaperonin (CCT, TRIC), intermediate domain [54853] (3)
    1. Thermosome, I domain [54854]
      1. Archaeon Thermoplasma acidophilum, alpha chain [TaxId: 2303] [100973] (2)
      2. Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679] [102951] (4)
      3. Archaeon Thermoplasma acidophilum, beta chain [TaxId: 2303] [100974] (2)
PX domain [64267] (1)
beta(3)-alpha(4); meander beta-sheet packed against array of helices; contains Pro-rich stretch
1. PX domain [64268] (1)
  uperfamily
  1. PX domain [64269] (5)
    Pfam 00787
    1. p40phox NADPH oxidase [69718]
      1. Human (Homo sapiens) [TaxId: 9606] [69719] (1)
    2. p47phox NADPH oxidase [64270]
      1. Human (Homo sapiens) [TaxId: 9606] [64271] (3)
    3. Vam7p [75424]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75425] (1)
    4. Sorting nexin grd19 [102952]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102953] (2)
    5. Serine/threonine-protein kinase Sgk3, Cisk [117932]
      1. Mouse (Mus musculus) [TaxId: 10090] [117933] (2)
        SQ Q9ERE3 10-125 ! SQ Q9ERE3 11-121
Shew3726-like [160271] (1)
beta(3)-alpha(n)-beta; 2 layers, a/b; mixed beta-sheet, order 1234, strands 3 and 4 are parallel with a left-handed crossover connection
1. Shew3726-like [160272] (1)
  1. Shew3726-like [160273] (1)
    Pfam 07369; DUF1488
    1. Hypothetical protein Shew3726 [160274]
      1. Shewanella loihica [TaxId: 359303] [160275] (1)
        SQ A3QJE4 1-90
DsrC, the gamma subunit of dissimilatory sulfite reductase [69720] (1)
beta(3)-alpha(5); meander beta-sheet packed against array of helices
1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69721] (1)
  uperfamily
  1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69722] (2)
    1. DsrC, the gamma subunit of dissimilatory sulfite reductase [69723]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69724] (1)
      2. Desulfovibrio vulgaris [TaxId: 881] [160276] (2)
        SQ P45573 3-105
DNA damage-inducible protein DinI [54856] (1)
beta-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed sheet 213; crossing loops
1. DNA damage-inducible protein DinI [54857] (1)
  uperfamily
  1. DNA damage-inducible protein DinI [54858] (1)
    1. DNA damage-inducible protein DinI [54859]
      1. Escherichia coli [TaxId: 562] [54860] (1)
HSP90 C-terminal domain [110941] (1)
alpha-beta(3)-alpha(3); 2 layers, a/b; mixed beta-sheet, order:132; crossing loops
1. HSP90 C-terminal domain [110942] (1)
  uperfamily
  1. HSP90 C-terminal domain [110943] (1)
    C-terminal part of Pfam 00183
    1. Chaperone protein HtpG [110944]
      1. Escherichia coli [TaxId: 562] [110945] (1)
        SQ P10413 511-624
Ferredoxin-like [54861] (59)
alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1. 4Fe-4S ferredoxins [54862] (6)
  uperfamily
  1. Short-chain ferredoxins [54863] (5)
    contains two 4Fe-4S clusters
    1. Ferredoxin II [54864]
      1. Peptostreptococcus asaccharolyticus [TaxId: 1258] [54866] (1)
      2. Clostridium acidurici [TaxId: 1556] [54867] (3)
      3. Clostridium pasteurianum [TaxId: 1501] [54868] (1)
      4. Chromatium vinosum [TaxId: 1049] [54869] (1)
      5. Thauera aromatica [TaxId: 59405] [102954] (1)
  2. 7-Fe ferredoxin [54870] (5)
    has C-terminal extension to the common fold
    1. Ferredoxin [54871]
      1. Azotobacter vinelandii [TaxId: 354] [54872] (32)
      2. Bacillus schlegelii [TaxId: 1484] [54873] (4)
      3. Thermus thermophilus [TaxId: 274] [69725] (1)
    2. Photosystem I iron-sulfur protein PsaC [64272]
      1. Synechococcus elongatus [TaxId: 32046] [64273] (1)
      2. Synechococcus sp. pcc 7002 [TaxId: 32049] [75426] (1)
  3. Archaeal ferredoxins [54874] (1)
    1. Ferredoxin [54875]
      the N-terminal extension to the common fold forms a part of a Zn-binding site
      1. Archaeon Sulfolobus sp. [TaxId: 2288] [54876] (1)
  4. Single 4Fe-4S cluster ferredoxin [54877] (5)
    contains only one 4Fe-4S cluster
    1. Ferredoxin A [54878]
      1. Thermotoga maritima [TaxId: 2336] [54879] (2)
    2. Ferredoxin I [54880]
      1. Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873] [54881] (3)
      2. Desulfovibrio gigas [TaxId: 879] [54865] (2)
    3. Ferredoxin [54882]
      1. Bacillus thermoproteolyticus [TaxId: 1427] [54883] (6)
    4. Fe3S4-ferredoxin PF1909 [110946]
      1. Pyrococcus furiosus [TaxId: 2261] [110947] (2)
        SQ P29603
  5. Ferredoxin domains from multidomain proteins [54884] (15)
    members of this "family" may be more closely related to other ferredoxins than to each other
    1. Fe-only hydrogenase, second domain [54885]
      1. Clostridium pasteurianum [TaxId: 1501] [54886] (4)
    2. Fe-only hydrogenase larger subunit, N-domain [54887]
      1. Desulfovibrio desulfuricans [TaxId: 876] [54888] (1)
    3. Pyruvate-ferredoxin oxidoreductase, PFOR, domain V [54889]
      1. Desulfovibrio africanus [TaxId: 873] [54890] (17)
    4. Dihydropyrimidine dehydrogenase, C-terminal domain [54891]
      includes linker from domain 4
      1. Pig (Sus scrofa) [TaxId: 9823] [54892] (5)
    5. Adenylylsulfate reductase B subunit [69726]
      includes N-terminal partly folded tail
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69727] (10)
    6. Formate dehydrogenase N, iron-sulfur (beta) subunit [75427]
      1. Escherichia coli [TaxId: 562] [75428] (2)
    7. Tungsten containing formate dehydrogenase, small subunit [82664]
      1. Desulfovibrio gigas [TaxId: 879] [82665] (1)
    8. Respiratory nitrate reductase 1 beta chain [102955]
      1. Escherichia coli [TaxId: 562] [102956] (7)
        SQ P11349
    9. Transhydroxylase beta subunit, BthL, N-terminal domain [110948]
      1. Pelobacter acidigallici [TaxId: 35816] [110949] (6)
        SQ P80564
    10. NADH-quinone oxidoreductase chain 9, Nqo9 [143252]
      1. Thermus thermophilus [TaxId: 274] [143253] (4)
        SQ Q56224 26-179
    11. NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 [143254]
      1. Thermus thermophilus [TaxId: 274] [143255] (4)
        SQ Q56223 96-246
    12. DsrB insert domain [160277]
      1. Desulfovibrio vulgaris [TaxId: 881] [160278] (2)
        SQ P45575 209-277
      2. Archaeoglobus fulgidus [TaxId: 2234] [160279] (2)
        SQ Q59110 197-261
    13. DsrA insert domain [160280]
      1. Desulfovibrio vulgaris [TaxId: 881] [160281] (2)
        SQ P45574 242-322
      2. Archaeoglobus fulgidus [TaxId: 2234] [160282] (2)
        SQ Q59109 240-305
  6. ETF-QO domain-like [143256] (1)
    Pfam 05187; Electron transfer flavoprotein-ubiquinone oxidoreductase; contains single Fe4-S4 cluster
    1. Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO [143257]
      1. Pig (Sus scrofa) [TaxId: 9823] [143258] (4)
        SQ P55931 506-607
2. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54893] (1)
  uperfamily
  1. Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain [54894] (2)
    1. Aspartate carbamoyltransferase [54895]
      1. Escherichia coli [TaxId: 562] [54896] (59)
        SQ P00478
      2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [110950] (2)
3. Protease propeptides/inhibitors [54897] (3)
  uperfamily
  1. Pancreatic carboxypeptidase, activation domain [54898] (6)
    1. Procarboxypeptidase A [54899]
      1. Pig (Sus scrofa) [TaxId: 9823] [54900] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [54901] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [54902] (4)
        procarboxypeptidase A2
      4. Cotton bollworm (Helicoverpa armigera) [TaxId: 29058] [75429] (1)
    2. Procarboxypeptidase B [54903]
      1. Pig (Sus scrofa) [TaxId: 9823] [54904] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [75430] (1)
  2. Subtilase propeptides/inhibitors [54905] (4)
    decorated with additional structure
    1. Subtilisin prosegment [54906]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [54907] (1)
      2. Bacillus subtilis [TaxId: 1423] [54908] (1)
    2. Proteinase A inhibitor 1, POIA1 [69728]
      1. Oyster mushroom (Pleurotus ostreatus) [TaxId: 5322] [69729] (2)
    3. Pro-kumamolisin activation domain [110951]
      1. Bacillus sp. MN-32 [TaxId: 198803] [110952] (1)
        SQ Q8RR56
  3. Prohormone convertase 1 pro-domain [75431] (1)
    1. Prohormone convertase 1 pro-domain [75432]
      1. Mouse (Mus musculus) [TaxId: 10090] [75433] (1)
4. Dimeric alpha+beta barrel [54909] (23)
  dimerizes through the beta-sheet; forms beta-sheet barrel, closed (n=8, S=12); dimers may assemble in higher oligomers
  uperfamily
  1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82666] (1)
    1. Actinorhodin biosynthesis monooxygenase ActVa-Orf6 [82667]
      1. Streptomyces coelicolor [TaxId: 1902] [82668] (5)
  2. Plant stress-induced protein [89927] (3)
    1. Hypothetical protein AT3G17210.1 [89928]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [89929] (3)
    2. Hypothetical protein AT5G22580 [102957]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [102958] (1)
    3. Boiling stable protein 1 [110953]
      1. European aspen (Populus tremula) [TaxId: 113636] [110954] (2)
        SQ Q9AR79
  3. PG130-like [102959] (5)
    subfamily of Pfam 03992
    1. Hypothetical protein TT1380 [102960]
      1. Thermus thermophilus [TaxId: 274] [102961] (1)
    2. Hypothetical protein PG130 (SAV0165) [110955]
      1. Staphylococcus aureus [TaxId: 1280] [110956] (3)
        SQ Q99X56
    3. Hypothetical protein BC2969 [110957]
      1. Bacillus cereus [TaxId: 1396] [110958] (1)
        SQ Q81C15
    4. Hypothetical protein IsdG [117934]
      1. Staphylococcus aureus [TaxId: 1280] [117935] (1)
        SQ Q8NX62
    5. Hypothetical protein YqjZ [160283]
      1. Bacillus subtilis [TaxId: 1423] [160284] (1)
        SQ P54563 3-110
  4. Hypothetical protein YjcS [102962] (1)
    1. Hypothetical protein YjcS [102963]
      1. Bacillus subtilis [TaxId: 1423] [102964] (1)
  5. YciI-like [102965] (1)
    structural similarity to MLI extends to the active site cavity location
    1. Hypothetical protein HI0828 [102966]
      1. Haemophilus influenzae [TaxId: 727] [102967] (1)
  6. Muconalactone isomerase, MLI [54910] (1)
    decamer: pentamer of dimers
    1. Muconalactone isomerase, MLI [54911]
      1. Pseudomonas putida [TaxId: 303] [54912] (10)
  7. Lrp/AsnC-like transcriptional regulator C-terminal domain [69733] (4)
    octamer: tetramer of dimers
    1. LprA [69734]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [69735] (1)
    2. Putative transcriptional regulator PH1519 [102968]
      archaeal feast/famine regulatory protein
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102969] (3)
        identical sequence to Pyrococcus sp. ot3 protein
    3. Transcriptional regulator LrpC [143259]
      1. Bacillus subtilis [TaxId: 1423] [143260] (8)
        SQ P96582 64-140
    4. Regulatory protein AsnC [143261]
      1. Escherichia coli [TaxId: 562] [143262] (2)
        SQ P0ACI6 67-152
  8. Polyketide synthesis cyclase [110959] (1)
    Pfam 04673
    1. Tetracenomycin polyketide synthesis protein TcmI [110960]
      1. Streptomyces glaucescens [TaxId: 1907] [110961] (1)
        SQ P39890
  9. DGPF domain (Pfam 04946) [110962] (1)
    there is the putative active site cavity in the equivalent location location to the MLI and YciI active sites
    1. Hypothetical protein PA1349 [110963]
      1. Pseudomonas aeruginosa [TaxId: 287] [110964] (1)
        SQ Q9I3Z5
  10. Chlorite dismutase-like [110965] (2)
    Pfam 06778; duplication: consists of two similar domains; forms a pentamer similar to the MLI decamer
    1. YwfI homologue [110966]
      1. Bacillus stearothermophilus [TaxId: 1422] [110967] (1)
        SQ Q5KUD5 # 98% sequence identity; Geobacillus kaustophilus TaxID:1462
    2. Polyketide synthase CurD homologue TTHA1714/TTC1352 [110968]
      1. Thermus thermophilus [TaxId: 274] [110969] (1)
        SQ Q5SHL6
  11. PA3566-like [110970] (5)
    subfamily of Pfam 03992
    1. Hypothetical protein PA3566 [110971]
      1. Pseudomonas aeruginosa [TaxId: 287] [110972] (1)
        SQ Q9HY51
    2. Hypothetical protein YgiN [117936]
      1. Escherichia coli [TaxId: 562] [117937] (2)
        SQ P0ADU2 P40718
    3. Hypothetical protein Rv0793 [117938]
      1. Mycobacterium tuberculosis [TaxId: 1773] [117939] (1)
        SQ O86332
    4. Hypothetical protein NE2512 [160285]
      1. Nitrosomonas europaea [TaxId: 915] [160286] (4)
        SQ Q82S47 1-100
    5. Hypothetical protein NE0621 [160287]
      1. Nitrosomonas europaea [TaxId: 915] [160288] (8)
        SQ Q82WP3 1-98
  12. Hypothetical protein YdhR [117940] (1)
    1. Hypothetical protein YdhR [117941]
      1. Escherichia coli [TaxId: 562] [117942] (5)
        SQ P77225
  13. NIPSNAP [117943] (2)
    Pfam 07978
    1. Hypothetical protein Atu4242 [117944]
      1. Agrobacterium tumefaciens [TaxId: 358] [117945] (9)
        SQ Q8U857
    2. Hypothetical protein Atu5224 [143263]
      1. Agrobacterium tumefaciens [TaxId: 358] [143264] (8)
        SQ Q8UK99 1-104
  14. Dyp-type peroxidase-like [143265] (3)
    Pfam 04261
    1. Hypothetical protein BT1219 [143266]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143267] (1)
        SQ Q8A8E8 8-316
    2. Decolorizing peroxidase DyP [143268]
      1. Geotrichum candidum [TaxId: 27317] [143269] (2)
        SQ Q8WZK8 60-498
        species assignment from the UniProt sequence (Id 100%); 2d3q species is Thanatephorus cucumeris
    3. Melanin biosynthesis protein TyrA [143270]
      1. Shewanella oneidensis [TaxId: 70863] [143271] (2)
        SQ Q8EIU4 5-311
  15. EthD-like [143272] (1)
    Pfam 07110
    1. Hypothetical protein BH0200 [143273]
      1. Bacillus halodurans [TaxId: 86665] [143274] (2)
        SQ Q9KGB0 4-106
  16. Atu0297-like [143275] (1)
    Pfam 07045; DUF1330
    1. Hypothetical protein Atu0297 [143276]
      1. Agrobacterium tumefaciens [TaxId: 358] [143277] (2)
        SQ Q8UIJ7 1-95
  17. SOR-like [143278] (1)
    Pfam 07682; duplication: consists of two similar domains
    1. Sulfur oxygenase reductase SOR [143279]
      1. Acidianus ambivalens [TaxId: 2283] [143280] (1)
        SQ P29082 2-308
  18. YbaA-like [160289] (1)
    Pfam 07237; DUF1428
    1. Hypothetical protein YbaA [160290]
      1. Shigella flexneri [TaxId: 623] [160291] (2)
        SQ P0AAQ9 1-117
  19. MmlI-like [160292] (1)
    Pfam 09448; Methylmuconolactone methyl-isomerase
    1. Hypothetical protein Reut_A1503 [160293]
      1. Ralstonia eutropha [TaxId: 106590] [160294] (2)
        SQ Q471R3 1-108
  20. Marine metagenome family DABB2 [160295] (1)
    1. Hypothetical protein GOS_3280838 [160296]
      1. environmental samples [160297] (2)
  21. YiiL-like [160298] (1)
    Pfam 05336; DUF718
    1. L-rhamnose mutarotase YiiL [160299]
      1. Escherichia coli [TaxId: 562] [160300] (4)
        SQ P32156 1-104
  22. Marine metagenome family DABB1 [160301] (2)
    1. Hypothetical protein GOS_7213774 [160302]
      1. environmental samples [160303] (6)
        marine metagenome
    2. Hypothetical protein GOS_2359375 [160304]
      1. environmental samples [160305] (4)
        marine metagenome
  23. Marine metagenome family DABB3 [160306] (1)
    duplication: consists of two similar domains; forms a pentamer similar to the Chlorite dismutase-like pentamer and the MLI decamer
    1. Uncharacterized protein GOS_2596953 [160307]
      1. environmental samples [160308] (5)
5. GlnB-like [54913] (5)
  form timeric structures with the orthogonally packed beta-sheets
  uperfamily
  1. Prokaryotic signal transducing protein [54914] (8)
    1. PII (product of glnB) [54915]
      trimer with orthogonal packing of beta-sheets around the threefold axis
      1. Escherichia coli [TaxId: 562] [54916] (2)
      2. Herbaspirillum seropedicae [TaxId: 964] [89930] (1)
      3. Cyanobacteria (Synechococcus sp.) pcc 7942 [TaxId: 1131] [102970] (1)
      4. Cyanobacteria (Synechococcus sp.) pcc pcc 6803 [TaxId: 1131] [102971] (1)
      5. Thermus thermophilus [TaxId: 274] [102972] (5)
        SQ P83820
    2. PII-homolog GlnK [54917]
      1. Escherichia coli [TaxId: 562] [54918] (8)
      2. Shigella flexneri [TaxId: 623] [160309] (1)
        SQ P0AC58 1-112
    3. Hypothetical protein TTHA0516 [143281]
      1. Thermus thermophilus [TaxId: 274] [143282] (3)
        SQ Q5SKX7 1-100
  2. Divalent ion tolerance proteins CutA (CutA1) [75434] (7)
    1. Cut A1 [89931]
      1. Thermus thermophilus [TaxId: 274] [89932] (2)
      2. Escherichia coli [TaxId: 562] [102973] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102974] (15)
        SQ O58720
      4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89933] (1)
    2. Hypothetical protein TM1056 [75435]
      1. Thermotoga maritima [TaxId: 2336] [75436] (3)
    3. Mammalian CutA-like protein [102975]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [102976] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [117946] (7)
        SQ O60888 40-146
  3. DUF190/COG1993 [89934] (1)
    1. Hypothetical protein TM0021 [89935]
      1. Thermotoga maritima [TaxId: 2336] [89936] (1)
  4. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [88851] (2)
    1. ATP phosphoribosyltransferase (ATP-PRTase, HisG), regulatory C-terminal domain [82669]
      binds allosteric inhibitor histidine
      1. Mycobacterium tuberculosis [TaxId: 1773] [82670] (2)
      2. Escherichia coli [TaxId: 562] [102977] (2)
  5. RPA1041-like [160310] (1)
    PF09413; DUF2007; provisional superfamily assignment based on a single monomeric solution structure
    1. Hypothetical protein RPA1041 [160311]
      1. Rhodopseudomonas palustris [TaxId: 1076] [160312] (1)
        SQ Q6NAY9 1-75
        missannotated in PDB 2HFV as Pseudomonas aeruginosa
6. SEA domain [82671] (1)
  uperfamily
  1. SEA domain [82672] (1)
    1. SEA domain from the hypothetical protein homologous to mucin 16 [82673]
      1. Mouse (Mus musculus) [TaxId: 10090] [82674] (1)
7. Nucleoside diphosphate kinase, NDK [54919] (1)
  uperfamily
  1. Nucleoside diphosphate kinase, NDK [54920] (20)
    1. Nucleoside diphosphate kinase, NDK [54921]
      1. Human (Homo sapiens) [TaxId: 9606] [54922] (14)
      2. Human (Homo sapiens), NDK4 [TaxId: 9606] [54923] (1)
      3. Human (Homo sapiens), NDKA [TaxId: 9606] [75437] (5)
      4. Cow (Bos taurus) [TaxId: 9913] [54924] (2)
      5. Dictyostelium discoideum [TaxId: 44689] [54925] (27)
      6. Drosophila melanogaster [TaxId: 7227] [54926] (2)
      7. Myxococcus xanthus [TaxId: 34] [54927] (3)
      8. Mycobacterium tuberculosis [TaxId: 1773] [75438] (1)
      9. Bacillus halodenitrificans [TaxId: 1482] [89937] (1)
      10. Plasmodium falciparum, isolate 3D7 [TaxId: 5833] [117947] (1)
        SQ Q8ID43
      11. Pea (Pisum sativum) [TaxId: 3888] [117948] (1)
        SQ Q9SP13 81-231
      12. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117949] (1)
        SQ P39207
      13. Thale cress (Arabidopsis thaliana), chloroplast NDK2 [TaxId: 3702] [117950] (2)
        SQ O64903 79-231
      14. Human(Homo sapiens), NDK3 [TaxId: 9606] [143283] (3)
        SQ Q13232 18-169
      15. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143284] (12)
        SQ O58429 3-155
      16. Rice(Oryza sativa) [TaxId: 4530] [143285] (12)
        SQ Q07661 1-148
      17. Mimivirus [TaxId: 315393] [143286] (8)
        SQ Q5UQL3 2-137
      18. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [143287] (3)
        SQ Q8ZWY4 2-183
      19. Archaeon Halobacterium salinarum [TaxId: 2242] [143288] (15)
        SQ P61136 4-158
      20. Thermus thermophilus [TaxId: 274] [143289] (6)
        SQ Q5SLV5 1-137
8. RNA-binding domain, RBD [54928] (5)
  uperfamily
  1. Canonical RBD [54929] (71)
    1. Nuclear ribonucleoprotein A1 (RNP A1, UP1) [54930]
      duplication: contains two domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [54931] (14)
        SQ P09651 7-188
    2. Nuclear ribonucleoprotein D0 (AUF1) [75439]
      1. Human (Homo sapiens) [TaxId: 9606] [75440] (3)
    3. Splicesomal U1A protein [54932]
      duplication: contains two domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [54933] (38)
        SQ P09012 1-97 ! SQ P09012 4-98 ! SQ P09012 1-98
      2. Drosophila melanogaster [TaxId: 7227] [160313] (3)
        SQ P43332 1-104! SQ P43332 134-216
    4. Splicing factor U2B'' [54934]
      1. Human (Homo sapiens) [TaxId: 9606] [54935] (1)
    5. Splicing factor U2AF 65 KDa subunit [54936]
      1. Human (Homo sapiens) [TaxId: 9606] [54937] (4)
    6. Sex-lethal protein [54938]
      1. Drosophila melanogaster [TaxId: 7227] [54939] (4)
    7. Hu antigen C (Huc) [54940]
      1. Mouse (Mus musculus) [TaxId: 10090] [54941] (3)
    8. Hu antigen D (Hud) [54942]
      1. Human (Homo sapiens) [TaxId: 9606] [54943] (2)
    9. Heterogeneous nuclear ribonucleoprotein d0 [54944]
      1. Human (Homo sapiens) [TaxId: 9606] [54945] (2)
    10. Neural RNA-binding protein Musashi-1 [54946]
      1. Mouse (Mus musculus) [TaxId: 10090] [54947] (2)
    11. Poly(A)-binding protein [54948]
      1. Human (Homo sapiens) [TaxId: 9606] [54949] (1)
    12. Polypyrimidine tract-binding protein [54950]
      1. Human (Homo sapiens) [TaxId: 9606] [54951] (9)
        SQ P26599 54-141, 177-284, 335-531
    13. Nucleolin [54952]
      1. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [54953] (4)
    14. CBP20, 20KDa nuclear cap-binding protein [64274]
      1. Human (Homo sapiens) [TaxId: 9606] [64275] (6)
    15. RNA-binding protein 8 [89938]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89939] (3)
        CG8781 protein
      2. Human (Homo sapiens) [TaxId: 9606] [102978] (6)
        RBM8A, Y14
    16. Lupus LA protein [89940]
      1. Human (Homo sapiens) [TaxId: 9606] [89941] (13)
    17. Nuclear factor Aly [102979]
      1. Mouse (Mus musculus) [TaxId: 10090] [102980] (1)
    18. Musashi-1 [102981]
      1. Mouse (Mus musculus) [TaxId: 10090] [102982] (1)
    19. Cleavage stimulation factor, 64 kda subunit [102983]
      1. Human (Homo sapiens) [TaxId: 9606] [102984] (1)
    20. Synaptojanin 2 [102985]
      1. Human (Homo sapiens) [TaxId: 9606] [102986] (1)
    21. Heterogeneous nuclear ribonucleoprotein L-like [117951]
      1. Mouse (Mus musculus) [TaxId: 10090] [117952] (1)
        SQ Q921F4 116-207
    22. Calcipressin-1 [117953]
      1. Mouse (Mus musculus) [TaxId: 10090] [117954] (1)
        SQ Q9JHG6 14-103
    23. Heterogeneous nuclear ribonucleoprotein H' [117955]
      1. Human (Homo sapiens) [TaxId: 9606] [117956] (2)
        SQ P55795 103-193; 280-369
    24. TAR DNA-binding protein 43, TDP-43 [117957]
      1. Human (Homo sapiens) [TaxId: 9606] [117958] (2)
        SQ Q13148 193-267
    25. RNA-binding protein Raly (Autoantigen p542) [117959]
      1. Human (Homo sapiens) [TaxId: 9606] [117960] (1)
        SQ Q9UKM9 1-97
    26. Heterogeneous nuclear ribonucleoproteins C1/C2 [117961]
      1. Human (Homo sapiens) [TaxId: 9606] [117962] (1)
        SQ P07910 8-92
    27. Probable RNA-binding protein KIAA1579 [117963]
      1. Human (Homo sapiens) [TaxId: 9606] [117964] (1)
        SQ Q9HCJ3 71-145
    28. Splicing factor, arginine/serine-rich 9 (SFRS9) [117965]
      1. Mouse (Mus musculus) [TaxId: 10090] [117966] (1)
        SQ Q9D0B0 104-188
    29. Poly(A)-specific ribonuclease PARN [117967]
      1. Mouse (Mus musculus) [TaxId: 10090] [117968] (1)
        SQ Q8VDG3 430-516; structure of the R3H domain (162-248) is also known (scop_sp 111031)
    30. Probable RNA-binding protein 19, Rbm19 [117969]
      1. Mouse (Mus musculus) [TaxId: 10090] [117970] (4)
        SQ Q8R3C6 399-484; 581-678
    31. Putative RNA-binding protein 15B, Rbm15b [117971]
      1. Mouse (Mus musculus) [TaxId: 10090] [117972] (1)
        SQ Q6PHZ5 81-164
    32. Eukaryotic translation initiation factor 4B [117973]
      1. Human (Homo sapiens) [TaxId: 9606] [117974] (1)
        SQ P23588 88-178
    33. HIV Tat-specific factor 1 [143290]
      1. Human (Homo sapiens) [TaxId: 9606] [143291] (1)
        SQ O43719 256-354
    34. Ataxin-2-binding protein 1 [143292]
      1. Human (Homo sapiens) [TaxId: 9606] [143293] (1)
        SQ Q9NWB1 109-196
    35. E3 ubiquitin protein ligase CNOT4 [143294]
      CCR4-NOT transcription complex subunit 4
      1. Mouse (Mus musculus) [TaxId: 10090] [143295] (1)
        SQ Q8BT14 101-198
    36. RNA-binding protein 41, RBM41 [143296]
      1. Human (Homo sapiens) [TaxId: 9606] [143297] (1)
        SQ Q96IZ5 291-392
    37. Nucleolysin TIAR [143298]
      1. Human (Homo sapiens) [TaxId: 9606] [143299] (2)
        SQ Q01085 1-90! SQ Q01085 187-282
    38. Cold-inducible RNA-binding protein [143300]
      1. Human (Homo sapiens) [TaxId: 9606] [143301] (1)
        SQ Q14011 1-90
    39. Negative elongation factor E, NELF-E [143302]
      1. Human (Homo sapiens) [TaxId: 9606] [143303] (3)
        SQ P18615 257-335! SQ P18615 258-341
    40. Eukaryotic translation initiation factor 3 subunit 4 [143304]
      1. Human (Homo sapiens) [TaxId: 9606] [143305] (1)
        SQ O75821 231-320
    41. Matrin 3 [143306]
      1. Mouse (Mus musculus) [TaxId: 10090] [143307] (2)
        SQ Q8K310 390-478! SQ Q8K310 478-576
    42. Ribonucleoprotein PTB-binding 1, Raver-1 [143308]
      1. Mouse (Mus musculus) [TaxId: 10090] [143309] (1)
        SQ Q9CW46 61-135
    43. Peptidyl-prolyl cis-trans isomerase E, N-terminal domain [143310]
      1. Human (Homo sapiens) [TaxId: 9606] [143311] (1)
        SQ Q9UNP9 1-89
    44. Arginine/serine-rich splicing factor 10 [143312]
      1. Human (Homo sapiens) [TaxId: 9606] [143313] (1)
        SQ P62995 109-191
    45. RNA-binding protein 9 [143314]
      1. Human (Homo sapiens) [TaxId: 9606] [143315] (1)
        SQ O43251 110-202
    46. Pre-mRNA branch site protein p14 [143316]
      1. Human (Homo sapiens) [TaxId: 9606] [143317] (4)
        SQ Q9Y3B4 12-125
    47. Splicing factor 3B subunit 4 [143318]
      1. Human (Homo sapiens) [TaxId: 9606] [143319] (2)
        SQ Q15427 102-184! SQ Q15427 4-96
    48. RNA-binding motif, single-stranded-interacting protein 2, RBMS2 [143320]
      1. Human (Homo sapiens) [TaxId: 9606] [143321] (1)
        SQ Q15434 58-129
    49. RNA-binding protein UBP1 [143322]
      1. Trypanosoma cruzi [TaxId: 5693] [143323] (1)
        SQ Q967R0 1-139
    50. Limkain-b1, LKAP [143324]
      KIAA0430
      1. Human (Homo sapiens) [TaxId: 9606] [143325] (1)
        SQ Q9Y4F3 788-870
    51. APOBEC1 stimulating protein [143326]
      1. Human (Homo sapiens) [TaxId: 9606] [143327] (1)
        SQ Q9NQ94 223-308
    52. Hypothetical protein FLJ20273 [143328]
      1. Human (Homo sapiens) [TaxId: 9606] [143329] (1)
        SQ Q8NI52 150-245
    53. Nucleoporin 35 [143330]
      1. Mouse (Mus musculus) [TaxId: 10090] [143331] (4)
        SQ Q8R4R6 169-249
    54. Polypyrimidine tract-binding protein 2, PTBP2 [143332]
      1. Human (Homo sapiens) [TaxId: 9606] [143333] (1)
        SQ Q9UKA9 51-138
    55. Alkylation repair AlkB homolog 8, ALKBH8 [143334]
      1. Human (Homo sapiens) [TaxId: 9606] [143335] (1)
        SQ Q96BT7 25-125
    56. CUG triplet repeat RNA-binding protein 1 [143336]
      1. Human (Homo sapiens) [TaxId: 9606] [143337] (1)
        SQ Q92879 383-484
    57. U4/U6 snRNA-associated-splicing factor PRP24 [143338]
      contains three RBDs
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143339] (24)
        SQ P49960 116-196! SQ P49960 206-291! SQ P49960 41-115
    58. RNA-binding protein EWS [143340]
      1. Human (Homo sapiens) [TaxId: 9606] [143341] (1)
        SQ Q01844 353-453
    59. Heterogeneous nuclear ribonucleoproteins A2/B1 [143342]
      1. Human (Homo sapiens) [TaxId: 9606] [143343] (1)
        SQ P22626 1-103
    60. IGF-II mRNA-binding protein 2 isoform A [143344]
      1. Human (Homo sapiens) [TaxId: 9606] [143345] (1)
        SQ Q9Y6M1 2-81
    61. Splicing factor, arginine/serine-rich 1, SFRS1 [143346]
      1. Human (Homo sapiens) [TaxId: 9606] [143347] (3)
        SQ Q07955 1-95
      2. Mouse (Mus musculus) [TaxId: 10090] [143348] (1)
        SQ Q6PDM2 112-206
    62. RNA-binding protein 12 [143349]
      3rd RBD
      1. Human (Homo sapiens) [TaxId: 9606] [143350] (2)
        SQ Q9NTZ6 412-523! SQ Q9NTZ6 536-638
      2. Mouse (Mus musculus) [TaxId: 10090] [143351] (1)
        SQ Q8R4X3 917-1002
    63. RNA binding protein 23 [143352]
      1. Human (Homo sapiens) [TaxId: 9606] [143353] (1)
        SQ Q86U06 148-248
    64. Non-POU domain-containing octamer-binding protein, NonO [143354]
      1. Mouse (Mus musculus) [TaxId: 10090] [143355] (1)
        SQ Q99K48 68-153
    65. RNA-binding motif, single-stranded-interacting protein 1, RBMS1 [143356]
      1. Human (Homo sapiens) [TaxId: 9606] [143357] (1)
        SQ P29558 123-223
    66. RNA-binding protein 28 [143358]
      1. Mouse (Mus musculus) [TaxId: 10090] [143359] (1)
        SQ Q8CGC6 316-413
    67. RNA-binding region containing protein 1 [143360]
      1. Human (Homo sapiens) [TaxId: 9606] [143361] (1)
        SQ Q9H0Z9 1-103
  2. Non-canonical RBD domain [54954] (1)
    1. mRNA export factor tap [54955]
      1. Human (Homo sapiens) [TaxId: 9606] [54956] (5)
  3. Splicing factor U2AF subunits [64276] (1)
    1. U2AF35 (35 KDa subunit) [64277]
      1. Human (Homo sapiens) [TaxId: 9606] [64278] (1)
  4. Smg-4/UPF3 [102987] (1)
    Pfam 03467
    1. RNA processing protein UPF3x, RRM domain [102988]
      1. Human (Homo sapiens) [TaxId: 9606] [102989] (1)
  5. GUCT domain [160314] (1)
    Pfam 08152
    1. ATP-dependent RNA helicase DDX50 [160315]
      1. Human (Homo sapiens) [TaxId: 9606] [160316] (1)
        SQ Q9BQ39 575-659
9. Viral DNA-binding domain [54957] (1)
  uperfamily
  1. Viral DNA-binding domain [54958] (6)
    1. Papillomavirus-1 E2 protein [54959]
      forms dimers with subunit beta-sheets making (8,12) barrel
      1. Bovine papillomavirus type 1 [TaxId: 10559] [54960] (3)
      2. Human papillomavirus type 31 [TaxId: 10585] [54961] (2)
      3. Human papillomavirus type 16 [TaxId: 333760] [54962] (5)
        SQ P03120 286-365
      4. Human papillomavirus type 18 [TaxId: 333761] [54963] (2)
      5. Human papillomavirus type 6a [TaxId: 37122] [102990] (11)
    2. Epstein barr virus nuclear antigen-1 (ebna1) [54964]
      DNA-binding mode differs from that of E2 protein
      1. Epstein-Barr virus [TaxId: 10376] [54965] (2)
10. RuBisCO, large subunit, small (N-terminal) domain [54966] (1)
  C-terminal domain is beta/alpha barrel
  uperfamily
  1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54967] (12)
    1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [54968]
      1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [54969] (5)
      2. Spinach (Spinacia oleracea) [TaxId: 3562] [54970] (11)
      3. Galdieria partita [TaxId: 83374] [54971] (2)
      4. Chlamydomonas reinhardtii [TaxId: 3055] [69730] (74)
      5. Alcaligenes eutrophus [TaxId: 106590] [54972] (1)
      6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [54973] (16)
      7. Rhodospirillum rubrum [TaxId: 1085] [54974] (5)
      8. Archaeon Thermococcus kodakaraensis [TaxId: 311400] [69731] (1)
      9. Chlorobium tepidum [TaxId: 1097] [117975] (3)
        SQ Q8KBL4 1-428
      10. Rice (Oryza sativa) [TaxId: 4530] [117976] (1)
        SQ P12089
      11. Archaeon Halothiobacillus neapolitanus [TaxId: 927] [143362] (1)
        SQ O85040 16-142
      12. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143363] (10)
        SQ O58677 8-133
11. Acylphosphatase/BLUF domain-like [54975] (2)
  uperfamily
  1. Acylphosphatase-like [54976] (6)
    1. Acylphosphatase [54977]
      1. Cow (Bos taurus) [TaxId: 9913] [54978] (1)
      2. Horse (Equus caballus) [TaxId: 9796] [54979] (1)
      3. Pyrococcus horikoshii [TaxId: 53953] [110973] (2)
        SQ P84142
      4. Thermus thermophilus [TaxId: 274] [117977] (1)
        SQ Q5SKS6
    2. Hydrogenase maturation protein HypF N-terminal domain (HypF-ACP) [82675]
      1. Escherichia coli [TaxId: 562] [82676] (2)
    3. Acylphosphatase 2 (Cg18505) [110974]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110975] (1)
        SQ Q9VF36
  2. BLUF domain [143364] (3)
    Pfam 04940; sensors of blue-light using FAD
    1. Blue light receptor BlrB [143365]
      1. Rhodobacter sphaeroides [TaxId: 1063] [143366] (2)
        SQ Q3IYE4 1-136
    2. Sensor of blue light AppA [143367]
      1. Rhodobacter sphaeroides [TaxId: 1063] [143368] (4)
        SQ Q53119 17-130! SQ Q53119 5-125
    3. Hypothetical protein Tll0078 [143369]
      1. Thermosynechococcus elongatus [TaxId: 146786] [143370] (10)
        SQ Q8DMN3 2-143
12. EF-G C-terminal domain-like [54980] (3)
  uperfamily
  1. EF-G/eEF-2 domains III and V [54981] (3)
    domain III structure is lacking some of the superfamily characters and is often disordered in crystals
    1. Elongation factor G (EF-G) [54982]
      domain III is seen in 1FNM but disordered in the most of other PDB entries
      1. Thermus thermophilus [TaxId: 274] [54983] (12)
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [143371] (4)
        SQ Q5SI76 371-447! SQ Q5SI76 563-658
        TTHA1498
    2. Elongation factor 2 (eEF-2) [82677]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82678] (41)
        SQ P32324
  2. YigZ C-terminal domain-like [102991] (2)
    similar to EF-G domain V; N-terminal domain shares structural similarity with the EF-G domain IV
    1. Hypothetical protein YigZ, C-terminal domain [102992]
      1. Escherichia coli [TaxId: 562] [102993] (1)
    2. Hypothetical protein TTHA1053, C-terminal domain [143372]
      1. Thermus thermophilus [TaxId: 274] [143373] (1)
        SQ Q5SJF5 125-191
  3. Hypothetical protein AF0491, C-terminal domain [110976] (1)
    1. Hypothetical protein AF0491, C-terminal domain [110977]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [110978] (2)
        SQ O29759
13. eEF-1beta-like [54984] (1)
  uperfamily
  1. eEF-1beta-like [54985] (3)
    1. Guanine nucleotide exchange factor (GEF) domain from elongation factor-1 beta [54986]
      1. Human (Homo sapiens) [TaxId: 9606] [54987] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [54988] (6)
    2. aEF-1beta [54989]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [54990] (1)
14. eEF1-gamma domain [89942] (1)
  elaborated with additional structures
  uperfamily
  1. eEF1-gamma domain [89943] (1)
    1. Elongation factor 1-gamma C-terminal domain [89944]
      1. Human (Homo sapiens) [TaxId: 9606] [89945] (1)
15. Anticodon-binding domain of PheRS [54991] (1)
  uperfamily
  1. Anticodon-binding domain of PheRS [54992] (1)
    1. Phenylalanyl-tRNA synthetase [54993]
      1. Thermus thermophilus [TaxId: 274] [54994] (9)
        identical sequence to Thermus aquaticus, TaxId: 271
16. Ribosomal protein S6 [54995] (1)
  uperfamily
  1. Ribosomal protein S6 [54996] (4)
    1. Ribosomal protein S6 [54997]
      1. Thermus thermophilus [TaxId: 274] [54998] (54)
        SQ P23370
      2. Thermotoga maritima [TaxId: 2336] [117978] (1)
        SQ Q9WZ72
      3. Escherichia coli [TaxId: 562] [160317] (24)
        SQ P02358 1-100
      4. Aquifex aeolicus [TaxId: 63363] [160318] (1)
        SQ O66474 3-108
17. Ribosomal protein S10 [54999] (1)
  uperfamily
  1. Ribosomal protein S10 [55000] (2)
    1. Ribosomal protein S10 [55001]
      1. Thermus thermophilus [TaxId: 274] [55002] (45)
        SQ P80375
      2. Escherichia coli [TaxId: 562] [160319] (24)
        SQ P0A7R5 5-102
18. N-utilization substance G protein NusG, N-terminal domain [82679] (1)
  uperfamily
  1. N-utilization substance G protein NusG, N-terminal domain [82680] (2)
    1. N-utilization substance G protein NusG, N-terminal domain [82681]
      1. Aquifex aeolicus [TaxId: 63363] [82682] (4)
        interrupted by an insert beta-sandwich domain
      2. Thermus thermophilus [TaxId: 274] [102994] (1)
19. PAP/Archaeal CCA-adding enzyme, C-terminal domain [55003] (2)
  uperfamily
  1. Poly(A) polymerase, PAP, C-terminal domain [55004] (2)
    1. Poly(A) polymerase, PAP, C-terminal domain [55005]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55006] (7)
      2. Cow (Bos taurus) [TaxId: 9913] [55007] (3)
        SQ P25500 18-497
  2. Archaeal tRNA CCA-adding enzyme [102995] (1)
    decorated fold with a large insertion
    1. tRNA nucleotidyltransferase, C-terminal domain [102996]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102997] (28)
        SQ O28126
20. HMA, heavy metal-associated domain [55008] (1)
  uperfamily
  1. HMA, heavy metal-associated domain [55009] (12)
    1. Mercuric ion binding protein MerP [55010]
      1. Shigella flexneri [TaxId: 623] [55011] (3)
      2. Ralstonia metallidurans CH34 [TaxId: 266264] [110979] (1)
        SQ O66016 Q58AI1 Q5NUU9 Q6UP70 Q7BRH5 Q7BRH6 Q7X3A5 # 100% identity
    2. Potential copper-translocating P-type ATPase CopA (YvgX) [75441]
      duplication: contains tandem repeat of two HMA domains in the N-terminal region
      1. Bacillus subtilis [TaxId: 1423] [75442] (6)
    3. Metal ion-transporting ATPase ZntA, N-terminal domain [82683]
      1. Escherichia coli [TaxId: 562] [82684] (2)
    4. Copper transporter domain ccc2a [64279]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64280] (3)
    5. Menkes copper-transporting ATPase [55012]
      1. Human (Homo sapiens) [TaxId: 9606] [55013] (7)
    6. ATX1 metallochaperone protein (ATOX1) [55014]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55015] (5)
      2. Human (Homo sapiens), HAH1 [TaxId: 9606] [55016] (5)
        SQ O00244
    7. Copper chaperone [55017]
      1. Enterococcus hirae [TaxId: 1354] [55018] (1)
      2. Bacillus subtilis, CopZ [TaxId: 1423] [69736] (4)
      3. Synechocystis sp. pcc 6803, Scatx1 [TaxId: 1148] [102998] (1)
    8. Copper chaperone for superoxide dismutase, N-terminal domain [55019]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55020] (2)
21. Urease metallochaperone UreE, C-terminal domain [69737] (1)
  uperfamily
  1. Urease metallochaperone UreE, C-terminal domain [69738] (2)
    1. Urease metallochaperone UreE, C-terminal domain [69739]
      1. Klebsiella aerogenes [TaxId: 28451] [69740] (3)
      2. Bacillus pasteurii [TaxId: 1474] [69741] (2)
22. ACT-like [55021] (14)
  regulatory domain linked to a wide range of metabolic enzymes
  uperfamily
  1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55022] (2)
    1. Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain [55023]
      1. Escherichia coli [TaxId: 562] [55024] (18)
      2. Mycobacterium tuberculosis [TaxId: 1773] [143374] (2)
        SQ P0A544 451-528
        there is an intervening domain between the substrate-binding domain and this domain
  2. Allosteric threonine deaminase C-terminal domain [55025] (1)
    1. Allosteric threonine deaminase C-terminal domain [55026]
      duplication: consists of two homologous domains
      1. Escherichia coli [TaxId: 562] [55027] (1)
  3. Phenylalanine metabolism regulatory domain [55028] (2)
    1. Phenylalanine hydroxylase N-terminal domain [55029]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55030] (2)
    2. Prephenate dehydratase C-terminal domain [160320]
      1. Staphylococcus aureus [TaxId: 1280] [160321] (2)
        SQ Q99SX2 185-264
  4. Nickel responsive regulator NikR, C-terminal domain [102999] (2)
    1. Nickel responsive regulator NikR, C-terminal domain [103000]
      1. Escherichia coli [TaxId: 562] [103001] (21)
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143375] (12)
        SQ O58316 51-132
  5. Glycine cleavage system transcriptional repressor [110980] (1)
    tandem repeat of two ACT-like domains; swapped domain dimer
    1. putative transcriptional repressor VC2159 [110981]
      1. Vibrio cholerae [TaxId: 666] [110982] (1)
        SQ Q9KQ45
  6. IlvH-like [143376] (3)
    Duplication: tandem repeat of two ACT-like domains; dimer, the N- and C-terminal domains have different dimerisation modes
    1. Acetolactate synthase small subunit, IlvH [143377]
      1. Thermotoga maritima [TaxId: 2336] [143378] (2)
        SQ Q9WZ19 5-82! SQ Q9WZ19 83-165
      2. Escherichia coli [TaxId: 562] [143379] (4)
        SQ P00894 2-77! SQ P00894 78-163
      3. Nitrosomonas europaea [TaxId: 915] [143380] (8)
        SQ Q82UZ2 1-77! SQ Q82UZ2 78-163
  7. SP0238-like [143381] (1)
    stand-alone protein; dimer, the dimerization interface is formed by parallel packing of the subunit beta-sheets
    1. UPF0237 protein SP0238 [143382]
      1. Streptococcus pneumoniae [TaxId: 1313] [143383] (3)
        SQ P67382 1-83
  8. Atu0741-like [143384] (1)
    duplication: tandem repeat of two ACT-like domains; contains strand invasion of extra N-terminal strand into the C-terminal domain beta-sheet; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    1. Hypothetical protein Atu0741 [143385]
      1. Agrobacterium tumefaciens [TaxId: 358] [143386] (2)
        SQ Q8UHE1 2-61! SQ Q8UHE1 62-127
  9. VC0802-like [143387] (1)
    duplication: tandem repeat of two ACT-like domains; contains circular permutation (the C-terminal strand replacement with extra N-terminal strand); dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    1. Hypothetical protein VC0802 [143388]
      1. Vibrio cholerae [TaxId: 666] [143389] (8)
        SQ Q9KTT6 2-67! SQ Q9KTT6 68-131
  10. Aspartokinase allosteric domain-like [143390] (3)
    duplication: tandem repeat of two ACT-like domains; similar subunit and oligomeric structures to the VC0802-like family
    1. Aspartokinase [143391]
      1. Methanococcus jannaschii [TaxId: 2190] [143392] (8)
        SQ Q57991 304-403! SQ Q57991 404-470
      2. Escherichia coli [TaxId: 562] [143393] (6)
        SQ P08660 295-385! SQ P08660 386-449
        Lysine-sensitive aspartokinase 3
      3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143394] (4)
        SQ Q9LYU8 388-478! SQ Q9LYU8 479-553
  11. BT0572-like [143395] (1)
    duplication: tandem repeat of two ACT-like domains; dimerizes with the formation of orthogonally packed intersubunit beta-sheets
    1. Hypothetical protein BT0572 [143396]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143397] (4)
        SQ Q8AA93 1-70! SQ Q8AA93 71-141
  12. AF1403 N-terminal domain-like [143398] (1)
    dimerizes with the formation of a single intersubunit beta-sheet
    1. Hypothetical protein AF1403, N-terminal domain [143399]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143400] (3)
        SQ O28869 2-78
  13. NIL domain-like [160322] (4)
    Pfam 09383
    1. Methionine import ATP-binding protein MetN [160323]
      1. Vibrio parahaemolyticus [TaxId: 670] [160324] (2)
        SQ Q87RS1 248-344
      2. Escherichia coli [TaxId: 562] [160325] (6)
        SQ P30750 241-343! SQ P30750 247-343
    2. Methionine import ATP-binding protein MetN2 [160326]
      1. Enterococcus faecalis [TaxId: 1351] [160327] (1)
        SQ Q831K6 256-345
      2. Staphylococcus aureus [TaxId: 1280] [160328] (3)
        SQ Q99VG8 247-341
  14. TM1266-like [160329] (1)
    PfamB 015436; stand-alone tetrameric protein; there are single beta-sheet dimers, whose beta-sheets are packed in parallel fasion in the tetramer
    1. Hypothetical protein TM1266 [160330]
      1. Thermotoga maritima [TaxId: 2336] [160331] (4)
        SQ Q9X0Z3 2-81
23. Bacterial exopeptidase dimerisation domain [55031] (1)
  uperfamily
  1. Bacterial exopeptidase dimerisation domain [55032] (9)
    1. Carboxypeptidase G2 [55033]
      dimerisation mode is similar to that of 1PSD domain
      1. Pseudomonas sp., strain rs-16 [TaxId: 306] [55034] (1)
    2. Peptidase T (tripeptidase) [75443]
      1. Salmonella typhimurium [TaxId: 90371] [75444] (1)
      2. Escherichia coli [TaxId: 562] [103002] (1)
    3. Peptidase-like beta-alanine synthase [103003]
      1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [103004] (2)
    4. Succinyl-diaminopimelate desuccinylase [103005]
      1. Neisseria meningitidis [TaxId: 487] [103006] (1)
    5. IAA-amino acid hydrolase [117979]
      apparently monomeric
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [117980] (2)
        SQ P54970 37-428
    6. Aminopeptidase PepV [82685]
      contains insert sudbomain 205-292 mimicking the other half of the family-specific dimer
      1. Lactobacillus delbrueckii [TaxId: 1584] [82686] (1)
    7. Allantoate amidohydrolase AllC [143401]
      1. Escherichia coli [TaxId: 562] [143402] (4)
        SQ P77425 211-327
    8. Protein YxeP [143403]
      dimeric protein closely related to IAA-amino acid hydrolase
      1. Bacillus subtilis [TaxId: 1423] [143404] (2)
        SQ P54955 178-292
24. NAD-binding domain of HMG-CoA reductase [55035] (1)
  uperfamily
  1. NAD-binding domain of HMG-CoA reductase [55036] (2)
    1. NAD-binding domain of HMG-CoA reductase [55037]
      1. Human (Homo sapiens) [TaxId: 9606] [55038] (9)
      2. Pseudomonas mevalonii [TaxId: 32044] [55039] (5)
        SQ P13702 4-377
25. Molybdenum cofactor biosynthesis protein C, MoaC [55040] (1)
  uperfamily
  1. Molybdenum cofactor biosynthesis protein C, MoaC [55041] (1)
    1. Molybdenum cofactor biosynthesis protein C, MoaC [55042]
      1. Escherichia coli [TaxId: 562] [55043] (2)
26. TRADD, N-terminal domain [55044] (1)
  uperfamily
  1. TRADD, N-terminal domain [55045] (1)
    1. TRADD, N-terminal domain [55046]
      1. Human (Homo sapiens) [TaxId: 9606] [55047] (2)
27. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55048] (1)
  uperfamily
  1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55049] (2)
    1. Probable ACP-binding domain of malonyl-CoA ACP transacylase [55050]
      1. Escherichia coli [TaxId: 562] [55051] (1)
      2. Streptomyces coelicolor A3(2) [TaxId: 100226] [82687] (1)
28. CheY-binding domain of CheA [55052] (1)
  uperfamily
  1. CheY-binding domain of CheA [55053] (2)
    1. CheY-binding domain of CheA [55054]
      1. Escherichia coli [TaxId: 562] [55055] (6)
      2. Thermotoga maritima [TaxId: 2336] [110983] (1)
        SQ Q56310 175-260
        structurally distinct from the E.coli domain and possesses a different CheY-binding mode
29. D-ribose-5-phosphate isomerase (RpiA), lid domain [75445] (1)
  uperfamily
  1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75446] (4)
    1. D-ribose-5-phosphate isomerase (RpiA), lid domain [75447]
      1. Escherichia coli [TaxId: 562] [75448] (3)
      2. Haemophilus influenzae [TaxId: 727] [82688] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75449] (2)
      4. Thermus thermophilus [TaxId: 274] [110984] (3)
        SQ Q72J47
30. Killer toxin KP6 alpha-subunit [55056] (1)
  uperfamily
  1. Killer toxin KP6 alpha-subunit [55057] (1)
    1. Killer toxin KP6 alpha-subunit [55058]
      1. Smut fungus (Ustilago maydis) [TaxId: 5270] [55059] (1)
31. Hypothetical protein VC0424 [89946] (1)
  uperfamily
  1. Hypothetical protein VC0424 [89947] (1)
    1. Hypothetical protein VC0424 [89948]
      1. Vibrio cholerae [TaxId: 666] [89949] (1)
32. Hypothetical protein TT1725 [103007] (1)
  uperfamily
  1. Hypothetical protein TT1725 [103008] (1)
    1. Hypothetical protein TT1725 [103009]
      1. Thermus thermophilus [TaxId: 274] [103010] (1)
        structural genomics
33. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82689] (1)
  the last strand of the fold is flipped away and involved in oligomerisation
  uperfamily
  1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82690] (1)
    1. Mechanosensitive channel protein MscS (YggB), C-terminal domain [82691]
      1. Escherichia coli [TaxId: 562] [82692] (14)
34. GHMP Kinase, C-terminal domain [55060] (7)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. Galactokinase [103011] (3)
    1. Galactokinase [103012]
      1. Lactococcus lactis [TaxId: 1358] [103013] (1)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103014] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [117981] (1)
        SQ P51570
  2. Homoserine kinase [55061] (1)
    1. Homoserine kinase [55062]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55063] (5)
  3. Mevalonate kinase [75450] (2)
    1. Mevalonate kinase [75451]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [75452] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [75453] (2)
  4. Phosphomevalonate kinase (PMK) [75454] (1)
    1. Phosphomevalonate kinase (PMK) [75455]
      1. Streptococcus pneumoniae r6 [TaxId: 171101] [75456] (1)
  5. Mevalonate 5-diphosphate decarboxylase [64281] (1)
    1. Mevalonate 5-diphosphate decarboxylase [64282]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64283] (1)
  6. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89950] (2)
    1. 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE [89951]
      1. Thermus thermophilus [TaxId: 274] [89952] (1)
      2. Escherichia coli [TaxId: 562] [103015] (1)
  7. Early switch protein XOL-1 [89953] (1)
    lost the ATP-binding site
    1. Early switch protein XOL-1 [89954]
      primary determinant of sexual fate in C. elegans
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89955] (1)
35. Translational regulator protein regA [55064] (1)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. Translational regulator protein regA [55065] (1)
    1. Translational regulator protein regA [55066]
      1. Bacteriophage T4 [TaxId: 10665] [55067] (1)
36. Peptide methionine sulfoxide reductase [55068] (1)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. Peptide methionine sulfoxide reductase [55069] (3)
    1. Peptide methionine sulfoxide reductase [55070]
      1. Cow (Bos taurus) [TaxId: 9913] [55071] (2)
      2. Escherichia coli [TaxId: 562] [55072] (2)
      3. Mycobacterium tuberculosis [TaxId: 1773] [89956] (1)
37. Nucleotide cyclase [55073] (2)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. Adenylyl and guanylyl cyclase catalytic domain [55074] (5)
    Pfam 00211
    structurally similar to the "palm" domain of DNA/RNA polymerase superfamily
    1. Type II adenylyl cyclase C2 domain [55075]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55076] (5)
        SQ P26769 879-1077
    2. Adenylyl cyclase VC1, domain C1a [55077]
      1. Dog (Canis familiaris) [TaxId: 9615] [55078] (11)
        SQ P30803 458-646
    3. Adenylyl cyclase IIC1, domain C2a [55079]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55080] (7)
    4. Receptor-type monomeric adenylyl cyclase [55081]
      1. Trypanosome (Trypanosoma brucei), different isoform [TaxId: 5691] [55082] (2)
    5. Adenylate cyclase CyaC [117982]
      1. Spirulina platensis [TaxId: 118562] [117983] (6)
        SQ O32393 1004-1200
  2. GGDEF domain [117984] (1)
    Pfam 00990; less decorated than the adenylyl/guanylyl cyclase domain
    1. Response regulator PleD, C-terminal domain [117985]
      Diguanylate cyclase
      1. Caulobacter crescentus [TaxId: 155892] [117986] (3)
        SQ Q9A5I5
38. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55083] (1)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55084] (2)
    1. 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK [55085]
      1. Escherichia coli [TaxId: 562] [55086] (19)
        SQ P26281
      2. Haemophilus influenzae [TaxId: 727] [55087] (1)
39. Glutamyl tRNA-reductase catalytic, N-terminal domain [69742] (1)
  common fold is elaborated with additional secondary structures
  uperfamily
  1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69743] (1)
    1. Glutamyl tRNA-reductase catalytic, N-terminal domain [69744]
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [69745] (1)
40. MTH1187/YkoF-like [89957] (2)
  uperfamily
  1. MTH1187-like [89958] (5)
    Pfam 01910; two domains form a single beta-sheet dimer; two dimers pack sheet-to-sheet in a tetramer; contains extra C-terminal helix
    1. Hypothetical protein MTH1187 [89959]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89960] (1)
    2. Hypothetical protein YB1001C [89961]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89962] (1)
    3. Hypothetical protein TM0486 [110985]
      1. Thermotoga maritima [TaxId: 2336] [110986] (1)
        SQ Q9WYV6
    4. Hypothetical protein BC0424 [143405]
      1. Bacillus cereus [TaxId: 1396] [143406] (2)
        SQ Q81IG4 1-101
    5. Hypothetical protein SP2199 [143407]
      1. Streptococcus pneumoniae [TaxId: 1313] [143408] (4)
        SQ Q97N67 1-90
  2. Putative thiamin/HMP-binding protein YkoF [110987] (1)
    duplication: one subunit consists of two domains assembled as in the MHT1178-like dimer
    1. Putative thiamin/HMP-binding protein YkoF [110988]
      1. Bacillus subtilis [TaxId: 1423] [110989] (3)
        SQ O34911
41. Methyl-coenzyme M reductase subunits [55088] (2)
  each of the three different subunits, alpha, beta and gamma, contains this fold decorated with additional secondary structures
  uperfamily
  1. Methyl-coenzyme M reductase gamma chain [55089] (3)
    1. Methyl-coenzyme M reductase gamma chain [55090]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55091] (5)
      2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55092] (1)
      3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55093] (1)
  2. Methyl-coenzyme M reductase alpha and beta chain N-terminal domain [55094] (6)
    C-terminal domain is all-alpha
    1. Alpha chain [55095]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55096] (5)
      2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55097] (1)
      3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55098] (1)
    2. Beta chain [55099]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55100] (5)
      2. Archaeon Methanopyrus kandleri [TaxId: 2320] [55101] (1)
      3. Archaeon Methanosarcina barkeri [TaxId: 2208] [55102] (1)
42. FAD-linked oxidases, C-terminal domain [55103] (4)
  duplication: contains two subdomains of this fold
  uperfamily
  1. Vanillyl-alcohol oxidase-like [55104] (2)
    1. Vanillyl-alcohol oxidase [55105]
      1. Fungus (Penicillium simplicissimum) [TaxId: 69488] [55106] (16)
        SQ P56216
    2. Flavoprotein subunit of p-cresol methylhydroxylase [55107]
      the other subunit is a short-chain cytochrome c
      1. Pseudomonas putida [TaxId: 303] [55108] (5)
  2. D-lactate dehydrogenase [55109] (1)
    1. D-lactate dehydrogenase [55110]
      1. Escherichia coli [TaxId: 562] [55111] (1)
  3. Cholesterol oxidase [64284] (1)
    1. Cholesterol oxidase [64285]
      1. Brevibacterium sterolicum [TaxId: 1702] [64286] (2)
  4. Cytokinin dehydrogenase 1 [110990] (1)
    1. Cytokinin dehydrogenase 1 [110991]
      1. Maize (Zea mays) [TaxId: 4577] [110992] (4)
        SQ Q9T0N8
43. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55112] (1)
  duplication: contains two subdomains of this fold
  uperfamily
  1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55113] (3)
    1. Formylmethanofuran:tetrahydromethanopterin formyltransferase [55114]
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [55115] (17)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [75457] (1)
      3. Archaeon Methanosarcina barkeri [TaxId: 2208] [75458] (1)
44. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55116] (1)
  duplication: contains two subdomains of this fold
  uperfamily
  1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55117] (1)
    1. Formiminotransferase domain of formiminotransferase-cyclodeaminase. [55118]
      1. Pig (Sus scrofa) [TaxId: 9823] [55119] (1)
45. Nitrite/Sulfite reductase N-terminal domain-like [55124] (2)
  duplication: contains two subdomains of this fold
  uperfamily
  1. Duplicated SiR/NiR-like domains 1 and 3 [55125] (3)
    1. Sulfite reductase, domains 1 and 3 [55126]
      1. Escherichia coli [TaxId: 562] [55127] (12)
    2. Ferredoxin--nitrite reductase, NIR [160332]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [160333] (2)
        SQ P05314 378-462! SQ P05314 54-206
    3. Sulfite reductase NirA [160334]
      1. Mycobacterium tuberculosis [TaxId: 1773] [160335] (8)
        SQ P71753 10-161! SQ P71753 327-406
  2. DsrA/DsrB N-terminal-domain-like [160336] (4)
    Dissimilatory sulfite reductase is a heterodimer of homologous DsrA and DsrB subunits, the assembly of which is similar to the architecture of duplicated sulfite reductase CysI
    1. Dissimilatory sulfite reductase subunit alpha, DsrA [160337]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160338] (2)
        SQ Q59109 2-418
      2. Desulfovibrio vulgaris [TaxId: 881] [160339] (2)
        SQ P45574 2-437
    2. Dissimilatory sulfite reductase subunit beta, DsrB [160340]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160341] (2)
        SQ Q59110 4-122
      2. Desulfovibrio vulgaris [TaxId: 881] [160342] (2)
        SQ P45575 2-381
46. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82693] (1)
  duplication: the N- and C-terminal halves of the whole proteins are structurally similar; each half contains two domains of this fold
  uperfamily
  1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82694] (1)
    1. Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains [82695]
      PN2 and PC2 subdomains are interrupted by the inserted subdomains DN and DC, respectively
      1. Escherichia coli [TaxId: 562] [82696] (6)
47. YajQ-like [89963] (1)
  duplication: consists of two domains of this fold swapped with their N-terminal strands
  uperfamily
  1. YajQ-like [89964] (1)
    1. Hypothetical protein HI1034 [89965]
      1. Haemophilus influenzae [TaxId: 727] [89966] (1)
48. eIF-2-alpha, C-terminal domain [110993] (1)
  uperfamily
  1. eIF-2-alpha, C-terminal domain [110994] (2)
    1. eIF-2-alpha, C-terminal domain [110995]
      1. Human (Homo sapiens) [TaxId: 9606] [110996] (1)
        SQ P05198
      2. Sulfolobus solfataricus [TaxId: 2287] [143409] (3)
        SQ Q97Z79 176-264
49. Sporulation related repeat [110997] (1)
  duplication: one domain contains two repeats of similar sequence and structure
  uperfamily
  1. Sporulation related repeat [110998] (1)
    Pfam 05036; SPOR
    1. Cell division protein FtsN [110999]
      1. Escherichia coli [TaxId: 562] [111000] (1)
        SQ P29131 243-319
50. CRISPR-associated protein [117987] (1)
  duplication: contains two subdomains of this fold
  uperfamily
  1. CRISPR-associated protein [117988] (1)
    1. Hypothetical protein TTHB192 [117989]
      1. Thermus thermophilus [TaxId: 274] [117990] (1)
        SQ Q53WG9
51. YbeD/HP0495-like [117991] (2)
  uperfamily
  1. YbeD-like [117992] (1)
    Pfam 04359; DUF493
    1. Hypothetical protein ybeD [117993]
      1. Escherichia coli [TaxId: 562] [117994] (1)
        SQ P0A8J4
  2. HP0495-like [160343] (1)
    PfamB 045675
    1. Hypothetical protein HP0495 [160344]
      1. Helicobacter pylori [TaxId: 210] [160345] (2)
        SQ O25237 1-86
52. DOPA-like [143410] (1)
  probable biological unit is homodimer; the extra C-terminal strand, adjacent and antiparallel to strand 4, contributes to the dimerisation interface
  uperfamily
  1. DOPA dioxygenase-like [143411] (1)
    Pfam 08883
    1. Putative dioxygenase BxeB0224 [143412]
      Bxeno_B2751
      1. Burkholderia xenovorans [TaxId: 36873] [143413] (6)
        SQ Q13JM0 1-115
53. CcmK-like [143414] (1)
  contains extra C-terminal helix; forms compact hexameric 'tiles' of hexagonal shape
  uperfamily
  1. CcmK-like [143415] (3)
    Pfam 00936; BMC domain
    1. Major carboxysome shell protein 1A, CsoS1A [143416]
      1. Halothiobacillus neapolitanus [TaxId: 927] [143417] (2)
        SQ P45689 5-97
    2. Carboxysome shell protein CcmK4 [143418]
      1. Synechocystis sp. PCC 6803 [TaxId: 1148] [143419] (9)
        SQ P73407 3-106
    3. Carboxysome shell protein CcmK2 [143420]
      1. Synechocystis sp. PCC 6803 [TaxId: 1148] [143421] (12)
        SQ P72761 1-101
54. Transposase IS200-like [143422] (1)
  contains extra N-terminal hairpin and C-terminal helix, both are involved in dimerization; there can be helix-swapping in the dimer
  uperfamily
  1. Transposase IS200-like [143423] (3)
    Pfam 01797
    1. Putative transposase SSO1474 [143424]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [143425] (4)
        SQ Q97Y68 2-131
    2. ISHP608 transposase [143426]
      1. Helicobacter pylori [TaxId: 210] [143427] (14)
        SQ Q933Z0 4-133
    3. Putative transposase DR0177 [143428]
      1. Deinococcus radiodurans [TaxId: 1299] [143429] (2)
        SQ Q9RXX8 1-130
55. TTP0101/SSO1404-like [143430] (1)
  contains extra C-terminal beta-strand that integrates into the beta-sheet of the other subunit in the homodimer, a probable biological unit of this superfamily
  uperfamily
  1. TTP0101/SSO1404-like [143431] (3)
    Pfam 02647; DUF196; this family includes recent structure of SSO1404 (PDB entry 2IVY)
    1. Hypothetical protein TTP0101 (TT1823) [143432]
      1. Thermus thermophilus [TaxId: 274] [143433] (1)
        SQ Q746F4 2-83
    2. Hypothetical protein PF1117 [160346]
      1. Pyrococcus furiosus [TaxId: 2261] [160347] (1)
        SQ Q8U1T8 1-84
    3. Hypothetical protein SSO1404 [160348]
      predicted DNA repair associated protein
      1. Sulfolobus solfataricus [TaxId: 2287] [160349] (2)
        SQ Q97YC2 2-89
56. Rnp2-like [160350] (1)
  contains extra C-terminal helix
  1. Rpp14/Pop5-like [160351] (2)
    Pfam 01900
    1. RNase P protein component 2, Rnp2 [160352]
      1. Pyrococcus horikoshii [TaxId: 53953] [160353] (2)
        SQ O59150 3-120
      2. Pyrococcus furiosus [TaxId: 2261] [160354] (5)
        SQ Q8U151 15-120
57. Bacterial polysaccharide co-polymerase-like [160355] (1)
  Decorated common fold with extra helical regions, which facilitate oligomerization
  1. FepE-like [160356] (3)
    the ferredoxin-like fold resides mainly on in the N-terminal part that corresponds to Pfam 02706 (Wzz)
    1. Chain length determinant protein WzzB [160357]
      1. Salmonella typhimurium [TaxId: 90371] [160358] (5)
        SQ Q04866 54-292
    2. Lipopolysaccharide biosynthesis protein WzzE [160359]
      1. Escherichia coli [TaxId: 562] [160360] (8)
        SQ P0AG01 54-318
    3. Enterochelin transport protein FepE [160361]
      1. Escherichia coli [TaxId: 562] [160362] (12)
        SQ Q8XBV8 64-330! SQ Q8XBV8 65-330
58. MTH889-like [160363] (1)
  assembles into hexameric ring-like structures with the formation of a singe beta-barrel sheet of 24 strands
  1. MTH889-like [160364] (2)
    Pfam 02680; DUF211, COG1888
    1. Uncharacterized protein MTH889 [160365]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [160366] (7)
        SQ O26975 3-95
    2. Uncharacterized protein AF1549 [160367]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160368] (14)
        SQ O28723 1-91
59. Ribosomal protein L10-like [160369] (1)
  consists of globular N-terminal domain, structurally similar to NDK, and the L7/L12-binding C-terminal alpha-helical tail
  1. Ribosomal protein L10-like [160370] (1)
    Pfam 00466; covers globular domain only
    1. Ribosomal protein L10 [160371]
      see also scop_pr 64661 for a partial structure in the ribosome
      1. Thermotoga maritima [TaxId: 2336] [160372] (3)
        SQ P29394 1-177
PurS-like [109622] (1)
consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
1. PurS-like [82697] (2)
  segment-swapped dimer: the swapped segment is made of the first helix and second strand; a single long strand is formed by strands 2 and 3 of each subunit
  uperfamily
  1. PurS subunit of FGAM synthetase [82698] (3)
    1. PurS subunit of FGAM synthetase [82699]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [82700] (1)
        MTH169
      2. Bacillus subtilis [TaxId: 1423] [111001] (2)
        SQ P12049 # YexA
      3. Thermotoga maritima [TaxId: 2336] [117995] (1)
        SQ Q9X0X1
  2. FGAM synthase PurL, PurS-like domain [111002] (1)
    duplication: consists of 2 structural repeats of the PurS subunit fold, assembled like the PurS dimer
    1. FGAM synthase PurL, PurS-like domain [111003]
      1. Salmonella typhimurium [TaxId: 90371] [111004] (1)
        SQ P74881
RplX-like [160373] (1)
beta(2)-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 213; some structural similarity to the PurS subunit/repeat (scop_cf 109622)
1. RplX-like [160374] (1)
  similar structural motif to the Ribosomal S24e family (scop_fa 117786); possible structural permutation
  1. RplX-like [160375] (1)
    Pfam 01911
    1. Ribosomal protein LX, RplX [160376]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [160377] (1)
        SQ O27647 1-78
Dystroglycan, domain 2 [111005] (1)
beta-alpha-beta-X-beta(2)-alpha(2)-beta; antiparallel beta-sheet, order 24153; topological similarity to the ferredoxin-like fold (scop_cf 54861)
1. Dystroglycan, domain 2 [111006] (1)
  uperfamily
  1. Dystroglycan, domain 2 [111007] (1)
    1. Dystroglycan, domain 2 [111008]
      1. Mouse (Mus musculus) [TaxId: 10090] [111009] (1)
        SQ Q62165 58-303
Pseudouridine synthase [100877] (1)
consists of two alpha+beta subdomains with some similarity to the ferredoxin-like fold
1. Pseudouridine synthase [55120] (4)
  the active site is the most conserved structural region of the superfamily and is located between the subdomains
  uperfamily
  1. Pseudouridine synthase I TruA [55121] (1)
    1. Pseudouridine synthase I TruA [55122]
      1. Escherichia coli [TaxId: 562] [55123] (10)
  2. Pseudouridine synthase II TruB [69746] (5)
    contains C-terminal PUA domain
    1. Pseudouridine synthase II TruB [69747]
      1. Escherichia coli [TaxId: 562] [69748] (3)
      2. Thermotoga maritima [TaxId: 2336] [103016] (8)
      3. Mycobacterium tuberculosis [TaxId: 1773] [103017] (1)
      4. Archaeon Pyrococcus furiosus [TaxId: 2261] [143434] (4)
        SQ Q7LWY0 5-249
      5. Archaeon Methanococcus jannaschii [TaxId: 2190] [143435] (1)
        SQ Q57612 17-246
  3. Pseudouridine synthase RsuA/RluD [75459] (4)
    contains N-terminal alpha-L RNA-binding motif
    1. Ribosomal small subunit pseudouridine 516 synthase RsuA [75460]
      1. Escherichia coli [TaxId: 562] [75461] (3)
      2. Haemophilus influenzae [TaxId: 727] [103018] (1)
    2. Ribosomal large subunit pseudouridine synthase D, RluD [103019]
      1. Escherichia coli [TaxId: 562] [103020] (3)
        SQ P33643
    3. Ribosomal large subunit pseudouridine synthase C, RluC [111010]
      1. Escherichia coli [TaxId: 562] [111011] (1)
        SQ P23851
  4. tRNA pseudouridine synthase TruD [103021] (1)
    natural circular permutation in the catalytic domain; insertion of the family-specific alpha+beta subdomain
    1. tRNA pseudouridine synthase TruD [103022]
      1. Escherichia coli [TaxId: 562] [103023] (3)
        SQ Q57261
        family-specific insert subdomain: res. 158-301
SP0830-like [160378] (1)
duplication: two beta-alpha-beta(2)-alpha-beta-alpha motifs are organized in ferredoxin-like subdomains swapped with the extra C-terminal helices
1. SP0830-like [160379] (1)
  1. SP0830-like [160380] (1)
    Pfam 08002; DUF1697
    1. Hypothetical protein SP0830 [160381]
      1. Streptococcus pneumoniae [TaxId: 1313] [160382] (4)
        SQ Q97RI5 1-180
Folate-binding domain [103024] (1)
duplication: consists of two beta(2)-alpha-beta(3)-alpha subdomains swapped with the first strands
1. Folate-binding domain [103025] (2)
  some topological similarity to Formylmethanofuran:tetrahydromethanopterin formyltransferase
  uperfamily
  1. Aminomethyltransferase folate-binding domain [103026] (5)
    1. N,N-dimethylglycine oxidase domain 3 [103027]
      1. Arthrobacter globiformis [TaxId: 1665] [103028] (3)
    2. Hypothetical protein YgfZ, N-terminal domain [103029]
      1. Escherichia coli [TaxId: 562] [103030] (2)
        SQ P39179
    3. Glycine cleavage system T protein, GcvT [111012]
      1. Thermotoga maritima [TaxId: 2336] [111013] (4)
        SQ Q9WY54
      2. Escherichia coli [TaxId: 562] [111014] (1)
        SQ P27248
      3. Pyrococcus horikoshii [TaxId: 53953] [117996] (1)
        SQ O58888
  2. TrmE formyl-THF-binding domain [117997] (1)
    dimeric biological unit; one subunit domain corresponds to one "unswapped" subdomain of the other family
    1. TrmE formyl-THF-binding domain [117998]
      1. Thermotoga maritima [TaxId: 2336] [117999] (2)
        SQ Q9WYA4
THUMP domain [143436] (1)
contains mixed 8-stranded beta-sheet, folded into a half-barrel and covered with 4 helices on the outside; order 32148756; strands 5, 6 and 7 are parallel
1. THUMP domain-like [143437] (3)
  predicted RNA-binding function
  uperfamily
  1. THUMP domain [143438] (2)
    Pfam 02926
    1. Thiamine biosynthesis protein ThiI, N-terminal domain [143439]
      1. Bacillus anthracis [TaxId: 1392] [143440] (1)
        SQ Q81KU0 3-173
    2. Hypothetical protein PH1313, N-terminal domain [143441]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143442] (2)
        SQ O59053 1-175
  2. PAE0736-like [143443] (1)
    orphan protein; rudiment, disulfide-stabilized form of THUMP domain fold
    1. Hypothetical protein PAE0736 [143444]
      1. Pyrobaculum aerophilum [TaxId: 13773] [143445] (2)
        SQ Q8ZYK2 1-98
  3. Minimal THUMP [160383] (1)
    subfamily of Pfam 02926; 4 stranded mixed beta-sheet with 2 helices on one side and a crossover loop on the other side
    1. THUMP domain-containing protein 1 [160384]
      1. Human (Homo sapiens) [TaxId: 9606] [160385] (1)
        SQ Q9NXG2 170-254
AMMECR1-like [143446] (1)
duplication; contains two beta(2)-alpha-beta(2) structural repeats, swapped with C-terminal strands; extra N-terminal helix and C-terminal strand
1. AMMECR1-like [143447] (1)
  uperfamily
  1. AMMECR1-like [143448] (3)
    Pfam 01871
    1. Hypothetical protein MM0484 [143449]
      1. Methanosarcina mazei [TaxId: 2209] [143450] (4)
        SQ Q8PZK8 1-199
    2. Hypothetical protein PH0010 [143451]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143452] (1)
        SQ O57770 3-205
    3. Hypothetical protein ST0229 [143453]
      1. Sulfolobus tokodaii [TaxId: 111955] [143454] (1)
        SQ Q976G0 3-227
NosL/MerB-like [160386] (1)
unusual fold; comprises two structural repeats of beta(2)-alpha-beta motifs, forming separate beta-sheets; probable duplication
1. NosL/MerB-like [160387] (2)
  1. NosL-like [160388] (1)
    Pfam 05573
    1. NosL [160389]
      1. Achromobacter cycloclastes [TaxId: 223] [160390] (2)
        SQ O68481 53-178
  2. MerB-like [160391] (1)
    Pfam 03243
    1. Alkylmercury lyase MerB [160392]
      1. Escherichia coli [TaxId: 562] [160393] (1)
        SQ P77072 81-212
YehU-like [118000] (1)
beta-alpha(2)-beta(2)-alpha; 3 layers, alpha/beta/alpha; antiparallel beta-sheet: order 123
1. YehU-like [118001] (1)
  uperfamily
  1. YehU-like [118002] (1)
    Pfam 06794; UPF0270
    1. Hypothetical UPF0270 protein PA3463 [118003]
      1. Pseudomonas aeruginosa [TaxId: 287] [118004] (1)
        SQ Q9HYE3
Hypothetical protein YwqG [103031] (1)
duplication: contains two similar beta-x-beta(4) motifs swapped with the first strands
1. Hypothetical protein YwqG [103032] (1)
  uperfamily
  1. Hypothetical protein YwqG [103033] (1)
    1. Hypothetical protein YwqG [103034]
      1. Bacillus subtilis [TaxId: 1423] [103035] (1)
VC0467-like [143455] (1)
complex fold; contains bifurcated beta-sheet structure folded into pseudo barrel
1. VC0467-like [143456] (1)
  uperfamily
  1. VC0467-like [143457] (5)
    Pfam 02622; DUF179
    1. Hypothetical protein DIP2367 [143458]
      1. Corynebacterium diphtheriae [TaxId: 1717] [143459] (2)
        SQ Q6NEA9 1-191! SQ Q6NEA9 1-193
    2. Hypothetical protein HD1794 [143460]
      1. Haemophilus ducreyi [TaxId: 730] [143461] (1)
        SQ Q7VKS7 1-186
    3. Hypothetical protein VC0467 [143462]
      1. Vibrio cholerae [TaxId: 666] [143463] (2)
        SQ Q9KUP8 1-177! SQ Q9KUP8 1-179
    4. Hypothetical protein ACIAD0353 [143464]
      1. Acinetobacter sp. ADP1 [TaxId: 62977] [143465] (1)
        SQ Q6FF54 5-179
    5. Hypotheical protein SO3346 [143466]
      1. Shewanella oneidensis [TaxId: 70863] [143467] (1)
        SQ Q8EBZ9 1-187
Lesion bypass DNA polymerase (Y-family), little finger domain [100878] (1)
beta-alpha-beta(2)-alpha-beta; antiparallel beta-sheet: order 1423; "reversed" ferredoxin-like topology
1. Lesion bypass DNA polymerase (Y-family), little finger domain [100879] (1)
  uperfamily
  1. Lesion bypass DNA polymerase (Y-family), little finger domain [100880] (7)
    1. DinB homolog (DBH) [100881]
      1. Archaeon Sulfolobus solfataricus, DNA polymerase IV [TaxId: 2287] [100882] (62)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [100883] (2)
      3. Sulfolobus acidocaldarius Brock et al. 1972 (Sulfolobus acidocaldarius) [TaxId: 2285] [160394] (3)
    2. DNA polymerase eta [100884]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [100885] (5)
    3. DNA polymerase IV [103036]
      1. Escherichia coli [TaxId: 562] [103037] (1)
    4. DNA polymerase iota [111015]
      1. Human (Homo sapiens) [TaxId: 9606] [111016] (8)
        SQ Q9UNA4
    5. DNA polymerase kappa [111017]
      1. Human (Homo sapiens) [TaxId: 9606] [111018] (1)
        SQ Q9UBT6 71-517
ImmE5-like [143468] (1)
alpha-beta(2)-alpha-beta; 2 layers, a/b; antiparallel beta-sheet, order 213
1. ImmE5-like [143469] (1)
  uperfamily
  1. ImmE5-like [143470] (1)
    1. Colicin E5 immunity protein ImmE5 [143471]
      1. Escherichia coli [TaxId: 562] [143472] (2)
        SQ P13476 1-83
Ribosomal protein L30p/L7e [55128] (1)
core: beta-alpha-beta-alpha-beta; antiparallel beta-sheet: order 312; some similarity to the ferredoxin-like fold
1. Ribosomal protein L30p/L7e [55129] (1)
  uperfamily
  1. Ribosomal protein L30p/L7e [55130] (4)
    1. Prokaryotic ribosomal protein L30 [55131]
      short-chain member of the family
      1. Thermus thermophilus [TaxId: 274] [55132] (11)
      2. Escherichia coli [TaxId: 562] [160395] (29)
        SQ P02430 1-58
      3. Deinococcus radiodurans [TaxId: 1299] [160396] (6)
        SQ Q9RSL0 1-55
    2. Archaeal L30 (L30a) [55133]
      long-chain member of the family; contains additional C-terminal (sub)domain
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [55134] (40)
        SQ P14121
Chorismate lyase-like [64287] (1)
duplication of alpha(2)-beta(3) motif; antiparallel beta sheet, order 123654
1. Chorismate lyase-like [64288] (3)
  uperfamily
  1. Chorismate lyase [64289] (1)
    1. Chorismate lyase [64290]
      1. Escherichia coli [TaxId: 562] [64291] (10)
        SQ P26602
  2. UTRA domain [143473] (10)
    Pfam 07702
    1. Probable transcriptional regulator PhnF, receptor domain [143474]
      1. Escherichia coli [TaxId: 562] [143475] (2)
        SQ P16684 84-241
    2. Transcriptional regulator EF1328 [160397]
      1. Enterococcus faecalis [TaxId: 1351] [160398] (4)
        SQ Q835P8 93-235
    3. Histidine utilization repressor HutC [160399]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [160400] (8)
        SQ Q87UX0 109-249
    4. Trehalose operon transcriptional repressor TreR [160401]
      formerly YfxA
      1. Bacillus subtilis [TaxId: 1423] [160402] (1)
        SQ P39796 95-238
    5. Putative transcriptional regulator BB3683 [160403]
      1. Bordetella bronchiseptica [TaxId: 518] [160404] (4)
        SQ Q7WD95 98-259
    6. Hypothetical protein SA0254 [160405]
      1. Staphylococcus aureus [TaxId: 1280] [160406] (2)
        SQ Q7A7U1 73-233
    7. Hypothetical transcriptional regulator YurK [160407]
      1. Bacillus subtilis [TaxId: 1423] [160408] (2)
        SQ O32152 86-238
    8. Putative transcriptional regulator SCO6256 [160409]
      1. Streptomyces coelicolor [TaxId: 1902] [160410] (1)
        SQ Q9RKT6 66-245
    9. Transcriptional regulator Cgl0157/Cg0196 [160411]
      1. Corynebacterium glutamicum [TaxId: 1718] [160412] (3)
        SQ Q8NTZ4 106-253
    10. Transcriptional regulator YydK [160413]
      1. Bacillus subtilis [TaxId: 1423] [160414] (3)
        SQ Q45591 89-233
  3. AF1396-like [160415] (1)
    Pfam 01947; DUF98
    1. Hypothetical protein AF1396 [160416]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160417] (6)
        SQ O28875 1-160
YdfO-like [160418] (1)
duplication: two alpha(2)-beta(3) motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456
1. YdfO-like [160419] (1)
  1. YdfO-like [160420] (1)
    Pfam 07166; DUF1398
    1. Hypothetical protein YdfO [160421]
      1. Escherichia coli [TaxId: 562] [160422] (1)
        SQ P76156 2-128
TM1622-like [143476] (1)
alpha-beta(3)-alpha-beta(4)-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order: 1237654
1. TM1622-like [143477] (1)
  uperfamily
  1. TM1622-like [143478] (1)
    1. Hypothetical protein TM1622 [143479]
      annotated in PDB as GTP binding regulator
      1. Thermotoga maritima [TaxId: 2336] [143480] (1)
        SQ Q9X1V7 25-154
BH3703-like [160423] (1)
alpha-beta(3)-alpha-beta(2)-alpha(2); antiparallel beta-sheet, order:32145; duplication: two alpha-beta(2) structural repeats are arranged with pseudo twofold symmetry
1. BH3703-like [160424] (1)
  1. BH3703-like [160425] (1)
    Pfam 04634; DUF600
    1. Uncharacterized protein BH3703 [160426]
      1. Bacillus halodurans [TaxId: 86665] [160427] (2)
        SQ Q9K6M5 1-166
Probable bacterial effector-binding domain [55135] (1)
duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12)
1. Probable bacterial effector-binding domain [55136] (4)
  uperfamily
  1. Gyrase inhibitory protein GyrI (SbmC, YeeB) [75462] (1)
    1. Gyrase inhibitory protein GyrI (SbmC, YeeB) [75463]
      1. Escherichia coli [TaxId: 562] [75464] (1)
  2. Multidrug-binding domain of transcription activator BmrR [55137] (1)
    1. Multidrug-binding domain of transcription activator BmrR [55138]
      1. Bacillus subtilis [TaxId: 1423] [55139] (9)
        SQ P39075
  3. Rob transcription factor, C-terminal domain [55140] (1)
    1. Rob transcription factor, C-terminal domain [55141]
      1. Escherichia coli [TaxId: 562] [55142] (1)
  4. SOUL heme-binding protein [143481] (1)
    Pfam 04832
    1. Heme-binding protein 1 [143482]
      p22HBP
      1. Mouse (Mus musculus) [TaxId: 10090] [143483] (2)
        SQ Q9R257 1-190! SQ Q9R257 7-190
CheC-like [103038] (1)
duplication: tandem repeat of two intertwined alpha-beta-(X)-beta(2) motifs
1. CheC-like [103039] (1)
  uperfamily
  1. CheC-like [103040] (2)
    Pfam 04509
    1. Chemotaxis protein CheX [103041]
      1. Thermotoga maritima [TaxId: 2336] [103042] (2)
        SQ Q9X1V3
        TM1618
    2. Chemotaxis protein CheC [118005]
      1. Thermotoga maritima [TaxId: 2336] [118006] (3)
        SQ Q9X006 # TM0904
LigT-like [55143] (1)
duplication of beta-alpha-beta-alpha-beta motif: antiparallel beta sheet forms barrel (n=6, S=8) similar to the barrel of prokaryotic DNA topoisomerases I and III
1. LigT-like [55144] (4)
  uperfamily
  1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [55145] (1)
    1. tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [55146]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [55147] (3)
  2. 2'-5' RNA ligase LigT [89967] (1)
    1. 2'-5' RNA ligase LigT [89968]
      1. Thermus thermophilus [TaxId: 274] [89969] (1)
        TT0787
  3. 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [103043] (1)
    1. 2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [103044]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [103045] (1)
  4. Atu0111-like [143484] (1)
    1. Putative phosphoesterase Atu0111 [143485]
      1. Agrobacterium tumefaciens [TaxId: 358] [143486] (1)
        SQ Q8UJ27 6-237
Pepsin inhibitor-3 [55148] (1)
duplication of beta(3)-alpha(2) motif: meander beta sheets form barrel-like structure
1. Pepsin inhibitor-3 [55149] (1)
  uperfamily
  1. Pepsin inhibitor-3 [55150] (1)
    1. Pepsin inhibitor-3 [55151]
      1. Pig roundworm (Ascaris suum) [TaxId: 6253] [55152] (2)
CYTH-like phosphatases [55153] (1)
duplication of beta-alpha-beta(3) motif: antiparallel beta sheet forms wide barrel (n=8, S=16) with a channel running through it
1. CYTH-like phosphatases [55154] (2)
  uperfamily
  1. mRNA triphosphatase CET1 [55155] (1)
    Pfam 02940
    1. mRNA triphosphatase CET1 [55156]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55157] (2)
  2. CYTH domain [118007] (4)
    Pfam 01928
    1. Hypothetical protein PF0863 [118008]
      1. Pyrococcus furiosus [TaxId: 2261] [118009] (1)
        SQ Q8U2H2 2-171
    2. Putative adenylate cyclase VP1760 [143487]
      1. Vibrio parahaemolyticus [TaxId: 670] [143488] (2)
        SQ Q87NV8 8-181
    3. Hypothetical protein NE1496 [143489]
      shape-shifter; open beta-sheet instead of beta-barrel
      1. Nitrosomonas europaea [TaxId: 915] [143490] (2)
        SQ Q82UI9 2-151
    4. Thiamine-triphosphatase (ThTPase) [160428]
      1. Mouse (Mus musculus) [TaxId: 10090] [160429] (1)
        SQ Q8JZL3 2-224
Antiparallel beta/alpha barrel (PT-barrel) [143491] (1)
tandem repeat of five alpha(2)-beta(2) motifs; antiparallel beta-sheet barrel, closed; n=10, S=10; order 123456789A; there is a channel along the barrel axis
1. Prenyltransferase-like [143492] (1)
  the barrel channel harbours the substrate-binding site
  uperfamily
  1. Prenyltransferase-like [143493] (1)
    1. Aromatic prenyltransferase [143494]
      1. Streptomyces sp. CL190 [TaxId: 93372] [143495] (4)
        SQ Q4R2T2 3-303
eIF1-like [55158] (2)
beta(2)-alpha-beta(2)-alpha-beta; 2 layers: alpha/beta; mixed beta-sheet: order 51243
1. eIF1-like [55159] (1)
  uperfamily
  1. eIF1-like [55160] (2)
    1. Eukaryotic translation initiation factor eIF-1 (SUI1) [55161]
      1. Human (Homo sapiens) [TaxId: 9606] [55162] (1)
    2. YciH [55163]
      1. Escherichia coli [TaxId: 562] [55164] (1)
2. TM1457-like [118010] (1)
  forms a homodimer via alpha-helical interface
  uperfamily
  1. TM1457-like [118011] (4)
    Pfam 04327; DUF464
    1. Hypothetical protein TM1457 [118012]
      1. Thermotoga maritima [TaxId: 2336] [118013] (1)
        SQ Q9X1G8
    2. Hypothetical protein SAV1646 [160430]
      1. Staphylococcus aureus [TaxId: 1280] [160431] (2)
        SQ Q931Q2 1-106
    3. Hypothetical protein SP1106 [160432]
      1. Streptococcus pneumoniae [TaxId: 1313] [160433] (2)
        SQ Q97QU3 1-112
    4. Hypothetical protein Smu.848 [160434]
      1. Streptococcus mutans [TaxId: 1309] [160435] (6)
        SQ Q8DUQ5 1-111
Hedgehog/DD-peptidase [55165] (1)
alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
1. Hedgehog/DD-peptidase [55166] (5)
  zinc-binding motif
  uperfamily
  1. Muramoyl-pentapeptide carboxypeptidase [55167] (1)
    1. Zn2+ DD-carboxypeptidase C-terminal catalytic domain [55168]
      1. Streptomyces albus G [TaxId: 1962] [55169] (1)
  2. MepA-like [111019] (1)
    1. D-alanyl-D-alanine-endopeptidase MepA [111020]
      1. Escherichia coli [TaxId: 562] [111021] (2)
        SQ P14007
  3. VanX-like [111022] (1)
    Pfam 01427
    1. D-Ala-D-Ala dipeptidase VanX [111023]
      1. Enterococcus faecium [TaxId: 1352] [111024] (1)
        SQ Q06241
  4. Hedgehog (development protein), N-terminal signaling domain [55170] (2)
    1. Sonic hedgehog [55171]
      1. Mouse (Mus musculus) [TaxId: 10090] [55172] (3)
    2. Hedgehog [143496]
      lacks the conserved metal ion-binding site
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143497] (4)
        SQ Q02936 50-198
  5. VanY-like [160436] (1)
    Pfam 02557
    1. L-alanyl-D-glutamate peptidase Ply [160437]
      1. Listeria phage A500 [TaxId: 40522] [160438] (3)
        SQ Q37979 1-148
Alpha-L RNA-binding motif [55173] (1)
alpha(2)-beta(2)-loop-beta; 2 layers: alpha/beta
1. Alpha-L RNA-binding motif [55174] (5)
  common motif in otherwise different folds
  uperfamily
  1. Ribosomal protein S4 [55178] (3)
    has a RRF/tRNA synthetase additional domain-like fold
    1. Ribosomal protein S4 [55179]
      also contains a Zn-binding N-terminal subdomain
      1. Thermus thermophilus [TaxId: 274] [55180] (45)
      2. Bacillus stearothermophilus [TaxId: 1422] [55181] (2)
      3. Escherichia coli [TaxId: 562] [160439] (26)
        SQ P0A7V8 1-205
  2. Heat shock protein 15 kD [55182] (1)
    there are additional C-terminal structures
    1. Heat shock protein 15 kD [55183]
      ribosome-binding protein
      1. Escherichia coli [TaxId: 562] [55184] (2)
  3. Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [75465] (2)
    there are additional N-terminal structures
    1. Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain [75466]
      1. Thermus thermophilus [TaxId: 274] [82701] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [75467] (1)
  4. YbcJ-like [103046] (1)
    overall topological similarity to the TyrRS C-domain
    1. Hypothetical protein YbcJ [103047]
      1. Escherichia coli [TaxId: 562] [103048] (1)
  5. Pseudouridine synthase RsuA N-terminal domain [75468] (2)
    1. Pseudouridine synthase RsuA N-terminal domain [75469]
      1. Escherichia coli [TaxId: 562] [75470] (3)
      2. Haemophilus influenzae [TaxId: 727] [103049] (1)
RRF/tRNA synthetase additional domain-like [55185] (4)
core: alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
1. ThrRS/AlaRS common domain [55186] (2)
  putative editing domain found in the N-terminal part of ThrRS, the C-terminal of AlaRS, and as a stand-alone protein; probable circular permutation of LuxS (d.185.1.2)
  uperfamily
  1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain [55187] (2)
    1. Threonyl-tRNA synthetase (ThrRS), second 'additional' domain [55188]
      1. Escherichia coli [TaxId: 562] [55189] (5)
        SQ P0A8M3
      2. Staphylococcus aureus [TaxId: 1280] [103050] (2)
  2. AlaX-like [103051] (2)
    1. Hypothetical protein PH0574 [103052]
      stand-alone protein related to the AlaRS domain
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103053] (7)
        SQ P27248
    2. AlaX-M trans-editing enzyme, C-terminal domain [160440]
      1. Pyrococcus horikoshii [TaxId: 53953] [160441] (1)
        SQ O57848 88-216
2. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55190] (1)
  uperfamily
  1. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55191] (2)
    1. Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain [55192]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55193] (3)
      2. Thermus thermophilus [TaxId: 274] [69749] (1)
3. Ribosome recycling factor, RRF [55194] (1)
  uperfamily
  1. Ribosome recycling factor, RRF [55195] (7)
    1. Ribosome recycling factor, RRF [55196]
      1. Thermotoga maritima [TaxId: 2336] [55197] (1)
      2. Thermus thermophilus [TaxId: 274] [55198] (9)
      3. Escherichia coli [TaxId: 562] [64292] (5)
      4. Aquifex aeolicus [TaxId: 63363] [64293] (1)
      5. Vibrio parahaemolyticus [TaxId: 670] [89970] (1)
      6. Mouse (Mus musculus), mitochondrial [TaxId: 10090] [118014] (1)
        SQ Q9D6S7 116-186
      7. Mycobacterium tuberculosis [TaxId: 1773] [160442] (3)
        SQ Q10794 2-184
4. General secretion pathway protein M, EpsM [103054] (1)
  uperfamily
  1. General secretion pathway protein M, EpsM [103055] (1)
    1. General secretion pathway protein M, EpsM [103056]
      1. Vibrio cholerae [TaxId: 666] [103057] (1)
LuxS/MPP-like metallohydrolase [63410] (1)
core: beta-alpha-beta(2)-alpha(2); 2 layers: alpha/beta
1. LuxS/MPP-like metallohydrolase [63411] (2)
  Share the same "active site motif" HxxEH located in the first core helix, but differ in one of the zinc-binding residues
  uperfamily
  1. Autoinducer-2 production protein LuxS [64294] (4)
    contains additional N-terminal strand; possible relationships to the putative editing domain of ThrRS (d.67.1)
    1. Autoinducer-2 production protein LuxS [64295]
      S-ribosylhomocysteinase
      1. Bacillus subtilis [TaxId: 1423] [64296] (6)
      2. Deinococcus radiodurans [TaxId: 1299] [64297] (5)
      3. Haemophilus influenzae [TaxId: 727] [64298] (2)
      4. Helicobacter pylori [TaxId: 210] [64299] (1)
  2. MPP-like [63412] (10)
    Common fold elaborated with many additional structures; duplication: each family member consists of two similar domains of beta(2)-alpha(2)-beta(2)-alpha(5)-beta structure, but only the N-terminal domain of MPP beta chain binds the catalytic metal
    1. Mitochondrial processing peptidase (MPP) beta chain [64300]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64301] (4)
    2. Mitochondrial processing peptidase (MPP) alpha chain [64302]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64303] (4)
    3. Cytochrome bc1 core subunit 1 [63408]
      1. Cow (Bos taurus) [TaxId: 9913] [55997] (26)
        SQ P31800
      2. Chicken (Gallus gallus) [TaxId: 9031] [55998] (3)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64304] (14)
    4. Cytochrome bc1 core subunit 2 [63409]
      1. Cow (Bos taurus) [TaxId: 9913] [56000] (12)
        SQ P23004
      2. Chicken (Gallus gallus) [TaxId: 9031] [56001] (17)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64305] (14)
    5. Presequence protease 1, PREP1 [143498]
      duplication: comprises four domains of this fold; similar to the MPP alpha-beta heterodimer
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [143499] (8)
        SQ Q9LJL3 100-356! SQ Q9LJL3 357-624! SQ Q9LJL3 625-882! SQ Q9LJL3 883-1078
    6. Protease III [143500]
      duplication: comprises four domains of this fold
      1. Escherichia coli [TaxId: 562] [143501] (4)
        SQ P05458 24-263! SQ P05458 264-503! SQ P05458 504-732! SQ P05458 733-960
IF3-like [55199] (8)
beta-alpha-beta-alpha-beta(2); 2 layers; mixed sheet 1243, strand 4 is antiparallel to the rest
1. Translation initiation factor IF3, C-terminal domain [55200] (1)
  uperfamily
  1. Translation initiation factor IF3, C-terminal domain [55201] (3)
    1. Translation initiation factor IF3, C-terminal domain [55202]
      1. Bacillus stearothermophilus [TaxId: 1422] [55203] (1)
      2. Escherichia coli [TaxId: 562] [55204] (1)
      3. Thermus thermophilus [TaxId: 274] [64306] (1)
2. YhbY-like [75471] (1)
  uperfamily
  1. YhbY-like [75472] (3)
    Pfam 01985
    1. hypothetical protein YhbY [75473]
      1. Escherichia coli [TaxId: 562] [75474] (1)
    2. YhbY homologue HI1333 [82702]
      1. Haemophilus influenzae [TaxId: 727] [82703] (1)
    3. Hypothetical protein SAV1595 [111025]
      1. Staphylococcus aureus, (strain Mu50 / ATCC 700699) [TaxId: 1280] [111026] (1)
        SQ Q99TQ4
3. SirA-like [64307] (1)
  uperfamily
  1. SirA-like [88852] (4)
    predicted redox protein, regulator of disulfide bond formation
    1. SirA [64309]
      implicated in cell division
      1. Escherichia coli [TaxId: 562] [64310] (1)
        formerly hypothetical protein YhhP
    2. Hypothetical protein Ta1170/Ta1414 [89971]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89972] (1)
    3. hypothetical protein YedF (EC005) [75475]
      1. Escherichia coli [TaxId: 562] [75476] (1)
    4. Hypothetical protein TM0983 [69751]
      1. Thermotoga maritima [TaxId: 2336] [69752] (1)
4. AlbA-like [82704] (2)
  uperfamily
  1. DNA-binding protein AlbA [82705] (4)
    1. DNA-binding protein AlbA [82706]
      an archaeal chromatin protein modulated by acetylation, a Sir2 substrate
      1. Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287] [82707] (4)
        gene SSO0962 (AlbA1)
      2. Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287] [103058] (5)
        gene SSO6877 (AlbA2)
      3. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103059] (2)
        gene AF1956
      4. Archaeon Methanococcus jannaschii [TaxId: 2190] [103060] (1)
  2. Hypothetical protein At2g34160 [111027] (1)
    1. Hypothetical protein At2g34160 [111028]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111029] (3)
        SQ O22969 19-117
5. C-terminal domain of ProRS [64586] (1)
  contains a metal (zinc)-binding site
  uperfamily
  1. C-terminal domain of ProRS [64587] (3)
    1. C-terminal domain of ProRS [64588]
      1. Thermus thermophilus [TaxId: 274] [64589] (4)
      2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [89973] (4)
      3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [89974] (1)
6. R3H domain [82708] (1)
  possibly lacks the N-terminal strand of the common fold
  uperfamily
  1. R3H domain [82709] (3)
    Pfam 01424; predicted nucleic acid-binding domain
    1. SmuBP-2 [82710]
      1. Human (Homo sapiens) [TaxId: 9606] [82711] (1)
    2. Poly(A)-specific ribonuclease PARN [111030]
      1. Mouse (Mus musculus) [TaxId: 10090] [111031] (1)
        SQ Q8VDG3 162-248; structure of an RNA-binding domain (430-516) is also known: 1WHV
    3. R3H domain protein KIAA1002 [118015]
      1. Human (Homo sapiens) [TaxId: 9606] [118016] (1)
        SQ Q9Y2K5 133-343
7. EPT/RTPC-like [55205] (2)
  uperfamily
  1. RNA 3'-terminal phosphate cyclase, RPTC [55206] (1)
    duplication: 3 repeats of this fold are packed together around the pseudo threefold axis
    1. RNA 3'-terminal phosphate cyclase, RPTC [55207]
      also contains an insert alpha+beta domain of the thioredoxin-like topology
      1. Escherichia coli [TaxId: 562] [55208] (2)
  2. Enolpyruvate transferase, EPT [55209] (4)
    duplication: 6 repeats of this fold are organized in two RPTC-like domains
    1. UDP-N-acetylglucosamine enolpyruvyl transferase (EPT, MurA, MurZ) [55210]
      1. Escherichia coli [TaxId: 562] [55211] (2)
      2. Enterobacter cloacae [TaxId: 550] [55212] (11)
        SQ P33038
    2. 5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase [55213]
      1. Escherichia coli [TaxId: 562] [55214] (12)
        SQ P07638
      2. Streptococcus pneumoniae [TaxId: 1313] [103061] (3)
8. SMR domain-like [160443] (1)
  1. Smr domain [160444] (1)
    Pfam 01713
    1. Nedd4-binding protein 2 [160445]
      1. Human (Homo sapiens) [TaxId: 9606] [160446] (1)
        SQ Q86UW6 1688-1770
PUG domain-like [143502] (1)
alpha(2)-beta-alpha(2)-beta(2)-alpha; cluster of helices with a small antiparallel beta-sheet on one side; order 132; topological similarity to the fold of an extended R3H domain (PDB 1whr)
1. PUG domain-like [143503] (1)
  uperfamily
  1. PUG domain [143504] (2)
    SMART 00580; domain in protein kinases, N-glycanases and other nuclear proteins
    1. N-glycanase 1, N-terminal domain [143505]
      1. Mouse (Mus musculus) [TaxId: 10090] [143506] (1)
        SQ Q9JI78 1-119
      2. Human (Homo sapiens) [TaxId: 9606] [143507] (2)
        SQ Q96IV0 11-109
PG1857-like [160447] (1)
alpha-beta-alpha-beta(2)-alpha(3); 3 layers, a/b/a; antiparallel beta-sheet, order: 132
1. PG1857-like [160448] (1)
  1. PG1857-like [160449] (1)
    Pfam 09633; DUF2023
    1. Hypothetical protein PG1857 [160450]
      1. Porphyromonas gingivalis [TaxId: 837] [160451] (2)
        SQ Q7MTT4 4-114
PB2 C-terminal domain-like [160452] (1)
alpha-beta-alpha-X-alpha-beta(2); 3 layers, a/b/a; antiparallel beta-sheet, order 132; connection between helices 2 and 3 runs over the edge of the beta-sheet
1. PB2 C-terminal domain-like [160453] (1)
  1. PB2 C-terminal domain-like [160454] (1)
    C-terminal part of Pfam 00604
    1. Polymerase basic protein 2, BP2 [160455]
      1. Influenza A virus [TaxId: 11320] [160456] (3)
        SQ P31345 685-759
Ribosome binding protein Y (YfiA homologue) [69753] (1)
beta-alpha-beta(3)-alpha; 2 layers; mixed sheet 1234, strand 3 is antiparallel to the rest
1. Ribosome binding protein Y (YfiA homologue) [69754] (1)
  uperfamily
  1. Ribosome binding protein Y (YfiA homologue) [69755] (3)
    1. Ribosome binding protein Y (YfiA homologue) [69756]
      Ribosome associated factor; cold-shock response protein
      1. Haemophilus influenzae [TaxId: 727] [69757] (1)
        HI0257
      2. Escherichia coli [TaxId: 562] [82712] (2)
      3. Thermus thermophilus [TaxId: 274] [160457] (4)
        SQ Q5SIS0 1-95
TolA/TonB C-terminal domain [74652] (1)
beta(2)-alpha-beta; 2 layers, alpha/beta; left-handed beta-alpha-beta unit in non-swapped monomer
1. TolA/TonB C-terminal domain [74653] (2)
  uperfamily
  1. TolA [55217] (2)
    contains extra N-terminal helix
    1. TolA [55218]
      1. Escherichia coli [TaxId: 562] [55219] (2)
      2. Pseudomonas aeruginosa [TaxId: 287] [75477] (1)
  2. TonB [64326] (1)
    isolated domain can form different segment-swapped dimers depending on the fragment length
    1. TonB [64327]
      1. Escherichia coli [TaxId: 562] [64328] (7)
        SQ P02929 150-239
Yeast killer toxins [55220] (1)
beta-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta; left-handed crossover connection
1. Yeast killer toxins [55221] (2)
  uperfamily
  1. Virally encoded KP4 toxin [55222] (1)
    1. Virally encoded KP4 toxin [55223]
      1. Ustilago maydis, P4 strain [TaxId: 5270] [55224] (1)
  2. SMK toxin [55225] (1)
    1. SMK toxin [55226]
      cleaved into alpha and beta chains
      1. Halotolerant yeast (Pichia farinosa) [TaxId: 4920] [55227] (2)
Cell division protein MinE topological specificity domain [55228] (1)
dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
1. Cell division protein MinE topological specificity domain [55229] (1)
  uperfamily
  1. Cell division protein MinE topological specificity domain [55230] (1)
    1. Cell division protein MinE topological specificity domain [55231]
      1. Escherichia coli [TaxId: 562] [55232] (1)
Hypothetical protein YoaG [103062] (1)
dimer of beta(2)-alpha motifs ; 2 layers, alpha/beta; reverse MinE topology
1. Hypothetical protein YoaG [103063] (1)
  uperfamily
  1. Hypothetical protein YoaG [103064] (1)
    1. Hypothetical protein YoaG [103065]
      1. Escherichia coli [TaxId: 562] [103066] (1)
BLRF2-like [160458] (1)
homodimer of alpha(2)-beta motif; also includes extra N-terminal helix of variable position
1. BLRF2-like [160459] (1)
  1. BLRF2-like [160460] (1)
    Pfam 05812; Herpesvirus BLRF2 protein
    1. Uncharacterized protein BQLF2 [160461]
      1. Murid herpesvirus 4 [TaxId: 33708] [160462] (6)
        SQ P88989 7-102
Nucleocapsid protein dimerization domain [103067] (1)
dimer of alpha-beta(2)-alpha motifs ; 2 layers, alpha/beta
1. Nucleocapsid protein dimerization domain [103068] (2)
  uperfamily
  1. Arterivirus nucleocapsid protein [103069] (2)
    1. Arterivirus nucleocapsid protein [103070]
      1. PRRSV (Porcine reproductive and respiratory syndrome virus) [TaxId: 28344] [103071] (1)
      2. Equine arteritis virus [TaxId: 11047] [160463] (4)
        SQ Q66526 50-105
  2. Coronavirus nucleocapsid protein [143508] (2)
    C-terminal part of Pfam 00937
    1. Coronavirus nucleocapsid protein [143509]
      1. Avian infectious bronchitis virus [TaxId: 11120] [143510] (12)
        SQ P32923 222-333! SQ P32923 226-332! SQ Q4ZJS4 218-326
        different strains
      2. SARS coronavirus [TaxId: 227859] [143511] (12)
        SQ P59595 270-366
Cyanase C-terminal domain [55233] (1)
intertwined dimer of alpha-beta(2) motifs ; 2 layers, alpha/beta
1. Cyanase C-terminal domain [55234] (1)
  uperfamily
  1. Cyanase C-terminal domain [55235] (1)
    active form is a decamer formed by five dimers
    1. Cyanase C-terminal domain [55236]
      1. Escherichia coli [TaxId: 562] [55237] (22)
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82713] (1)
Intertwined pseudo hexamer of an alpha+beta motif
1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82714] (1)
  duplication: the N- and C-terminal halves of the whole proteins are structurally similar
  uperfamily
  1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82715] (1)
    1. Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains [82716]
      1. Escherichia coli [TaxId: 562] [82717] (6)
RuBisCO, small subunit [55238] (1)
alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
1. RuBisCO, small subunit [55239] (1)
  uperfamily
  1. RuBisCO, small subunit [55240] (8)
    1. Ribulose 1,5-bisphosphate carboxylase-oxygenase [55241]
      1. Tobacco (Nicotiana tabacum), variant turkish samsun [TaxId: 4097] [55242] (5)
      2. Spinach (Spinacia oleracea) [TaxId: 3562] [55243] (11)
      3. Galdieria partita [TaxId: 83374] [55244] (2)
      4. Chlamydomonas reinhardtii [TaxId: 3055] [69758] (74)
      5. Alcaligenes eutrophus [TaxId: 106590] [55245] (1)
      6. Synechococcus sp., strain pcc 6301 [TaxId: 1131] [55246] (16)
      7. Rice (Oryza sativa) [TaxId: 4530] [118017] (1)
        SQ P18567
      8. Halothiobacillus neapolitanus [TaxId: 927] [143512] (1)
        SQ P45686 3-110
DCoH-like [55247] (5)
beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
1. PCD-like [55248] (1)
  has additional alpha helix at the N-terminus
  uperfamily
  1. PCD-like [55249] (3)
    Pfam 01329
    1. Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) [55250]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55251] (4)
      2. Thermus thermophilus [TaxId: 274] [103072] (2)
    2. DcoH-like protein DCoH2 [118018]
      1. Mouse (Mus musculus) [TaxId: 10090] [118019] (1)
        SQ Q9CZL5
2. C-terminal domain of arginine repressor [55252] (1)
  forms trimers with three closely packed beta-sheets
  uperfamily
  1. C-terminal domain of arginine repressor [55253] (3)
    1. C-terminal domain of arginine repressor [55254]
      1. Escherichia coli [TaxId: 562] [55255] (3)
      2. Bacillus stearothermophilus [TaxId: 1422] [55256] (2)
      3. Bacillus subtilis [TaxId: 1423] [69759] (4)
3. RBP11-like subunits of RNA polymerase [55257] (2)
  form homo and heterodimers
  uperfamily
  1. RBP11/RpoL [64311] (2)
    1. RPB11 [64312]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64313] (25)
        SQ P38902; part of multichain biological unit
    2. DNA-directed RNA polymerase subunit L, RpoL [118020]
      1. Thermoplasma acidophilum [TaxId: 2303] [118021] (1)
        SQ Q9HIC5
  2. RNA polymerase alpha subunit dimerisation domain [55258] (4)
    1. RNA polymerase alpha [55259]
      1. Escherichia coli [TaxId: 562] [55260] (1)
      2. Thermus aquaticus [TaxId: 271] [64314] (7)
      3. Thermus thermophilus [TaxId: 274] [75478] (30)
        SQ Q9Z9H6; part of multichain biological unit
    2. RPB3 [64315]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64316] (25)
        SQ P16370; part of multichain biological unit
4. GAD domain-like [55261] (2)
  uperfamily
  1. GAD domain [55262] (4)
    has additional structures inserted in the common fold loops
    1. Prokaryotic AspRS, insert domain [55263]
      1. Escherichia coli [TaxId: 562] [55264] (3)
      2. Thermus thermophilus, AspRS-1 [TaxId: 274] [55265] (3)
    2. Glutamyl-tRNA(gln) amidotransferase subunit E, GatE, insert domain [143513]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [143514] (2)
        SQ O26803 271-395
      2. Pyrococcus abyssi [TaxId: 29292] [143515] (2)
        SQ Q9V0U0 277-407
  2. PH0730 C-terminal domain-like [160464] (1)
    1. Hypothetical protein PH0730 [160465]
      1. Pyrococcus horikoshii [TaxId: 53953] [160466] (1)
        SQ O58461 97-213
5. PH0987 N-terminal domain-like [160467] (1)
  1. PH0987 N-terminal domain-like [160468] (1)
    corresponds to the N-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
    1. Uncharacterized protein PH0987 [160469]
      1. Pyrococcus horikoshii [TaxId: 53953] [160470] (1)
        SQ O58715 2-85
TRCF domain-like [143516] (1)
beta-alpha(3)-beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; mixed beta sheet, order 12354, strands 1 and 2 are parallel; some topological similarity to the DCoH-like fold (scop_cf 55247)
1. TRCF domain-like [143517] (1)
  uperfamily
  1. TRCF domain [143518] (1)
    Pfam 03461
    1. Transcription-repair coupling factor, TRCF, C-terminal domain [143519]
      1. Escherichia coli [TaxId: 562] [143520] (2)
        SQ P30958 990-1147
NMB0513-like [160471] (1)
alpha(3)-beta(2)-alpha-beta(2); some similarity to the "winged helix" DNA-binding domain fold
1. NMB0513-like [160472] (1)
  1. NMB0513-like [160473] (1)
    C-terminal part corresponds to Pfam 04591, DUF596
    1. Hypothetical protein NMB0513 [160474]
      1. Neisseria meningitidis [TaxId: 487] [160475] (1)
        SQ Q9K0R7 1-131
PA1123-like [160476] (1)
irregular array of short helices and two three-stranded beta-sheets
1. PA1123-like [160477] (1)
  1. PA1123-like [160478] (1)
    Pfam 09634; DUF2025
    1. Hypothetical protein PA1123 [160479]
      1. Pseudomonas aeruginosa [TaxId: 287] [160480] (1)
        SQ Q9I4L2 1-106
Hypothetical protein Yml108w [100886] (1)
beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta; mixed beta-sheet 2143, strands 1 and 4 are parallel
1. Hypothetical protein Yml108w [89975] (1)
  uperfamily
  1. Hypothetical protein Yml108w [89976] (1)
    1. Hypothetical protein Yml108w [89977]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89978] (1)
MutS N-terminal domain-like [55266] (2)
beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta
1. tRNA-intron endonuclease N-terminal domain-like [55267] (1)
  uperfamily
  1. tRNA-intron endonuclease N-terminal domain-like [55268] (2)
    1. Tetrameric tRNA splicing endonuclease, N-terminal domain [55269]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55270] (1)
    2. Dimeric tRNA splicing endonuclease, domains 1 and 3 [103073]
      duplication: one subunit consists of two tetrameric tRNA splicing endonuclease subunit-like repeats
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103074] (11)
2. DNA repair protein MutS, domain I [55271] (1)
  uperfamily
  1. DNA repair protein MutS, domain I [55272] (2)
    1. DNA repair protein MutS, domain I [55273]
      1. Thermus aquaticus [TaxId: 271] [55274] (3)
      2. Escherichia coli [TaxId: 562] [55275] (10)
        SQ P23909 2-800
GYF/BRK domain-like [55276] (2)
beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta
1. GYF domain [55277] (1)
  uperfamily
  1. GYF domain [55278] (2)
    Pfam 02213
    1. GYF domain from cd2bp2 protein [55279]
      1. Human (Homo sapiens) [TaxId: 9606] [55280] (5)
    2. Hypothetical rotein At5g08430 [118022]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118023] (1)
        SQ Q9FT92 444-508; structure of the N-terminal SWIB domain (25-112) is also known (scop_sp 101202)
2. BRK domain-like [160481] (1)
  1. BRK domain-like [160482] (2)
    Pfam 07533; TCH domain
    1. Chromodomain-helicase-dna-binding protein 8, CHD8 [160483]
      1. Human (Homo sapiens) [TaxId: 9606] [160484] (2)
        SQ Q9HCK8 2024-2093! SQ Q9HCK8 2028-2085
    2. Chromodomain-helicase-DNA-binding protein 7, CHD7 [160485]
      1. Human (Homo sapiens) [TaxId: 9606] [160486] (3)
        SQ Q9P2D1 1799-1852! SQ Q9P2D1 1801-1860! SQ Q9P2D1 1869-1953
GTP cyclohydrolase I feedback regulatory protein, GFRP [69760] (1)
beta(2)-alpha-beta(2)-alpha-beta(2); 2 layers, alpha/beta, antiparallel beta-sheet: order 342165
1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69761] (1)
  uperfamily
  1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69762] (1)
    1. GTP cyclohydrolase I feedback regulatory protein, GFRP [69763]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69764] (4)
        SQ P70552
RL5-like [55281] (1)
beta-alpha-beta(2)-alpha-beta(3)-alpha; 2 layers, alpha/beta; antiparallel beta-sheet: order 231654
1. RL5-like [55282] (2)
  uperfamily
  1. Ribosomal protein L5 [55283] (5)
    1. Ribosomal protein L5 [55284]
      synonym: 50S ribosomal protein L5p, HMAL5, HL13
      1. Bacillus stearothermophilus [TaxId: 1422] [64317] (1)
      2. Thermus thermophilus [TaxId: 274] [82718] (6)
      3. Archaeon Haloarcula marismortui [TaxId: 2238] [55285] (40)
        SQ P14124
      4. Deinococcus radiodurans [TaxId: 1299] [160487] (6)
        SQ Q9RXJ0 3-179
      5. Escherichia coli [TaxId: 562] [160488] (29)
        SQ P62399 1-178
  2. SSO1042-like [160489] (4)
    Pfam 01877; DUF54
    1. Hypothetical protein SSo1042 [160490]
      1. Sulfolobus solfataricus [TaxId: 2287] [160491] (2)
        SQ Q97Z89 3-144
    2. Hypothetical protein AF2318 [160492]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160493] (4)
        SQ O27966 3-143
    3. Hypothetical protein SSO0741 [160494]
      1. Sulfolobus solfataricus [TaxId: 2287] [160495] (1)
        SQ Q9UXC9 4-144
    4. Hypotheical protein MJ1564 [160496]
      1. Methanocaldococcus jannaschii [TaxId: 2190] [160497] (1)
        SQ Q58959 1-133
RPB5-like RNA polymerase subunit [55286] (1)
core: beta-alpha-beta-alpha-beta(2); 2 layers, alpha/beta
1. RPB5-like RNA polymerase subunit [55287] (1)
  uperfamily
  1. RPB5 [55288] (3)
    1. RNA polymerase subunit RBP5 (RNA polymerase subunit H) [55289]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [55290] (1)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [55291] (1)
    2. Eukaryotic RPB5 C-terminal domain [55292]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55293] (26)
        SQ P20434; part of multichain biological unit
Bacillus chorismate mutase-like [55297] (9)
core: beta-alpha-beta-alpha-beta(2); mixed beta-sheet: order: 1423, strand 4 is antiparallel to the rest
1. YjgF-like [55298] (2)
  forms trimers with three closely packed beta-sheets; possibly related to the IspF (d.79.5) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
  uperfamily
  1. YjgF/L-PSP [55299] (15)
    some members possess an endoribonuclease activity inhibiting mRNA translation
    1. Conserved 'hypothetical' protein YjgF [55300]
      1. Escherichia coli [TaxId: 562] [55301] (1)
      2. Haemophilus influenzae [TaxId: 727] [82719] (1)
        YjgF homologue HI0719
    2. Hypothetical protein YjgH [103075]
      1. Escherichia coli [TaxId: 562] [103076] (1)
    3. Purine regulatory protein YabJ [55302]
      1. Bacillus subtilis [TaxId: 1423] [55303] (1)
      2. Clostridium thermocellum [TaxId: 1515] [118024] (1)
        SQ Q4CI45
    4. Highdosage growth inhibitor YER057cp (YEO7_YEAST) [64319]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64320] (1)
    5. 14.5 kda translational inhibitor protein, L-PSP [89979]
      mammalian tumor associated antigen UK114
      1. Human (Homo sapiens) [TaxId: 9606] [89980] (1)
      2. Goat (Capra hircus) [TaxId: 9925] [103077] (1)
      3. Rat (Rattus norvegicus) [TaxId: 10116] [103078] (1)
        Perchloric acid soluble protein
    6. Hypothetical protein ST0811 [143521]
      1. Sulfolobus tokodaii [TaxId: 111955] [143522] (2)
        SQ Q973T6 1-124
    7. Putative endonuclease APE1501 [143523]
      1. Aeropyrum pernix [TaxId: 56636] [143524] (1)
        SQ Q9YBU8 4-119
    8. Putative protein synthesis inhibitor TM0215 [143525]
      1. Thermotoga maritima [TaxId: 2336] [143526] (2)
        SQ Q9WY58 2-127
    9. Hypothetical protein SPy2060 [143527]
      1. Streptococcus pyogenes [TaxId: 1314] [143528] (12)
        SQ Q99XS4 3-122
    10. Putative translation intiation inhibitor TTHA0137 [143529]
      1. Thermus thermophilus [TaxId: 274] [143530] (13)
        SQ Q5SM06 1-124
    11. Hypothetical protein SO1960 [160498]
      1. Shewanella oneidensis [TaxId: 70863] [160499] (3)
        SQ Q8EFL1 2-153
  2. Chorismate mutase [55304] (3)
    1. Chorismate mutase [55305]
      1. Bacillus subtilis [TaxId: 1423] [55306] (6)
      2. Thermus thermophilus [TaxId: 274] [89981] (3)
      3. Clostridium thermocellum [TaxId: 1515] [118025] (1)
        SQ Q5KXU6 5-114 # 53% sequence identity
2. IpsF-like [69765] (1)
  forms trimers with three closely packed beta-sheets; possible link between the YjgF-like (d.79.1) and 4'-phosphopantetheinyl transferase superfamilies (d.150.1)
  uperfamily
  1. IpsF-like [69766] (5)
    1. 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF [69767]
      1. Escherichia coli [TaxId: 562] [69768] (11)
        SQ P62617 ! SQ P36663
      2. Haemophilus influenzae [TaxId: 727] [75479] (3)
      3. Thermus thermophilus [TaxId: 274] [82720] (4)
      4. Shewanella oneidensis [TaxId: 70863] [118026] (1)
        SQ Q8EBR3
    2. IspD/ispF bifunctional enzyme, MECDP synthase domain [118027]
      1. Campylobacter jejuni [TaxId: 197] [118028] (2)
        SQ Q9PM68
3. Tubulin C-terminal domain-like [55307] (1)
  uperfamily
  1. Tubulin, C-terminal domain [55308] (9)
    1. Cell-division protein FtsZ [55309]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55310] (7)
        SQ Q57816 23-360
      2. Pseudomonas aeruginosa [TaxId: 287] [89982] (2)
      3. Mycobacterium tuberculosis [TaxId: 1773] [111032] (7)
        SQ O08378
      4. Thermotoga maritima [TaxId: 2336] [118029] (1)
        SQ O08398 22-335
    2. Tubulin alpha-subunit [55311]
      1. Pig (Sus scrofa) [TaxId: 9823] [55312] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [64321] (6)
        SQ P02550
      3. Prosthecobacter dejongeii [TaxId: 48465] [160500] (3)
        SQ Q8GCC5 253-432
        bacterial tubulin BtubA
    3. Tubulin beta-subunit [55313]
      1. Pig (Sus scrofa) [TaxId: 9823] [55314] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [64322] (8)
        SQ P02554
4. L30e-like [55315] (3)
  uperfamily
  1. L30e/L7ae ribosomal proteins [55316] (11)
    1. Eukaryotic ribosomal protein L30 (L30e) [55317]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55318] (4)
        SQ P14120
      2. Archaeon Thermococcus celer [TaxId: 2264] [89986] (8)
    2. Ribosomal protein L7ae [55319]
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [103081] (2)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [55320] (58)
        SQ P12743
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [111033] (3)
        SQ P54066
      4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111034] (1)
        SQ O29494 # AF0764
      5. Aeropyrum pernix [TaxId: 56636] [160501] (1)
        SQ Q9YAX7 4-127
      6. Pyrococcus furiosus [TaxId: 2261] [160502] (1)
        SQ Q8U160 3-123
      7. Cryptosporidium parvum [TaxId: 5807] [160503] (1)
        SQ Q7YYQ3 17-131
    3. Spliceosomal 15.5kd protein [55321]
      1. Human (Homo sapiens) [TaxId: 9606] [55322] (4)
    4. Small nuclear ribonucleoprotein-associated protein 1, Snu13p [160504]
      1. Saccharomyces cerevisiae [TaxId: 4932] [160505] (3)
        SQ P39990 1-126! SQ P39990 2-126
  2. RNA 2'-O ribose methyltransferase substrate binding domain [75480] (2)
    1. RrmA (RrmH), N-terminal domain [75481]
      23S rRNA methyltransferase; proposed gene names are as appear in the original publication (and the PDB entry)
      1. Thermus thermophilus [TaxId: 274] [75482] (1)
    2. RlmB, N-terminal domain [82721]
      23S rRNA G2251 2'O-methytransferase
      1. Escherichia coli [TaxId: 562] [82722] (1)
  3. ERF1/Dom34 C-terminal domain-like [55323] (4)
    1. C-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55324]
      contains a large insertion forming a separate (sub)domain
      1. Human (Homo sapiens) [TaxId: 9606] [55325] (1)
    2. Cell division protein pelota [160506]
      1. Human (Homo sapiens) [TaxId: 9606] [160507] (1)
        SQ Q9BRX2 261-371
      2. Thermoplasma acidophilum [TaxId: 2303] [160508] (1)
        SQ Q9HJ74 244-338
    3. Dom34 [160509]
      1. Saccharomyces cerevisiae [TaxId: 4932] [160510] (3)
        SQ P33309 278-381
5. PurM N-terminal domain-like [55326] (1)
  uperfamily
  1. PurM N-terminal domain-like [55327] (6)
    1. Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain [55328]
      1. Escherichia coli [TaxId: 562] [55329] (1)
    2. Phosphoribosylformylglycinamidine synthase II, domains 1 and 3 [103082]
      duplication: tandem repeats of two PurM-like units arranged like the PurM subunits in the dimer
      1. Thermotoga maritima [TaxId: 2336] [103083] (17)
        TM1246
    3. FGAM synthase PurL, PurM-like module, N1 and N2 domains [111035]
      1. Salmonella typhimurium [TaxId: 90371] [111036] (1)
        SQ P74881
    4. Thiamine monophosphate kinase (ThiL) N-terminal domain [118030]
      1. Aquifex aeolicus [TaxId: 63363] [118031] (9)
        SQ O67883
    5. Selenide, water dikinase SelD [160511]
      1. Aquifex aeolicus [TaxId: 63363] [160512] (7)
        SQ O67139 1-154! SQ O67139 28-154
    6. Hydrogenase expression/formation protein HypE [160513]
      1. Thermococcus kodakaraensis [TaxId: 311400] [160514] (2)
        SQ Q5JII7 41-155
6. Holliday junction resolvase RusA [103084] (1)
  uperfamily
  1. Holliday junction resolvase RusA [103085] (1)
    1. Holliday junction resolvase RusA [103086]
      1. Escherichia coli [TaxId: 562] [103087] (1)
7. OmpA-like [103088] (1)
  uperfamily
  1. OmpA-like [103089] (3)
    Pfam 00691
    1. Peptidoglycan-associated lipoprotein, PAL, periplasmic domain [103090]
      1. Escherichia coli [TaxId: 562] [103091] (5)
      2. Haemophilus influenzae [TaxId: 727] [143531] (1)
        SQ P10324 20-153
    2. Outer membrane protein class 4, RmpM, C-terminal domain [103092]
      1. Neisseria meningitidis [TaxId: 487] [103093] (1)
8. YueI-like [160515] (1)
  1. YueI-like [160516] (1)
    Pfam 07997; DUF1694
    1. Uncharacterized protein YueI [160517]
      1. Bacillus subtilis [TaxId: 1423] [160518] (2)
        SQ O32092 3-130
9. BB2672-like [160519] (1)
  contains extra N-terminal strand and a beta-hairpin insertion between strands 3 and 4 that packs against the main beta-sheet
  1. BB2672-like [160520] (2)
    Pam 06684; DUF1185
    1. Uncharacterized protein BB2672 [160521]
      1. Bordetella bronchiseptica [TaxId: 518] [160522] (3)
        SQ Q7WJ28 2-192
    2. Uncharacterized protein SPO0826 [160523]
      1. Silicibacter pomeroyi [TaxId: 89184] [160524] (1)
        SQ Q5LV76 3-171
YjbQ-like [111037] (1)
beta(2)-alpha-beta(2)-alpha(2)-beta(3); contains a beta-sandwich: 7 strands in 2 sheets; trimerizes with orthogonally packed beta-sheets
1. YjbQ-like [111038] (1)
  uperfamily
  1. YjbQ-like [111039] (4)
    Pfam 01894
    1. B.subtilis YugU ortolog CAC0907 [111040]
      1. Clostridium acetobutylicum [TaxId: 1488] [111041] (2)
        SQ Q97KL0
    2. Hypothetical protein BH3498 [118032]
      1. Bacillus halodurans [TaxId: 86665] [118033] (1)
        SQ Q9K772
    3. Hypothetical protein TM0723 [118034]
      1. Thermotoga maritima [TaxId: 2336] [118035] (1)
        SQ Q9WZI2
    4. Hypothetical protein SSO2532 [118036]
      1. Sulfolobus solfataricus [TaxId: 2287] [118037] (1)
        SQ Q97VS8
Tautomerase/MIF [55330] (1)
(beta-alpha-beta)2; 2 layers: alpha/beta; mixed beta-sheet
generally forms trimers with three closely packed beta-sheets
1. Tautomerase/MIF [55331] (6)
  uperfamily
  1. 4-oxalocrotonate tautomerase-like [55332] (5)
    dimer of beta-alpha-beta subunits: may assemble further in hexamer (trimer of the dimers)
    1. 4-oxalocrotonate tautomerase [55333]
      1. Pseudomonas sp., DmpI [TaxId: 306] [55334] (1)
      2. Pseudomonas putida, XylH [TaxId: 303] [55335] (4)
    2. Trans-3-chloroacrylic acid dehalogenase alpha-subunit, CaaD1 [103094]
      forms heterohexamer with beta-subunit
      1. Pseudomonas pavonaceae [TaxId: 47881] [103095] (1)
    3. Trans-3-chloroacrylic acid dehalogenase beta-subunit, CaaD2 [103096]
      forms heterohexamer with alpha-subunit
      1. Pseudomonas pavonaceae [TaxId: 47881] [103097] (1)
    4. 4-oxalocrotonate tautomerase homologue YdcE [82723]
      forms stable dimer without further oligomerisation
      1. Escherichia coli [TaxId: 562] [82724] (3)
  2. 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) [55336] (1)
    1. 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) [55337]
      1. Escherichia coli [TaxId: 562] [55338] (1)
  3. MIF-related [55339] (6)
    1. Microphage migration inhibition factor (MIF) [55340]
      synonym: glycosylation-inhibiting factor (GIF)
      1. Human (Homo sapiens) [TaxId: 9606] [55341] (20)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [55342] (1)
      3. Mouse (Mus musculus) [TaxId: 10090] [55343] (5)
      4. Trichinella spiralis [TaxId: 6334] [64323] (1)
      5. African clawed frog (Xenopus laevis) [TaxId: 8355] [111042] (1)
        SQ Q76BK2
    2. D-dopachrome tautomerase [55344]
      1. Human (Homo sapiens) [TaxId: 9606] [55345] (1)
  4. Hypothetical protein HI1388.1 [103098] (1)
    lacks the N-terminal proline
    1. Hypothetical protein HI1388.1 [103099]
      1. Haemophilus influenzae [TaxId: 727] [103100] (1)
  5. VC0714-like [111043] (1)
    1. Hypothetical protein VC0714 [111044]
      1. Vibrio cholerae [TaxId: 666] [111045] (1)
        SQ Q9KU16
  6. MSAD-like [143532] (1)
    1. Malonate semialdehyde decarboxylase, MSAD [143533]
      1. Pseudomonas pavonaceae [TaxId: 47881] [143534] (14)
        SQ Q9EV83 2-130! SQ Q9EV83 2-230
FwdE/GAPDH domain-like [55346] (4)
core: alpha-beta-alpha-beta(3); mixed sheet: 2134, strand 2 is parallel to strand 1
1. Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain [55347] (5)
  N-terminal domain is the classic Rossmann-fold
  uperfamily
  1. GAPDH-like [55348] (29)
    has many additional secondary structures
    1. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [55349]
      1. Escherichia coli [TaxId: 562] [55350] (13)
        SQ P06977
      2. Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [55351] (14)
      3. Achromobacter xylosoxidans [TaxId: 85698] [89987] (1)
        formerly Alcaligenes xylosoxidans
      4. Thermus aquaticus [TaxId: 271] [55352] (13)
      5. Thermus thermophilus [TaxId: 274] [103101] (1)
      6. Thermotoga maritima [TaxId: 2336] [55353] (1)
      7. Archaeon Sulfolobus solfataricus [TaxId: 2287] [55354] (1)
      8. Archaeon Methanothermus fervidus [TaxId: 2180] [55355] (1)
      9. Trypanosoma brucei brucei, glycosome [TaxId: 5702] [55356] (1)
      10. Trypanosoma cruzi [TaxId: 5693] [75483] (7)
      11. Leishmania mexicana [TaxId: 5665] [55357] (5)
      12. American lobster (Homarus americanus) [TaxId: 6706] [55358] (2)
      13. South China Sea lobster (Palinurus versicolor) [TaxId: 150436] [55359] (5)
      14. Human (Homo sapiens) [TaxId: 9606] [55360] (1)
      15. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [103102] (1)
      16. Spinach (Spinacia oleracea) [TaxId: 3562] [69769] (24)
        SQ P19866
      17. Human(Homo sapiens), liver isoform [TaxId: 9606] [143535] (8)
        SQ P04406 151-314
      18. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [143536] (12)
        SQ Q8IKK7 153-318! SQ Q8T6B1 153-318
      19. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143537] (4)
        SQ O59494 140-301
    2. Aspartate beta-semialdehyde dehydrogenase [55361]
      1. Escherichia coli [TaxId: 562] [55362] (4)
        SQ P00353
      2. Vibrio cholerae [TaxId: 666] [82725] (2)
      3. Haemophilus influenzae [TaxId: 727] [103103] (12)
        SQ P44801
      4. Streptococcus pneumoniae [TaxId: 1313] [143538] (11)
        SQ Q8DQ00 128-329
    3. Acetaldehyde dehydrogenase (acylating) [89988]
      1. Pseudomonas sp. [TaxId: 306] [89989] (1)
    4. N-acetyl-gamma-glutamyl-phosphate reductase ArgC [111046]
      1. Thermotoga maritima [TaxId: 2336] [111047] (1)
        SQ Q9X2A2
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118038] (5)
        SQ O82187 15-359
      3. Salmonella typhimurium [TaxId: 90371] [143539] (1)
        SQ Q8ZKL8 154-308
    5. Putative semialdehyde dehydrogenase [143540]
      1. Rice (Oryza sativa) [TaxId: 4530] [143541] (4)
        SQ Q6AV34 219-383
    6. Usg-1 protein homolog PA3116 [143542]
      1. Pseudomonas aeruginosa [TaxId: 287] [143543] (1)
        SQ O87014 130-319
  2. Homoserine dehydrogenase-like [55363] (2)
    1. Homoserine dehydrogenase [55364]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55365] (4)
        SQ P31116
    2. Saccharopine reductase [55366]
      contains an alpha-helical subdomain inserted in the common fold and other additional secondary structures
      1. Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [55367] (3)
  3. Dihydrodipicolinate reductase-like [55368] (12)
    1. Diaminopimelic acid dehydrogenase (DAPDH) [55369]
      distantly related to dihydrodipicolinate reductase
      larger alpha+beta subdomain substitutes for one helix and one strand of the common fold
      1. Corynebacterium glutamicum [TaxId: 1718] [55370] (4)
    2. Dihydrodipicolinate reductase [55371]
      1. Escherichia coli [TaxId: 562] [55372] (5)
      2. Mycobacterium tuberculosis [TaxId: 1773] [103104] (14)
      3. Thermotoga maritima [TaxId: 2336] [111048] (1)
        SQ Q9X1K8
    3. Myo-inositol 1-phosphate synthase [75484]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75485] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75486] (9)
        SQ P11986
      3. Archaeoglobus fulgidus [TaxId: 2234] [111049] (1)
        SQ O28480
      4. Caenorhabditis elegans [TaxId: 6239] [111050] (1)
        SQ Q18664
    4. Hypothetical protein TM1419 [103105]
      myo-inositol 1-phosphate synthase-related protein
      1. Thermotoga maritima [TaxId: 2336] [103106] (1)
    5. Hypothetical protein TM1643 [75487]
      1. Thermotoga maritima [TaxId: 2336] [75488] (2)
    6. 1-deoxy-D-xylulose-5-phosphate reductoisomerase [69770]
      1. Escherichia coli [TaxId: 562] [69771] (12)
        SQ P45568
      2. Zymomonas mobilis [TaxId: 542] [111051] (2)
        SQ Q9X5F2
  4. Biliverdin reductase [55373] (1)
    1. Biliverdin reductase [55374]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55375] (3)
  5. Glucose 6-phosphate dehydrogenase-like [55376] (8)
    has many additional secondary structures
    1. Glucose-fructose oxidoreductase [55377]
      very similar to the glucose 6-phosphate dehydrogenase domain
      1. Zymomonas mobilis [TaxId: 542] [55378] (12)
    2. Glucose 6-phosphate dehydrogenase [55379]
      1. Leuconostoc mesenteroides [TaxId: 1245] [55380] (9)
      2. Human (Homo sapiens) [TaxId: 9606] [55381] (1)
    3. Virulence factor MviM [111052]
      1. Escherichia coli [TaxId: 562] [111053] (1)
        SQ P75931
    4. Putative oxidoreductase VCA1048 [111054]
      1. Vibrio cholerae [TaxId: 666] [111055] (1)
        SQ Q9KKQ4
    5. Probable oxidoreductase At4g09670 [118039]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118040] (1)
        SQ Q9SZ83
    6. Hypothetical protein TM0312 [143544]
      1. Thermotoga maritima [TaxId: 2336] [143545] (2)
        SQ Q9WYE8 132-275
    7. Galactose/lactose metabolism regulatory protein GAL80 [143546]
      1. Yeast (Kluyveromyces lactis) [TaxId: 28985] [143547] (9)
        SQ Q06433 155-373
2. Serine metabolism enzymes domain [143548] (2)
  contains extra C-terminal beta-hairpin
  uperfamily
  1. Serine dehydratase beta chain-like [143549] (1)
    Pfam 03315
    1. L-serine dehydratase SdhL, N-terminal domain [143550]
      1. Legionella pneumophila [TaxId: 446] [143551] (3)
        SQ Q5ZXE1 17-161
  2. SerA intervening domain-like [143552] (1)
    PfamB 001360; this domain is found in some but not all D-3-phosphoglycerate dehydrogenases (SerA) and related enzymes
    1. D-3-phosphoglycerate dehydrogenase SerA [143553]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143554] (2)
        SQ P0A544 316-450
3. FwdE-like [143555] (1)
  contains extra N-terminal and C-terminal structures
  uperfamily
  1. FwdE-like [143556] (2)
    Pfam 02663; Tungsten formylmethanofuran dehydrogenase, subunit E, FwdE, is a stand-alone domain of this fold
    1. FwdE-like protein DSY1837 (Dhaf_2201) [143557]
      1. Desulfitobacterium hafniense [TaxId: 49338] [143558] (2)
        SQ Q24WG6 3-151
    2. Uncharacterized protein Ta1109 [160525]
      1. Thermoplasma acidophilum [TaxId: 2303] [160526] (1)
        SQ Q9HJ63 1-168
4. V-type ATPase subunit E-like [160527] (1)
  extra N-terminal helix and extra C-terminal helix form dimerisation subdomain
  1. V-type ATPase subunit E [160528] (1)
    Pfam 01991
    1. V-type ATP synthase subunit E [160529]
      1. Pyrococcus horikoshii [TaxId: 53953] [160530] (3)
        SQ O57724 81-198
Ava3019-like [160531] (1)
alpha(2)-beta-alpha-beta(4); 2 layers, a/b; antiparallel beta-sheet, order: 32145; similarity to the insert domain of Glucose 6-phosphate dehydrogenase-like family (sop_fa 55376)
1. Ava3019-like [160532] (1)
  1. Ava3019-like [160533] (1)
    Pfam 08854; DUF1824
    1. Uncharacterized protein Ava3019 [160534]
      1. Anabaena variabilis [TaxId: 1172] [160535] (3)
        SQ Q3M8Q7 8-138
Hypothetical protein PF0899 [111056] (1)
alpha-beta-alpha-beta(4); 2 layers: a/b; mixed beta-sheet, order 23145, strands 1 and 3 are parallel; similar to the GAPDH C-terminal domain-like fold (scop_cf 55346)
1. Hypothetical protein PF0899 [111057] (1)
  possibly related to Major capsid protein gp5 (scop_sf 56563)63566
  uperfamily
  1. Hypothetical protein PF0899 [111058] (1)
    1. Hypothetical protein PF0899 [111059]
      1. Pyrococcus furiosus [TaxId: 2261] [111060] (1)
        SQ Q8U2E0
Major capsid protein gp5 [56562] (1)
unusual fold; contains PF0899-like core, decorated with additional structure
1. Major capsid protein gp5 [56563] (1)
  possibly related to the hypothetical protein PF0899 superfamily (scop_sf 111057)
  uperfamily
  1. Major capsid protein gp5 [56564] (1)
    1. Major capsid protein gp5 [56565]
      1. Bacteriophage HK97 [TaxId: 37554] [56566] (21)
MK0786-like [143559] (1)
alpha(2)-beta(4); 2 layers: a/b; antiparallel beta-sheet, order 1234 (meander)
1. MK0786-like [143560] (1)
  probable biological unit is a teramer; all subunit interfaces are provided by helices
  uperfamily
  1. MK0786-like [143561] (2)
    single domain; the N-terminal half is covered by Pfam 04036 (DUF372) and the C-terminal half by Pfam 04038 (DUF381)
    1. Hypothetical protein PTO0218 [143562]
      1. Picrophilus torridus [TaxId: 82076] [143563] (6)
        SQ Q6L2J9 1-120
    2. Hypothetical protein MK0786 [143564]
      1. Methanopyrus kandleri [TaxId: 2320] [143565] (4)
        SQ Q8TX89 7-119
YkuJ-like [143566] (1)
alpha-beta(4)-alpha; 2 layers a/b; antiparallel beta-sheet, order 1234
1. YkuJ-like [143567] (1)
  uperfamily
  1. YkuJ-like [143568] (1)
    1. Hypothetical protein YkuJ [143569]
      1. Bacillus subtilis [TaxId: 1423] [143570] (2)
        SQ O34588 2-79
N domain of copper amine oxidase-like [55382] (5)
alpha-beta(5)-alpha; 2 layers: alpha/beta; meander antiparallel sheet
1. Copper amine oxidase, domain N [55383] (1)
  uperfamily
  1. Copper amine oxidase, domain N [55384] (1)
    1. Copper amine oxidase, domain N [55385]
      non-conserved N-terminal domain
      1. Escherichia coli [TaxId: 562] [55386] (11)
2. Frataxin/Nqo15-like [55387] (2)
  uperfamily
  1. Frataxin-like [55388] (3)
    iron homeostasis proteins
    1. C-terminal domain of frataxin [55389]
      protein responsible for Friedreich ataxia
      1. Human (Homo sapiens) [TaxId: 9606] [55390] (2)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [143571] (2)
        SQ Q07540 52-174! SQ Q07540 61-172
    2. CyaY [55391]
      1. Escherichia coli [TaxId: 562] [55392] (4)
        SQ P27838
  2. Nqo15-like [143572] (1)
    overall structural similarity to the frataxin-like family
    1. NADH-quinone oxidoreductase subunit 15, Nqo15 [143573]
      1. Thermus thermophilus [TaxId: 274] [143574] (4)
        SQ Q5SKZ7 3-129
3. Hypothetical protein c14orf129, hspc210 [103107] (1)
  uperfamily
  1. Hypothetical protein c14orf129, hspc210 [103108] (1)
    Pfam 05303
    1. Hypothetical protein c14orf129, hspc210 [103109]
      1. Human (Homo sapiens) [TaxId: 9606] [103110] (1)
4. GAS2 domain-like [143575] (1)
  this superfamily may include the most C-terminal domain of IBP39 (scop_fa 103410); the preceeding (middle) domain of IBP39 may be split and reassigned to the EF-hand superfamily (scop_sf 47473)
  uperfamily
  1. GAS2 domain [143576] (1)
    Pfam 02187
    1. Growth-arrest-specific protein 2, GAS2 [143577]
      1. Mouse (Mus musculus) [TaxId: 10090] [143578] (1)
        SQ P11862 200-284
5. GK1464-like [143579] (1)
  dimer; pseudo barrel; the true dimeric barrel formation requires swapping of the C-ternimal beta-alpha units
  uperfamily
  1. GK1464-like [143580] (1)
    1. Hypothetical protein, GK1464 ortholog [143581]
      MCSG target ID: APC35702
      1. Bacillus stearothermophilus [TaxId: 1422] [143582] (2)
        SQ Q5KZY7 1-100
Aha1/BPI domain-like [55393] (2)
core: [beta]-alpha-beta(5)-alpha; 2 layers: alpha/beta; antiparallel beta-sheet, meander
1. Activator of Hsp90 ATPase, Aha1 [103111] (1)
  consists of a single domain of this fold
  uperfamily
  1. Activator of Hsp90 ATPase, Aha1 [103112] (1)
    1. Activator of Hsp90 ATPase, Aha1 [103113]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103114] (2)
2. Bactericidal permeability-increasing protein, BPI [55394] (1)
  duplication: consists of two clear structural repeats of this fold also containing an extra C-terminal beta-hairpin
  uperfamily
  1. Bactericidal permeability-increasing protein, BPI [55395] (1)
    1. Bactericidal permeability-increasing protein, BPI [55396]
      1. Human (Homo sapiens) [TaxId: 9606] [55397] (2)
SpoVG-like [160536] (1)
beta(5)-alpha; comprises a coiled antiparallel beta-sheet (order: 12345) packed against the C-terminal helix; the extensions of strands 4 and 5 form an isolated beta-hairpin
1. SpoVG-like [160537] (1)
  probable biological unit is a hexamer (trimer of dimers)
  1. SpoVG-like [160538] (2)
    Pfam 04026
    1. Putative septation protein SpoVG [160539]
      1. Bacillus subtilis [TaxId: 1423] [160540] (6)
        SQ P28015 1-92
      2. Staphylococcus epidermidis [TaxId: 1282] [160541] (4)
        SQ Q8CML1 1-84! SQ Q8CML1 1-87
Subtilisin inhibitor [55398] (1)
alpha+beta sandwich
1. Subtilisin inhibitor [55399] (1)
  uperfamily
  1. Subtilisin inhibitor [55400] (2)
    1. Subtilisin inhibitor [55401]
      1. Streptomyces lividans [TaxId: 1916] [55402] (3)
      2. Streptomyces albogriseolus, s-3253 [TaxId: 1887] [55403] (2)
RNA bacteriophage capsid protein [55404] (1)
6-standed beta-sheet followed with 2 helices; meander
1. RNA bacteriophage capsid protein [55405] (1)
  uperfamily
  1. RNA bacteriophage capsid protein [55406] (5)
    1. MS2 virus coat protein [55407]
      1. Bacteriophage MS2 [TaxId: 12022] [55408] (48)
        SQ P03612
    2. GA coat protein [55409]
      1. Bacteriophage GA [TaxId: 12018] [55410] (2)
    3. fr coat protein [55411]
      1. Bacteriophage FR [TaxId: 12017] [55412] (2)
    4. Qbeta coat protein [55413]
      1. Bacteriophage Qbeta [TaxId: 39803] [55414] (1)
    5. PP7 coat protein [55415]
      1. Bacteriophage PP7 [TaxId: 12023] [55416] (1)
eIF4e-like [55417] (1)
beta(2)-alpha-beta(2)-alpha-beta(2)-alpha-beta-2; 2 layers: alpha/beta; antiparallel sheet: 21356478
1. eIF4e-like [55418] (2)
  uperfamily
  1. Translation initiation factor eIF4e [55419] (3)
    1. Translation initiation factor eIF4e [55420]
      messenger RNA 5' cap-binding protein
      1. Mouse (Mus musculus) [TaxId: 10090] [55421] (7)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55422] (2)
      3. Homo sapiens [TaxId: 9606] [160542] (6)
  2. BLES03-like [143583] (1)
    the N-terminal strand is missing, but there extra C-terminal strands in the beta-sheet
    1. Basophilic leukemia expressed protein BLES03 [143584]
      1. Human (Homo sapiens) [TaxId: 9606] [143585] (4)
        SQ Q9H3H3 17-250
CO dehydrogenase flavoprotein C-domain-like [55423] (2)
core: beta(3,4)-alpha(3); alpha+beta sandwich
1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55424] (1)
  both first two domains are of same beta/beta/alpha fold
  uperfamily
  1. FAD/NAD-linked reductases, dimerisation (C-terminal) domain [55425] (22)
    1. Glutathione reductase [55426]
      1. Human (Homo sapiens) [TaxId: 9606] [55427] (17)
      2. Plasmodium falciparum [TaxId: 5833] [89990] (1)
      3. Escherichia coli [TaxId: 562] [55428] (4)
    2. Trypanothione reductase [55429]
      1. Crithidia fasciculata [TaxId: 5656] [55430] (6)
      2. Trypanosoma cruzi [TaxId: 5693] [55431] (6)
    3. Mammalian thioredoxin reductase [64329]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [64330] (1)
    4. Apoptosis-inducing factor (AIF) [75489]
      contains a large loop insertion in this domain
      1. Human (Homo sapiens) [TaxId: 9606] [75490] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [75491] (1)
    5. NADH peroxidase [55432]
      1. Enterococcus faecalis [TaxId: 1351] [55433] (8)
    6. NADH-dependent ferredoxin reductase, BphA4 [55434]
      1. Pseudomonas sp., KKS102 [TaxId: 306] [55435] (2)
    7. Putidaredoxin reductase [103115]
      1. Pseudomonas putida [TaxId: 303] [103116] (2)
    8. Dihydrolipoamide dehydrogenase [55436]
      1. Pseudomonas putida [TaxId: 303] [55437] (1)
      2. Pseudomonas fluorescens [TaxId: 294] [55438] (1)
      3. Azotobacter vinelandii [TaxId: 354] [55439] (1)
      4. Bacillus stearothermophilus [TaxId: 1422] [55440] (1)
      5. Neisseria meningitidis [TaxId: 487] [55441] (2)
      6. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64331] (3)
      7. Garden pea (Pisum sativum) [TaxId: 3888] [55442] (1)
      8. Mycobacterium tuberculosis [TaxId: 1773] [118041] (1)
        SQ O53355
    9. NADH-dependent 2-ketopropyl coenzyme M oxidoreductase/carboxylase [82726]
      1. Xanthobacter sp., py2 [TaxId: 35809] [82727] (6)
    10. Flavocytochrome c sulfide dehydrogenase, FCSD, flavin-binding subunit [55443]
      rudiment "interface" domain of smaller size; beta(3)-alpha
      1. Purple phototrophic bacterium (Chromatium vinosum) [TaxId: 1049] [55444] (1)
    11. NADH oxidase /nitrite reductase [118042]
      1. Pyrococcus furiosus [TaxId: 2261] [118043] (1)
        SQ Q8U1K9
2. CO dehydrogenase flavoprotein C-terminal domain-like [55447] (1)
  uperfamily
  1. CO dehydrogenase flavoprotein C-terminal domain-like [55448] (6)
    1. Carbon monoxide (CO) dehydrogenase flavoprotein, C-terminal domain [55449]
      1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [55450] (7)
      2. Hydrogenophaga pseudoflava [TaxId: 47421] [55451] (2)
    2. Xanthine oxidase, domain 4 (?) [55452]
      1. Cow (Bos taurus) [TaxId: 9913] [55453] (7)
        SQ P80457
    3. Xanthine dehydrogenase chain A, domain 4 [69772]
      1. Rhodobacter capsulatus [TaxId: 1061] [69773] (2)
    4. Quinoline 2-oxidoreductase medium subunit QorM [111061]
      1. Pseudomonas putida [TaxId: 303] [111062] (1)
        SQ P72222
    5. 4-hydroxybenzoyl-CoA reductase beta subunit HrcB, C-terminal domain [118044]
      1. Thauera aromatica [TaxId: 59405] [118045] (2)
        SQ O33820
SRF-like [55454] (1)
alpha-beta(2)-alpha; dimer; 3 layers a/b/a; antiparallel beta-sheet
1. SRF-like [55455] (1)
  uperfamily
  1. SRF-like [55456] (4)
    1. Serum response factor (SRF) core [55457]
      1. Human (Homo sapiens) [TaxId: 9606] [55458] (3)
    2. MCM1 transcriptional regulator [55459]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55460] (1)
    3. Myocyte enhancer factor Mef2a core [55461]
      1. Human (Homo sapiens) [TaxId: 9606] [55462] (2)
    4. Myocyte enhancer factor Mef2b core [103117]
      1. Human (Homo sapiens) [TaxId: 9606] [103118] (2)
        SQ Q02080 2-91
Origin of replication-binding domain, RBD-like [55463] (1)
alpha-beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel sheet 41325
1. Origin of replication-binding domain, RBD-like [55464] (5)
  uperfamily
  1. The origin DNA-binding domain of SV40 T-antigen [55465] (1)
    1. The origin DNA-binding domain of SV40 T-antigen [55466]
      1. Simian virus 40, Sv40 [TaxId: 10633] [55467] (14)
  2. DNA-binding domain of REP protein [82728] (1)
    1. DNA-binding domain of REP protein [82729]
      1. Geminivirus (Tomato yellow leaf curl virus - sardinia) [TaxId: 123735] [82730] (2)
  3. Replication initiation protein E1 [64332] (2)
    1. Replication initiation protein E1 [64333]
      1. Bovine papillomavirus [TaxId: 10571] [64334] (3)
      2. Human papillomavirus type 18 [TaxId: 333761] [103119] (1)
  4. Replication protein Rep, nuclease domain [75492] (1)
    1. Replication protein Rep, nuclease domain [75493]
      1. Adeno-associated virus, aav-5 [TaxId: 272636] [75494] (3)
  5. Relaxase domain [103120] (2)
    circular permutation of the common fold
    1. F factor TraI relaxase [103121]
      1. Escherichia coli [TaxId: 562] [103122] (1)
    2. TrwC relaxase [103123]
      1. Escherichia coli [TaxId: 562] [103124] (5)
SARS receptor-binding domain-like [143586] (1)
core: 3 layers, a/b/a; antiparallel beta-sheet of 5 strands, order 13542
1. SARS receptor-binding domain-like [143587] (1)
  uperfamily
  1. SARS receptor-binding domain-like [143588] (1)
    part of PfamB 000266
    1. Spike protein S1 [143589]
      1. SARS coronavirus [TaxId: 227859] [143590] (9)
        SQ P59594 320-502! SQ P59594 321-512! SQ P59594 323-502
Hut operon positive regulatory protein HutP [111063] (1)
alpha(2)-beta-alpha(2)-beta(3); 3 layers: a/b/a; antiparallel beta-sheet: order 1234
1. Hut operon positive regulatory protein HutP [111064] (1)
  uperfamily
  1. Hut operon positive regulatory protein HutP [111065] (1)
    1. Hut operon positive regulatory protein HutP [111066]
      an RNA-binding antitermination protein
      1. Bacillus subtilis [TaxId: 1423] [111067] (23)
        SQ P10943
Hypothetical protein yfbM [111068] (1)
beta-alpha(2)-beta-alpha(2)-beta(2)-alpha(n)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 21543
1. Hypothetical protein yfbM [111069] (1)
  uperfamily
  1. Hypothetical protein yfbM [111070] (1)
    1. Hypothetical protein yfbM [111071]
      1. Escherichia coli [TaxId: 562] [111072] (1)
        SQ P76483
TTHA1528-like [143591] (1)
beta-alpha-beta(3)-alpha-beta-alpha(2)-beta; 3 layers: a/b/a; mixed beta-sheet, order: 143256, parallel strands' pairs are 1-4 and 2-5
1. TTHA1528-like [143592] (1)
  uperfamily
  1. TTHA1528-like [143593] (1)
    1. Hypothetical protein TTHA1528 (TT1805) [143594]
      1. Thermus thermophilus [TaxId: 274] [143595] (2)
        SQ Q5SI52 1-127
YojJ-like [143596] (1)
alpha-beta-X-beta-alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; 7-stranded mixed beta-sheet, order 2431567; strands 1 and 3 are parallel to each other
1. YojJ-like [143597] (1)
  uperfamily
  1. YojJ-like [143598] (1)
    Pfam 02457; DUF147
    1. Hypothetical protein BC4920 (YojJ) [143599]
      contains extra N-terminal hairpin of long helices; possible membrane spanning region
      1. Bacillus cereus [TaxId: 1396] [143600] (3)
        SQ Q812L9 1-201
STIV B116-like [143601] (1)
subunit fold consists of mixed 5-stranded beta-sheet, order:31452, strand 5 is antiparallel to the rest, with 3 helices on one side; dimerises with the formation of a single 10-stranded beta-sheet; strand 2 is in the dimer interface
1. STIV B116-like [143602] (1)
  uperfamily
  1. STIV B116-like [143603] (2)
    1. Hypothetical protein B116 [143604]
      1. Sulfolobus turreted icosahedral virus, STIV [TaxId: 269145] [143605] (2)
        SQ Q6Q0K9 2-116
    2. Afv3-109 [143606]
      1. Acidianus filamentous virus 1 [TaxId: 235266] [143607] (2)
Bacillus phage protein [111073] (1)
alpa-beta(3)-alpha-beta(3)-alpha; 3 layers: b/a/b, 3-helical bundle flanked by two 3-stranded meander beta-sheets
1. Bacillus phage protein [111074] (1)
  uperfamily
  1. Bacillus phage protein [111075] (1)
    1. Bacillus phage protein [111076]
      1. Bacillus cereus [TaxId: 1396] [111077] (1)
        SQ Q81EU2; 100% sequence identity to a Bacteriophage phBC6A51 protein
FMN-dependent nitroreductase-like [55468] (1)
core: (alpha-beta-alpha-beta)2; 3 layers a/b/a; antiparallel beta-sheet: 1243
1. FMN-dependent nitroreductase-like [55469] (2)
  uperfamily
  1. NADH oxidase/flavin reductase [55470] (11)
    1. NADH oxidase [55471]
      1. Thermus thermophilus, HB8 [TaxId: 274] [55472] (1)
    2. Flavin reductase P (NADPH:FMN oxidoreductase) [55473]
      1. Vibrio harveyi [TaxId: 669] [55474] (2)
      2. Vibrio fischeri [TaxId: 668] [55475] (5)
    3. Oxygen-insensitive NAD(P)H nitroreductase [55476]
      1. Enterobacter cloacae [TaxId: 550] [55477] (4)
      2. Escherichia coli, minor form, NfnB [TaxId: 562] [55478] (17)
      3. Escherichia coli, major form, NfsA [TaxId: 562] [55479] (1)
    4. Hypothetical oxidoreductase SP0622 [143608]
      1. Streptococcus pneumoniae [TaxId: 1313] [143609] (4)
        SQ Q97S03 1-201
    5. Hypothetical protein Smu.260 [143610]
      1. Streptococcus mutans [TaxId: 1309] [143611] (6)
        SQ Q8DW21 2-200
    6. Hypothetical oxidoreductase BC1844 [143612]
      1. Bacillus cereus [TaxId: 1396] [143613] (1)
        SQ Q81EW9 2-200
    7. Hypothetical oxidoreductase YcnD [143614]
      1. Bacillus subtilis [TaxId: 1423] [143615] (1)
        SQ P94424 1-249
    8. NAD(P)H-flavin oxidoreductase Atu0013 [143616]
      1. Agrobacterium tumefaciens [TaxId: 358] [143617] (2)
        SQ Q8UJB5 1-200
  2. Putative nitroreductase TM1586 [111078] (1)
    duplication: consists of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site
    1. Putative nitroreductase TM1586 [111079]
      1. Thermotoga maritima [TaxId: 2336] [111080] (1)
        SQ Q9X1S2
N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55480] (1)
alpha-beta-alpha(2)-beta(3)-alpha; 3 layers a/b/a; antiparallel beta-sheet: 4123
1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55481] (1)
  uperfamily
  1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55482] (1)
    1. N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 [55483]
      1. Human (Homo sapiens) [TaxId: 9606] [55484] (1)
EscU C-terminal domain-like [160543] (1)
alpha-beta(3)-alpha-beta-alpha(2); 3 layers, a/b/a; mixed beta-sheet, order: 4123, strand 2 is antiparallel to the rest
1. EscU C-terminal domain-like [160544] (1)
  1. EscU C-terminal domain-like [160545] (3)
    C-terminal part of Pfam 01312; self-cleaving type III secretion protein domain
    1. Type III secretion proteins EscU [160546]
      1. Escherichia coli [TaxId: 562] [160547] (8)
        SQ Q9AJ26 237-345! SQ Q9AJ26 244-262,263-343! SQ Q9AJ26 245-262,263-343! SQ Q9AJ26 245-345! SQ Q9AJ26 246-262,263-345! SQ Q9AJ26 246-345
    2. Surface presentation of antigens protein SpaS [160548]
      1. Shigella flexneri [TaxId: 623] [160549] (1)
        SQ P0A1M8 237-257,258-338
      2. Salmonella typhimurium [TaxId: 90371] [160550] (1)
        SQ P40702 239-258,259-346
Zincin-like [55485] (2)
contains mixed beta sheet with connection over free side of the sheet
1. Metalloproteases ("zincins"), catalytic domain [55486] (17)
  uperfamily
  1. Zinc protease [55487] (1)
    single domain
    1. Zinc protease [55488]
      1. Streptomyces caespitosus [TaxId: 53502] [55489] (2)
  2. Fungal zinc peptidase [64335] (2)
    single domain with insertions in the common fold
    1. Fungal zinc peptidase [64336]
      1. Grifola frondosa [TaxId: 5627] [64337] (4)
      2. Aspergillus oryzae, deuterolysin [TaxId: 5062] [69774] (1)
  3. Thermolysin-like [55490] (4)
    includes alpha-helical C-terminal domain characteristic for the family
    1. Elastase [63413]
      1. Pseudomonas aeruginosa [TaxId: 287] [55492] (2)
        SQ P14756 198-495
    2. Thermolysin [63414]
      1. Bacillus thermoproteolyticus [TaxId: 1427] [55494] (59)
        SQ P00800
    3. Neutral protease [63415]
      1. Bacillus cereus, strain dsm 3101 [TaxId: 1396] [55496] (2)
    4. Aureolysin [63416]
      1. Staphylococcus aureus [TaxId: 1280] [55498] (1)
  4. Leukotriene A4 hydrolase catalytic domain [64338] (1)
    adopts thermolysin-like fold
    1. Leukotriene A4 hydrolase catalytic domain [64339]
      1. Human (Homo sapiens) [TaxId: 9606] [64340] (15)
        SQ P09960
  5. Neutral endopeptidase (neprilysin) [55502] (1)
    1. Neutral endopeptidase (neprilysin) [55503]
      contains thermolysin-like catalytic domain (residues 419-749)
      the N-terminal half of the structure is multihelical
      1. Human (Homo sapiens) [TaxId: 9606] [55504] (6)
        SQ P08473 54-749
  6. Neurolysin-like [55505] (6)
    combines M2, M3 and M32 families of metalloproteases
    the N-terminal half of the structure is multihelical; the C-terminal half contains the thermolysin-like catalytic domain
    1. Neurolysin (endopeptidase 24.16, thimet oligopeptidase) [55506]
      M3 family member; the thermolysin-like catalytic domain consists of residues 352-674
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55507] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [111081] (1)
        SQ P52888
    2. Thermostable carboxypeptidase 1 [82731]
      M32 (Taq) family member; overall fold is similar to that of neurolysin but is less elaborated
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82732] (3)
    3. Angiotensin converting enzyme, ACE [82733]
      M2 family member; overall fold is similar to that of neurolysin but is less elaborated
      1. Human (Homo sapiens) [TaxId: 9606] [82734] (5)
        SQ P22966
      2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89991] (3)
    4. Angiotensin converting enzyme 2, ACE2 [103125]
      1. Human (Homo sapiens) [TaxId: 9606] [103126] (4)
  7. Anthrax toxin lethal factor, N- and C-terminal domains [69775] (1)
    1. Anthrax toxin lethal factor, N- and C-terminal domains [69776]
      duplication: each domain adopts a thermolysin-like fold, but the proteolytic activity resides only in the C-terminal domain
      1. Bacillus anthracis [TaxId: 1392] [69777] (12)
  8. Leishmanolysin [55499] (1)
    1. Leishmanolysin [55500]
      the catalytic domain is N-terminal (residues 100-272)
      the rest of structure will be classified in future releases
      1. Leishmania major [TaxId: 5664] [55501] (1)
  9. Serralysin-like metalloprotease, catalytic (N-terminal) domain [55508] (4)
    characteristic HEXXHXXGXXH motif and Met located near C-terminus
    1. Metalloprotease [55509]
      the rest of protein is all-beta sandwich containing a parallel beta-helix
      1. Pseudomonas aeruginosa [TaxId: 287] [55510] (3)
        alkaline protease
      2. Serratia marcescens [TaxId: 615] [55511] (4)
        Serralysin
      3. Erwinia chrysanthemi [TaxId: 556] [82735] (5)
        Protease C
      4. Pseudomonas sp., tac ii 18 [TaxId: 306] [82736] (8)
        psychrophilic alkaline protease
  10. Clostridium neurotoxins, catalytic domain [55512] (4)
    1. Botulinum neurotoxin [55513]
      1. Clostridium botulinum, serotype A [TaxId: 1491] [55514] (15)
        SQ P10845 1-419
      2. Clostridium botulinum, serotype B [TaxId: 1491] [55515] (18)
      3. Clostridium botulinum, serotype E [TaxId: 1491] [111082] (2)
        SQ Q00496 1-421
      4. Clostridium butyricum [TaxId: 1492] [160551] (2)
  11. Astacin [55516] (1)
    1. Astacin [55517]
      1. European fresh water crayfish (Astacus astacus) [TaxId: 6715] [55518] (8)
  12. Reprolysin-like [55519] (8)
    Pfam 01421
    1. Snake venom metalloprotease [55520]
      1. Eastern diamondback rattlesnake (Crotalus adamanteus), adamalysin II [TaxId: 8729] [55521] (4)
      2. Western diamonback rattlesnake (Crotalus atrox), atrolysin C [TaxId: 8730] [55522] (3)
      3. Taiwan habu (Trimeresurus mucrosquamatus), atrolysin E [TaxId: 103944] [75495] (4)
      4. Five-pace snake (Agkistrodon acutus), acutolysin A [TaxId: 36307] [55523] (2)
      5. Chinese five-pace snake (Agkistrodon acutus), acutolysin C [TaxId: 36307] [55524] (1)
      6. Terciopelo (Bothrops asper), bap1 [TaxId: 8722] [103127] (1)
      7. Habu (Trimeresurus flavoviridis), Trimerelysin II [TaxId: 88087] [111083] (1)
        SQ P20165
    2. ADAM33 [118046]
      1. Human (Homo sapiens) [TaxId: 9606] [118047] (2)
        SQ Q9BZ11 204-409
  13. TNF-alpha converting enzyme, TACE, catalytic domain [55525] (1)
    1. TNF-alpha converting enzyme, TACE, catalytic domain [55526]
      1. Human (Homo sapiens) [TaxId: 9606] [55527] (12)
  14. Matrix metalloproteases, catalytic domain [55528] (15)
    1. Fibroblast collagenase (MMP-1) [55529]
      1. Human (Homo sapiens) [TaxId: 9606] [55530] (14)
        SQ P03956 32-466
      2. Pig (Sus scrofa) [TaxId: 9823] [55531] (3)
    2. MMP-2 [69778]
      1. Human (Homo sapiens) [TaxId: 9606] [69779] (1)
    3. Neutrophil collagenase (MMP-8) [55532]
      1. Human (Homo sapiens) [TaxId: 9606] [55533] (21)
    4. Gelatinase A [55534]
      1. Human (Homo sapiens) [TaxId: 9606] [55535] (4)
    5. Stromelysin-1 (MMP-3) [55536]
      1. Human (Homo sapiens), fibroblast [TaxId: 9606] [55537] (36)
    6. Matrilysin (MMP-7) [55538]
      1. Human (Homo sapiens) [TaxId: 9606] [55539] (4)
    7. Gelatinase B (MMP-9) [75496]
      1. Human (Homo sapiens) [TaxId: 9606] [75497] (13)
    8. Stromelysin-2 (MMP-10) [103128]
      1. Human (Homo sapiens) [TaxId: 9606] [103129] (1)
    9. Stromelysin-3 (MMP-11) [64341]
      1. Mouse (Mus musculus) [TaxId: 10090] [64342] (1)
    10. Macrophage elastase (MMP-12) [69780]
      1. Human (Homo sapiens) [TaxId: 9606] [69781] (18)
        SQ P39900 106-263 ! SQ P39900 106-264
    11. Collagenase-3 (MMP-13) [55540]
      1. Human (Homo sapiens) [TaxId: 9606] [55541] (34)
      2. Mouse (Mus musculus) [TaxId: 10090] [55542] (1)
    12. Membrane-type matrix metalloproteinase (CDMT1-MMP) [55543]
      1. Human (Homo sapiens) [TaxId: 9606] [55544] (2)
    13. Matrix metalloproteinase-16 (MMP-16) [103130]
      1. Human (Homo sapiens) [TaxId: 9606] [103131] (1)
  15. Predicted metal-dependent hydrolase [103132] (3)
    Pfam 02130; UPF0054; COG0319; MMP-like fold with a different sequence motif in the putative active site
    1. Hypothetical protein Aq_1354 [103133]
      1. Aquifex aeolicus [TaxId: 63363] [103134] (1)
    2. Hypothetical protein YbeY [118048]
      1. Escherichia coli [TaxId: 562] [118049] (1)
        SQ P77385
    3. Hypothetical protein TM1509 [118050]
      1. Thermotoga maritima [TaxId: 2336] [118051] (1)
        SQ Q9X1J7
  16. Caur0242-like [160552] (1)
    Pfam 10103; DUF2342; there is a characteristic HExxH motif but no metal ion bound to it in the first structure.
    1. Uncharacterized protein Caur0242 [160553]
      1. Chloroflexus aurantiacus [TaxId: 1108] [160554] (1)
        SQ A9WCA2 43-391
  17. TTHA0227-like [160555] (2)
    PF06262; DUF1025; minimal zincin fold that retains 3-stranded mixed beta-sheet and contains HExxH motif in the C-terminal helix; no metal ion bound to this motif is observed in the first determined structures
    1. Uncharacterized protein TTHA0227 [160556]
      1. Thermus thermophilus [TaxId: 274] [160557] (2)
        SQ Q5SLR6 2-108
    2. Uncharacterized protein Acel_2062 [160558]
      1. Acidothermus cellulolyticus [TaxId: 28049] [160559] (2)
        SQ A0LWM4 1-113
2. beta-N-acetylhexosaminidase-like domain [55545] (3)
  contains similar fold but lacks its catalytic centre
  uperfamily
  1. beta-N-acetylhexosaminidase domain [55546] (4)
    family GH20
    1. Bacterial chitobiase, Domain 2 [55547]
      1. Serratia marcescens [TaxId: 615] [55548] (4)
    2. beta-N-acetylhexosaminidase, N-terminal domain [64343]
      1. Streptomyces plicatus [TaxId: 1922] [64344] (6)
    3. beta-hexosaminidase B, N-terminal domain [89992]
      1. Human (Homo sapiens) [TaxId: 9606] [89993] (12)
    4. beta-hexosaminidase A [160560]
      1. Human (Homo sapiens) [TaxId: 9606] [160561] (8)
        SQ P06865 23-166
  2. alpha-D-glucuronidase, N-terminal domain [82737] (2)
    family GH67
    1. alpha-D-glucuronidase, N-terminal domain [82738]
      inverting reaction mechanism
      1. Pseudomonas cellulosa [TaxId: 155077] [82739] (5)
      2. Bacillus stearothermophilus [TaxId: 1422] [82740] (7)
  3. Hyaluronidase N-terminal domain-like [143618] (2)
    1. Hyaluronidase N-terminal domain [143619]
      1. Clostridium perfringens [TaxId: 1502] [143620] (6)
        SQ Q8XL08 41-178
    2. Glucosaminidase GH84, N-terminal domain [143621]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143622] (12)
        SQ Q89ZI2 25-147
SH2-like [55549] (1)
3 layers: a/b/a; antiparallel beta-sheet of 5 strands is flaked by two helices
1. SH2 domain [55550] (1)
  uperfamily
  1. SH2 domain [55551] (39)
    Pfam 00017
    1. p56-lck tyrosine kinase [55552]
      1. Human (Homo sapiens) [TaxId: 9606] [55553] (16)
    2. Carboxyl-terminal src kinase (csk) [75498]
      1. Human (Homo sapiens) [TaxId: 9606] [75499] (1)
    3. c-src tyrosine kinase [55556]
      1. Human (Homo sapiens) [TaxId: 9606] [55557] (42)
      2. Chicken (Gallus gallus) [TaxId: 9031] [55558] (3)
      3. Rous sarcoma virus [TaxId: 11886] [69782] (13)
    4. Tyrosine kinase Fyn [55559]
      1. Human (Homo sapiens) [TaxId: 9606] [55560] (3)
    5. Tyrosine phosphatase Syp [55561]
      1. Mouse (Mus musculus) [TaxId: 10090] [55562] (4)
    6. Growth factor receptor-bound protein 2 (GRB2) [55563]
      1. Human (Homo sapiens) [TaxId: 9606] [55564] (25)
    7. Hemopoetic cell kinase Hck [55565]
      1. Human (Homo sapiens) [TaxId: 9606] [55566] (4)
    8. Crk proto-oncogen [82741]
      1. Human (Homo sapiens) [TaxId: 9606] [82742] (3)
    9. Shc adaptor protein [55567]
      1. Human (Homo sapiens) [TaxId: 9606] [55568] (2)
    10. Phosphatidylinositol 3-kinase, p85-alpha subunit [55569]
      1. Cow (Bos taurus) [TaxId: 9913] [55570] (7)
      2. Human (Homo sapiens) [TaxId: 9606] [55571] (2)
      3. Rat (Rattus norvegicus) [TaxId: 10116] [55572] (2)
    11. Proto-oncogen tyrosine kinase [55573]
      1. Human (Homo sapiens) [TaxId: 9606] [55574] (2)
    12. Syk tyrosine kinase [55575]
      1. Human (Homo sapiens) [TaxId: 9606] [55576] (3)
    13. Growth factor receptor-bound protein 10, GRB10 [89994]
      1. Human (Homo sapiens) [TaxId: 9606] [89995] (1)
    14. Growth factor receptor-bound protein 7 [103135]
      1. Human (Homo sapiens) [TaxId: 9606] [103136] (5)
    15. Tyrosine-protein kinase zap-70 [89996]
      1. Human (Homo sapiens) [TaxId: 9606] [89997] (3)
    16. Phospholipase C-gamma-1 [55577]
      1. Cow (Bos taurus) [TaxId: 9913] [55578] (3)
    17. P55 Blk protein tyrosine kinase [55579]
      1. Mouse (Mus musculus) [TaxId: 10090] [55580] (2)
    18. Itk/tsk protein tyrosine kinase [82743]
      1. Mouse (Mus musculus) [TaxId: 10090] [82744] (6)
    19. Abl tyrosine kinase [55581]
      1. Human (Homo sapiens) [TaxId: 9606] [55582] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [89998] (2)
    20. Csk homologous kinase Chk [64345]
      1. Human (Homo sapiens) [TaxId: 9606] [64346] (1)
    21. STAT-1 [55583]
      1. Human (Homo sapiens) [TaxId: 9606] [55584] (1)
    22. STAT3b [55585]
      1. Mouse (Mus musculus) [TaxId: 10090] [55586] (1)
    23. STAT homologue [103137]
      1. Dictyostelium discoideum [TaxId: 44689] [103138] (2)
    24. Cbl [55587]
      1. Human (Homo sapiens) [TaxId: 9606] [55588] (12)
    25. Tyrosine phoshatase shp-2 [55589]
      1. Human (Homo sapiens) [TaxId: 9606] [55590] (1)
    26. The Xlp protein Sap [55591]
      1. Human (Homo sapiens) [TaxId: 9606] [55592] (6)
    27. Ews/fli1 activated transcript 2, Eat2 [89999]
      1. Mouse (Mus musculus) [TaxId: 10090] [90000] (1)
    28. Adaptor protein Aps [103139]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [103140] (2)
    29. Tyrosine-protein kinase 6 (Breast tumor kinase, Brk) [111084]
      1. Human (Homo sapiens) [TaxId: 9606] [111085] (1)
        SQ Q13882 75-174
    30. GRB2-related adaptor protein 2 (MONA, GRID) [111086]
      1. Mouse (Mus musculus) [TaxId: 10090] [111087] (3)
        SQ O89100 53-147
    31. Beta-chimaerin, N-terminal domain [118052]
      includes N-terminal tail and the linker to the next domain
      1. Human (Homo sapiens) [TaxId: 9606] [118053] (1)
        SQ P52757 23-468
    32. Hematopoietic SH2 domain containing protein HSH2D [143623]
      1. Human (Homo sapiens) [TaxId: 9606] [143624] (1)
        SQ Q96JZ2 24-129
    33. Suppressor of cytokine signaling 2, SOCS-2 [160562]
      1. Human (Homo sapiens) [TaxId: 9606] [160563] (1)
        SQ O14508 32-134
    34. Suppressor of cytokine signaling 4, SOCS-4 [160564]
      1. Human (Homo sapiens) [TaxId: 9606] [160565] (1)
        SQ Q8WXH5 274-385
HPr-like [55593] (2)
beta-alpha-beta(2)-alpha-beta-alpha; 2 layers: a/b; antiparallel sheet 1423
1. HPr-like [55594] (1)
  uperfamily
  1. HPr-like [55595] (8)
    1. Histidine-containing phosphocarrier protein (HPr) [55596]
      1. Bacillus subtilis [TaxId: 1423] [55597] (6)
      2. Enterococcus faecalis [TaxId: 1351] [55598] (3)
      3. Escherichia coli [TaxId: 562] [55599] (14)
      4. Mycoplasma capricolum [TaxId: 2095] [55600] (1)
      5. Staphylococcus aureus [TaxId: 1280] [55601] (1)
      6. Staphylococcus carnosus [TaxId: 1281] [55602] (1)
      7. Bacillus megaterium [TaxId: 1404] [118054] (4)
        SQ O69250
    2. Crh, catabolite repression HPr-like protein [69783]
      1. Bacillus subtilis [TaxId: 1423] [69784] (10)
2. Putative transcriptional regulator TM1602, C-terminal domain [75500] (1)
  uperfamily
  1. Putative transcriptional regulator TM1602, C-terminal domain [75501] (1)
    1. Putative transcriptional regulator TM1602, C-terminal domain [75502]
      1. Thermotoga maritima [TaxId: 2336] [75503] (1)
TrkA C-terminal domain-like [116725] (1)
beta-X-beta(2)-X-beta-alpha; pseudo barrel capped by helix at one end; topological similarity to the HPr-like fold
1. TrkA C-terminal domain-like [116726] (1)
  uperfamily
  1. TrkA C-terminal domain-like [116727] (2)
    Pfam 02080
    1. Potassium channel-related protein MthK, C-terminal domain [116728]
      1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [116729] (9)
    2. Hypothetical protein PH0236, C-terminal domain [143625]
      1. Pyrococcus horikoshii [TaxId: 53953] [143626] (4)
        SQ O57975 108-201
Hypothetical protein YjiA, C-terminal domain [90001] (1)
beta-alpha-beta(4)-alpha; 2 layers: a/b; antiparallel sheet 15234; topological similarity to the HPr-like fold
1. Hypothetical protein YjiA, C-terminal domain [90002] (1)
  uperfamily
  1. Hypothetical protein YjiA, C-terminal domain [90003] (1)
    1. Hypothetical protein YjiA, C-terminal domain [90004]
      homologue of the cobalamin biosynthesis protein CobW
      1. Escherichia coli [TaxId: 562] [90005] (1)
YggU-like [69785] (1)
beta(2)-loop-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243; some similarity to the Homing endonuclease-like fold
1. YggU-like [69786] (1)
  uperfamily
  1. YggU-like [69787] (2)
    1. Hypothetical protein YggU [82745]
      1. Escherichia coli, o157 [TaxId: 562] [82746] (2)
    2. Hypothetical protein MTH637 [69788]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69789] (1)
Homing endonuclease-like [55603] (2)
alpha-beta(2)-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel sheet 1243
1. Glucose permease domain IIB [55604] (1)
  uperfamily
  1. Glucose permease domain IIB [55605] (1)
    1. Glucose permease domain IIB [55606]
      1. Escherichia coli [TaxId: 562] [55607] (4)
        there are differences in secondary structure packing between the two NMR-determined structures
2. Homing endonucleases [55608] (2)
  uperfamily
  1. Group I mobile intron endonuclease [55609] (5)
    contains two extra helices in the C-terminal extension
    1. DNA endonuclease I-CreI [55610]
      1. Chlamydomonas reinhardtii [TaxId: 3055] [55611] (13)
        SQ P05725 2-154 ! SQ P05725
    2. DNA endonuclease I-dmoI [55612]
      duplication: contains tandem repeat of this fold
      1. Archaeon Desulfurococcus mobilis [TaxId: 2274] [55613] (2)
    3. DNA endonuclease I-MsoI [90006]
      1. Monomastix sp. cl-1997 [TaxId: 141716] [90007] (1)
    4. DNA endonuclease I-AniI [103141]
      duplication: contains tandem repeat of this fold
      1. Aspergillus nidulans [TaxId: 162425] [103142] (1)
        synonym: Emericella nidulans
    5. DNA endonuclease I-SceI [118055]
      duplication: contains tandem repeat of this fold
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118056] (1)
        SQ P03882
  2. Intein endonuclease [55614] (2)
    duplication: contains tandem repeat of this fold
    1. VMA1-derived endonuclease (VDE) PI-SceI [55615]
      homing endonuclease with protein splicing activity
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55616] (7)
        SQ P17255 284-737
    2. PI-Pfui intein [55617]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [55618] (1)
T-fold [55619] (2)
beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1234
tunnel-shaped: its known members form wide oligomeric barrels different sizes
1. Tetrahydrobiopterin biosynthesis enzymes-like [55620] (4)
  bind purine or pterin in topologically similar sites between subunits
  uperfamily
  1. GTP cyclohydrolase I [55621] (4)
    1. GTP cyclohydrolase I [55622]
      beta-sheets of five subunits form a barrel, closed: n=20, S=20
      1. Escherichia coli [TaxId: 562] [55623] (7)
      2. Human (Homo sapiens) [TaxId: 9606] [55624] (1)
      3. Rat (Rattus norvegicus) [TaxId: 10116] [69790] (3)
        SQ P22288
      4. Thermus thermophilus [TaxId: 274] [143627] (15)
        SQ Q5SH52 32-216
  2. 6-pyruvoyl tetrahydropterin synthase [55625] (4)
    1. 6-pyruvoyl tetrahydropterin synthase [55626]
      beta-sheets of three subunits form a barrel, closed: n=12, S=12
      1. Rat (Rattus norvegicus) [TaxId: 10116] [55627] (3)
      2. Plasmodium falciparum [TaxId: 5833] [118057] (1)
        SQ Q6LEZ4
      3. Caenorhabditis elegans [TaxId: 6239] [143628] (1)
        SQ O02058 1-139
      4. Plasmodium vivax [TaxId: 5855] [143629] (2)
        73% similarity to the Plasmodium falciparum enzyme
  3. DHN aldolase/epimerase [55628] (4)
    beta-sheets of four subunits form a barrel, closed: n=16, S=16
    1. 7,8-dihydroneopterin aldolase [55629]
      1. Staphylococcus aureus [TaxId: 1280] [55630] (15)
        SQ P56740
      2. Bacteria (Mycobacterium tuberculosis) [TaxId: 1773] [103143] (2)
        SQ O06275 2-115
      3. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [111088] (1)
        SQ Q9SF23
    2. 7,8-dihydroneopterin triphosphate epimerase [55631]
      1. Escherichia coli [TaxId: 562] [55632] (1)
  4. Urate oxidase (uricase) [55633] (3)
    1. Urate oxidase (uricase) [55634]
      duplication: one subunit consists of two domains of this fold; beta-sheets of two subunits form a barrel, closed: n=16, S=16
      1. Aspergillus flavus [TaxId: 5059] [55635] (72)
      2. Bacillus sp., strain TB-90 [TaxId: 1409] [111089] (1)
        SQ Q45697 177-482
      3. Arthrobacter globiformis [TaxId: 1665] [143630] (96)
2. ApbE-like [143631] (2)
  duplication: contains two differently decorated beta(2)-alpha(2)-beta(2) subdomains, similar to other T-fold domains; probably does not form the tunnel-shaped oligomers
  uperfamily
  1. ApbE-like [143632] (1)
    Pfam 02424
    1. Hypothetical protein TM1553 [143633]
      1. Thermotoga maritima [TaxId: 2336] [143634] (1)
        SQ Q9X1N9 44-352
  2. DVU1097-like [160566] (1)
    Pfam 04040; DUF375
    1. Hypothetical protein DVU1097 [160567]
      1. Desulfovibrio vulgaris [TaxId: 881] [160568] (1)
        SQ Q72D34 1-248
Cell cycle regulatory proteins [55636] (1)
beta(2)-alpha(2)-beta(2); 2 layers: alpha/beta; antiparallel sheet 1243
can form strand-exchange dimers
1. Cell cycle regulatory proteins [55637] (1)
  uperfamily
  1. Cell cycle regulatory proteins [55638] (4)
    1. suc1 [55639]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [55640] (2)
        in hexamer, the beta-sheets of three dimers form a barrel, closed: n=12, S=12
    2. cks1 [55641]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55642] (1)
    3. CksHs2 [55643]
      1. Human (Homo sapiens) [TaxId: 9606] [55644] (1)
    4. CksHs1 [55645]
      1. Human (Homo sapiens) [TaxId: 9606] [55646] (5)
YonK-like [160569] (1)
intertwined dimer of beta(3)-alpha-beta subunits; assembles further in octamer with formation of a wide 16-stranded beta-barrel
1. YonK-like [160570] (1)
  (Pro)phage and phage-related proteins
  1. Yonk-like [160571] (1)
    Pfam 09642
    1. Uncharacterized protein YonK [160572]
      1. Bacillus subtilis [TaxId: 1423] [160573] (4)
        SQ O31947 2-63
BLIP-like [55647] (2)
alpha(2)-beta(4); 2 layers: alpha/beta
1. beta-lactamase-inhibitor protein, BLIP [55648] (1)
  uperfamily
  1. beta-lactamase-inhibitor protein, BLIP [55649] (1)
    duplication: consists of two clear structural repeats each having this fold
    1. beta-lactamase-inhibitor protein, BLIP [55650]
      1. Streptomyces clavuligerus [TaxId: 1901] [55651] (6)
2. BT0923-like [160574] (1)
  Duplication: tandem repeat of two similar structural subdomains, which associate like the BLIP repeats but differ from them by transposition of the helices
  1. BT0923-like [160575] (2)
    after putative calcium-regulated periplasmic protein BT0923 (PDB ID 3DUE; new)
    1. Putative periplasmic protein BVU2443 [160576]
      1. Bacteroides vulgatus [TaxId: 821] [160577] (2)
        SQ A6L337 20-146
    2. Putative periplasmic protein BVU2987 [160578]
      1. Bacteroides vulgatus [TaxId: 821] [160579] (1)
        SQ A6L4L1 20-145
Ribosomal protein L9 C-domain [55652] (1)
alpha-beta-alpha(2)-beta(2); 2 layers: alpha/beta
1. Ribosomal protein L9 C-domain [55653] (1)
  uperfamily
  1. Ribosomal protein L9 C-domain [55654] (3)
    1. Ribosomal protein L9 C-domain [55655]
      1. Bacillus stearothermophilus [TaxId: 1422] [55656] (5)
      2. Thermus thermophilus [TaxId: 274] [143635] (5)
        SQ Q5SLQ1 55-146
      3. Escherichia coli [TaxId: 562] [160580] (29)
        SQ P0A7R1 59-149
MbtH/L9 domain-like [55657] (2)
beta(2)-alpha-beta-alpha; 3 layers: alpha/beta/alpha
1. L9 N-domain-like [55658] (2)
  uperfamily
  1. Ribosomal protein L9 N-domain [55659] (3)
    1. Ribosomal protein L9 N-domain [55660]
      1. Bacillus stearothermophilus [TaxId: 1422] [55661] (10)
      2. Thermus thermophilus [TaxId: 274] [143636] (5)
        SQ Q5SLQ1 1-55
      3. Escherichia coli [TaxId: 562] [160581] (29)
        SQ P0A7R1 1-58
  2. N-terminal domain of RNase HI [55662] (1)
    1. N-terminal domain of RNase HI [55663]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55664] (1)
2. MbtH-like [160582] (1)
  the first helix is replaced with an extended loop; contains extra C-terminal helix of variable position
  1. MbtH-like [160583] (1)
    Pfam 03621
    1. Uncharacterized protein PA2412 [160584]
      1. Pseudomonas aeruginosa [TaxId: 287] [160585] (2)
        SQ Q9I169 1-72
Tombusvirus P19 core protein, VP19 [103144] (1)
beta(2)-alpha-beta(2)-alpha; 2 layers: alpha/beta; antiparallel sheet: order 2134
1. Tombusvirus P19 core protein, VP19 [103145] (1)
  uperfamily
  1. Tombusvirus P19 core protein, VP19 [103146] (2)
    1. Tombusvirus P19 core protein, VP19 [103147]
      an RNA silencing suppressor
      1. Tomato bushy stunt virus, TBSV [TaxId: 12145] [103148] (1)
      2. Carnation italian ringspot virus, CIRV [TaxId: 39443] [103149] (1)
Ribonuclease PH domain 2-like [55665] (1)
beta(2)-alpha-beta(2)-alpha; 3 layers: alpha/beta/alpha; antiparallel sheet: order 2134
1. Ribonuclease PH domain 2-like [55666] (1)
  uperfamily
  1. Ribonuclease PH domain 2-like [55667] (14)
    1. Ribonuclease PH, domain 2 [103150]
      1. Aquifex aeolicus [TaxId: 63363] [103151] (4)
      2. Pseudomonas aeruginosa [TaxId: 287] [103152] (2)
      3. Bacillus subtilis [TaxId: 1423] [103153] (3)
    2. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5 [55668]
      duplication of two-domain units formed by domains 1-2 and 4-5
      1. Streptomyces antibioticus [TaxId: 1890] [55669] (2)
    3. Exosome complex exonuclease RRP45 [160586]
      1. Human (Homo sapiens) [TaxId: 9606] [160587] (1)
        SQ Q86Y41 185-302
    4. Exosome complex exonuclease RRP42 [160588]
      1. Human (Homo sapiens) [TaxId: 9606] [160589] (1)
        SQ Q15024 192-285
    5. Exosome complex exonuclease 1, ECX1 [160590]
      1. Sulfolobus solfataricus [TaxId: 2287] [160591] (50)
        SQ Q9UXC2 156-241! SQ Q9UXC2 156-248
      2. Archaeoglobus fulgidus [TaxId: 2234] [160592] (6)
        SQ O29757 154-252
    6. Exosome complex exonuclease RRP41 [160593]
      1. Human (Homo sapiens) [TaxId: 9606] [160594] (1)
        SQ Q9NPD3 152-241
    7. Exosome complex exonuclease RRP46 [160595]
      1. Human (Homo sapiens) [TaxId: 9606] [160596] (1)
        SQ Q9NQT4 147-235
    8. Exosome complex exonuclease 2, ECX2 [160597]
      1. Archaeoglobus fulgidus [TaxId: 2234] [160598] (6)
        SQ O29756 179-257
      2. Sulfolobus solfataricus [TaxId: 2287] [160599] (51)
        SQ Q9UXC0 192-275
    9. Exosome complex exonuclease MTR3 [160600]
      1. Human (Homo sapiens) [TaxId: 9606] [160601] (1)
        SQ Q5RKV6 176-270
    10. Exosome complex exonuclease RRP43 [160602]
      1. Human (Homo sapiens) [TaxId: 9606] [160603] (1)
        SQ Q96B26 188-276
Regulatory factor Nef [55670] (1)
alpha(2)-beta(4)-alpha; 3 layers: alpha/beta/alpha
1. Regulatory factor Nef [55671] (1)
  uperfamily
  1. Regulatory factor Nef [55672] (1)
    1. Regulatory factor Nef [55673]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [55674] (4)
CytB endotoxin-like [55675] (1)
core: beta-alpha(2)-beta-alpha(2)-beta(4); 3 layers: a/b/a
1. CytB endotoxin-like [55676] (1)
  uperfamily
  1. CytB endotoxin-like [55677] (2)
    Pfam 01338
    1. Mosquitocidal delta-endotoxin CytB [55678]
      1. Bacillus thuringiensis, strain Kyushuensis [TaxId: 1428] [55679] (1)
    2. Volvatoxin A2 [111090]
      1. Volvariella volvacea, different isoforms [TaxId: 36659] [111091] (4)
        SQ Q6USC4
Class II aaRS and biotin synthetases [55680] (1)
contains large mixed beta-sheet
1. Class II aaRS and biotin synthetases [55681] (4)
  uperfamily
  1. Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain [55682] (28)
    1. Seryl-tRNA synthetase (SerRS) [55683]
      1. Thermus thermophilus, strain hb27 [TaxId: 274] [55684] (4)
    2. Lysyl-tRNA synthetase (LysRS) [55685]
      contains an insertion of LEM/SAP-like HeH motif, residues 337-379
      1. Escherichia coli, gene lysU [TaxId: 562] [55686] (5)
      2. Escherichia coli, gene lysS [TaxId: 562] [55687] (2)
    3. Histidyl-tRNA synthetase (HisRS) [55688]
      1. Escherichia coli [TaxId: 562] [55689] (7)
      2. Staphylococcus aureus [TaxId: 1280] [55690] (1)
      3. Thermus thermophilus [TaxId: 274] [55691] (3)
      4. Archaeon Thermoplasma acidophilum [TaxId: 2303] [143637] (2)
        SQ Q9HLX5 3-329
    4. Glycyl-tRNA synthetase (GlyRS) [55692]
      1. Thermus thermophilus [TaxId: 274] [55693] (3)
    5. Threonyl-tRNA synthetase (ThrRS) [55694]
      1. Escherichia coli [TaxId: 562] [55695] (5)
      2. Staphylococcus aureus [TaxId: 1280] [103154] (2)
    6. Aspartyl-tRNA synthetase (AspRS) [55696]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55697] (3)
      2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [55698] (1)
      3. Thermus thermophilus, AspRS-2 [TaxId: 274] [90008] (1)
        non-discriminating and archaeal-type enzyme
      4. Escherichia coli [TaxId: 562] [55699] (3)
      5. Thermus thermophilus, AspRS-1 [TaxId: 274] [55700] (3)
    7. Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS [55701]
      1. Thermus thermophilus [TaxId: 274] [55702] (9)
        identical sequence to Thermus aquaticus, TaxId: 271
    8. Phenyl-tRNA synthetase (PheRS) beta subunit, PheT, central domain [55703]
      this domain is non-catalytic
      1. Thermus thermophilus [TaxId: 274] [55704] (9)
        identical sequence to Thermus aquaticus, TaxId: 271
    9. Glycyl-tRNA synthetase (GlyRS) alpha chain [75504]
      1. Thermotoga maritima [TaxId: 2336] [75505] (1)
        TM0216
    10. Alanyl-tRNA synthetase (AlaRS) [103155]
      1. Aquifex aeolicus [TaxId: 63363] [103156] (7)
    11. Prolyl-tRNA synthetase (ProRS) [64347]
      1. Thermus thermophilus [TaxId: 274] [64348] (4)
      2. Arhaeon (Methanothermobacter thermautotrophicus) [TaxId: 145262] [90009] (4)
      3. Archaeon (Methanocaldococcus jannaschii) [TaxId: 2190] [90010] (1)
    12. The aaRS-like accessory subunit of mitochondrial polymerase gamma, N-terminal domain [64349]
      1. Mouse (Mus musculus) [TaxId: 10090] [64350] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [143638] (4)
        SQ Q9UHN1 66-355
    13. Asparagine synthetase [55705]
      1. Escherichia coli [TaxId: 562] [55706] (2)
    14. Hypothetical protein PF1951 [103157]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [103158] (1)
        AspRS-related protein
    15. ATP phosphoribosyltransferase regulatory subunit HisZ [118058]
      shares histidine-binding site with the HisRS catalytic domain
      1. Thermotoga maritima [TaxId: 2336] [118059] (1)
        SQ Q9X0D3
      2. Lactococcus lactis [TaxId: 1358] [143639] (8)
        SQ Q02147 6-323
  2. Biotin holoenzyme synthetase [55707] (2)
    1. Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain [55708]
      this structure contains an SH2-like fold
      1. Escherichia coli [TaxId: 562] [55709] (5)
    2. Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain [143640]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [143641] (28)
        SQ O57883 1-188
  3. LplA-like [143642] (6)
    part of Pfam 03099
    1. Lipoyltransferase LipB [143643]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143644] (1)
        SQ Q10404 1-216
    2. LplA-like protein SP1160, N-terminal domain [143645]
      1. Streptococcus pneumoniae [TaxId: 1313] [143646] (1)
        SQ Q97QP1 1-241
    3. Lipoate-protein ligase A [160604]
      1. Streptococcus agalactiae [TaxId: 1311] [160605] (1)
        SQ Q3D8N4 2-270
      2. Thermoplasma acidophilum [TaxId: 2303] [160606] (11)
        SQ Q9HKT1 1-257
    4. Two-domain LplA, N-terminal domain [160607]
      1. Escherichia coli [TaxId: 562] [160608] (6)
        SQ P32099 1-246
    5. Hypothetical protein BH3822 [160609]
      1. Bacillus halodurans [TaxId: 86665] [160610] (1)
        SQ Q9K6A7 12-276
  4. PH0223-like [160611] (1)
    Pfam 04017; DUF366
    1. Uncharacterized protein PH0223 [160612]
      1. Pyrococcus horikoshii [TaxId: 53953] [160613] (6)
        SQ O57962 3-190
Subdomain of clathrin and coatomer appendage domain [55710] (1)
beta-alpha-beta-alpha-beta(4)-alpha; 3 layers: a/b/a; bifurcated antiparallel beta-sheet
1. Subdomain of clathrin and coatomer appendage domain [55711] (2)
  uperfamily
  1. Clathrin adaptor appendage, alpha and beta chain-specific domain [55712] (2)
    1. Alpa-adaptin AP2, C-terminal subdomain [55713]
      1. Mouse (Mus musculus) [TaxId: 10090] [55714] (10)
        SQ P17427 694-938 # 98% sequence identity
    2. Beta2-adaptin AP2, C-terminal subdomain [55715]
      1. Human (Homo sapiens) [TaxId: 9606] [55716] (5)
  2. Coatomer appendage domain [103159] (2)
    1. Coatomer gamma subunit, C-terminal subdomain [103160]
      1. Human (Homo sapiens) [TaxId: 9606] [103161] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [103162] (1)
SCP-like [55717] (1)
alpha-beta(3)-(crossover)-beta-(alpha)-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 32145
1. SCP-like [55718] (4)
  uperfamily
  1. Sterol carrier protein, SCP [55719] (5)
    Pfam 02036
    1. Sterol carrier protein 2 (SCP2) [55720]
      1. Human (Homo sapiens) [TaxId: 9606] [55721] (2)
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55722] (1)
      3. Yellow fever mosquito (Aedes aegypti) [TaxId: 7159] [103163] (1)
    2. SCP2-like domain of MFE-2 [69791]
      1. Human (Homo sapiens) [TaxId: 9606] [69792] (1)
    3. Hypothetical protein TT1886 (TTHA0401) [118060]
      1. Thermus thermophilus [TaxId: 274] [118061] (1)
        SQ Q5SL92
  2. Micothiol-dependent maleylpyruvate isomerase C-terminal domain-like [160614] (1)
    lacking the short edge strand 3
    1. Micothiol-dependent maleylpyruvate isomerase [160615]
      1. Corynebacterium glutamicum [TaxId: 1718] [160616] (2)
        SQ Q8NLC1 161-240
        Cgl3021
  3. Alkylsulfatase C-terminal domain-like [160617] (1)
    1. Alkylsulfatase SdsA1 [160618]
      1. Pseudomonas aeruginosa [TaxId: 287] [160619] (4)
        SQ Q9I5I9 530-655
  4. EF1021 C-terminal domain-like [160620] (3)
    1. Hypothetical protein EF1021 [160621]
      1. Enterococcus faecalis [TaxId: 1351] [160622] (6)
        SQ Q836T6 287-397
    2. Putative acetyltransferase EF2353 [160623]
      1. Enterococcus faecalis [TaxId: 1351] [160624] (6)
        SQ Q831Y9 301-406
    3. Putative acetyltransferase Ava4977 [160625]
      1. Anabaena variabilis [TaxId: 1172] [160626] (1)
        SQ Q3M362 291-395
Ta1353-like [103164] (1)
core: beta-alpha-beta(2)-alpha-beta-alpha-beta; 3 layers: a/b/a; antiparallel beta-sheet of 5 strands; order: 51423;
1. Ta1353-like [103165] (1)
  uperfamily
  1. Ta1353-like [103166] (2)
    Pfam 04008
    1. Hypothetical protein Ta1353 [103167]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [103168] (1)
    2. Hypothetical protein TT1634 (TTHA1091) [118062]
      1. Thermus thermophilus [TaxId: 274] [118063] (1)
        SQ Q5SJC3
Mog1p/PsbP-like [55723] (1)
(beta-hairpin)-beta(3)-alpha-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet of 7 strands; order: 1237654
1. Mog1p/PsbP-like [55724] (4)
  uperfamily
  1. Ran-binding protein mog1p [55725] (1)
    1. Ran-binding protein mog1p [55726]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55727] (2)
  2. PsbP-like [111092] (1)
    Pfam 01789
    1. Oxygen-evolving enhancer protein PsbP [111093]
      1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [111094] (1)
        SQ P18212
  3. PA0094-like [111095] (1)
    segment-swapped dimer; some sequence similarity to the PsbP-like family
    1. Hypothetical protein PA0094 [111096]
      1. Pseudomonas aeruginosa [TaxId: 287] [111097] (1)
        SQ Q9I738
  4. DIP2269-like [160627] (1)
    Pfam 09449; DUF2020
    1. Hypothetical protein DIP2269 [160628]
      1. Corynebacterium diphtheriae [TaxId: 1717] [160629] (2)
        SQ Q6NEK4 2-148
SMI1/KNR4-like [160630] (1)
alpha(4)-beta(4)-alpha; 3 layers: a/b/a; antiparallel beta-sheet, order 1234(meander)
1. SMI1/KNR4-like [160631] (1)
  1. SMI1/KNR4-like [160632] (3)
    Pfam 09346
    1. Uncharacterized protein Lin2918 [160633]
      1. Listeria innocua [TaxId: 1642] [160634] (1)
        SQ Q926X2 1-158
    2. Hypothetical protein PSPTO5518 [160635]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [160636] (1)
        SQ Q87TZ9 1-135
    3. Uncharacterized protein YobK [160637]
      1. Bacillus subtilis [TaxId: 1423] [160638] (2)
        SQ O34596 1-152
Acyl-CoA N-acyltransferases (Nat) [55728] (1)
3 layers: a/b/a; contains mixed beta-sheet
1. Acyl-CoA N-acyltransferases (Nat) [55729] (10)
  uperfamily
  1. N-acetyl transferase, NAT [55730] (60)
    1. Aminoglycoside 6'-N-acetyltransferase [55731]
      1. Enterococcus faecium [TaxId: 1352] [55732] (4)
    2. Aminoglycoside 3-N-acetyltransferase [55733]
      1. Serratia marcescens [TaxId: 615] [55734] (1)
    3. Aminoglycoside 2'-N-acetyltransferase [75506]
      1. Mycobacterium tuberculosis [TaxId: 1773] [75507] (4)
    4. Tabtoxin resistance protein [82747]
      possesses HAT activity
      1. Pseudomonas syringae [TaxId: 317] [82748] (2)
    5. Histone acetyltransferase domain of P300/CBP associating factor, PCAF [55735]
      1. Human (Homo sapiens) [TaxId: 9606] [55736] (1)
    6. Catalytic domain of GCN5 histone acetyltransferase [55737]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55738] (1)
      2. Tetrahymena thermophila [TaxId: 5911] [55739] (9)
        SQ Q27198 49-209
      3. Human (Homo sapiens) [TaxId: 9606] [143647] (1)
        SQ Q92830 497-658
    7. Histone acetyltransferase HPA2 [55740]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55741] (2)
    8. Histone acetyltransferase HAT1 [55742]
      contains additional N- and C-terminal (sub)domains
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55743] (1)
    9. Histone acetyltransferase ESA1 [55744]
      most similar to HAT1 including the N- and C-terminal (sub)domains; the N-terminal domain contains a rudiment CCHC zinc-finger (res. 191-220); the C-terminal domain (res. 351-434) has "winged helix" DNA-binding fold
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55745] (4)
    10. Serotonin N-acetyltranferase [55746]
      1. Sheep (Ovis aries) [TaxId: 9940] [55747] (7)
    11. Glucosamine-phosphate N-acetyltransferase GNA1 [64351]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64352] (3)
    12. Putative acetyltransferase YycN [90011]
      1. Bacillus subtilis [TaxId: 1423] [90012] (2)
    13. Hypothetical protein YqiY [90013]
      1. Bacillus subtilis [TaxId: 1423] [90014] (1)
    14. Probable acetyltransferase YdaF [90015]
      1. Bacillus subtilis [TaxId: 1423] [90016] (1)
    15. Probable acetyltransferase YjcF [103169]
      1. Bacillus subtilis [TaxId: 1423] [103170] (1)
    16. Putative phosphinothricin acetyltransferase YwnH [103171]
      1. Bacillus subtilis [TaxId: 1423] [103172] (1)
    17. Hypothetical protein SA2309 [103173]
      1. Staphylococcus aureus [TaxId: 1280] [103174] (2)
    18. Mycothiol synthase MshD [103175]
      duplication: consists of two NAT domains swapped with the C-terminal strands with both domains binding acetyl-CoA; structural link with the other families
      1. Mycobacterium tuberculosis [TaxId: 1773] [103176] (3)
        Rv0819
    19. Aminoglycoside N-acetyltransferase AAC(6')-IY [111098]
      1. Salmonella enteritidis [TaxId: 149539] [111099] (3)
        SQ Q9R381
      2. Salmonella choleraesuis [TaxId: 28901] [160639] (2)
    20. Protease synthase and sporulation negative regulatory protein PaiA [111100]
      1. Bacillus subtilis [TaxId: 1423] [111101] (1)
        SQ P21340
    21. Hypothetical protein AT1g77540 [118064]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118065] (3)
        SQ Q8LEN2
    22. Hypothetical protein PA0115 [118066]
      1. Pseudomonas aeruginosa [TaxId: 287] [118067] (1)
        SQ Q9I717
    23. Probable acetyltransferase TTHA1209 [118068]
      1. Thermus thermophilus [TaxId: 274] [118069] (2)
        SQ Q5SJ05
    24. Putative acetyltransferase EF0945 [118070]
      1. Enterococcus faecalis [TaxId: 1351] [118071] (1)
        SQ Q836Z8
    25. Putative acetyltransferase PF0028 [118072]
      1. Pyrococcus furiosus [TaxId: 2261] [118073] (1)
        SQ Q8U4Q2
    26. Hypothetical protein PH1933 [143648]
      1. Pyrococcus horikoshii [TaxId: 53953] [143649] (2)
        SQ O59596 1-157
    27. Probable acetyltransferase BC2806 [143650]
      1. Bacillus cereus [TaxId: 1396] [143651] (2)
        SQ Q81CG1 1-140
    28. Diamine acetyltransferase 1 [143652]
      1. Human (Homo sapiens) [TaxId: 9606] [143653] (18)
        SQ P21673 2-170! SQ P21673 3-169
    29. Hypothetical protein YsnE [143654]
      1. Bacillus subtilis [TaxId: 1423] [143655] (1)
        SQ P94562 1-151
    30. Probable acetyltransferase Atu2258 [143656]
      1. Agrobacterium tumefaciens [TaxId: 358] [143657] (1)
        SQ Q7CXI0 1-137
    31. Transcriptional regulator BH1968 [143658]
      1. Bacillus halodurans [TaxId: 86665] [143659] (2)
        SQ Q9KBG0 4-153
    32. Probable acetyltransferase Atu2290 [143660]
      1. Agrobacterium tumefaciens [TaxId: 358] [143661] (4)
        SQ Q8UD38 6-169
    33. Probable acetyltransferase EF1919 [143662]
      1. Enterococcus faecalis [TaxId: 1351] [143663] (2)
        SQ Q833M5 1-157
    34. Putative acetyltransferase EF0244 [143664]
      1. Enterococcus faecalis [TaxId: 1351] [143665] (4)
        SQ Q839D1 1-161
    35. Hypothetical protein PH0736 [143666]
      1. Pyrococcus horikoshii [TaxId: 53953] [143667] (2)
        SQ O58467 1-182
    36. Hypothetical protein Rv1347c/MT1389 [143668]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143669] (8)
        SQ P64819 10-207
    37. Probable acetyltransferase YitI [143670]
      1. Bacillus licheniformis [TaxId: 1402] [143671] (3)
        SQ Q65LG7 2-146
    38. Probable histone acetyltransferase MYST1 [143672]
      ESA1 orthologue
      1. Human (Homo sapiens) [TaxId: 9606] [143673] (1)
        SQ Q9H7Z6 178-448
    39. Hypothetical protein SA2161 [143674]
      1. Staphylococcus aureus [TaxId: 1280] [143675] (2)
        SQ Q7A3W2 1-133
    40. Probable N-acetyltransferase PA0478 [143676]
      1. Pseudomonas aeruginosa [TaxId: 287] [143677] (2)
        SQ Q9I640 3-158
    41. L7/L12-Ribosomal-protein-serine acetyltransferase RimL [143678]
      1. Salmonella typhimurium [TaxId: 90371] [143679] (9)
        SQ Q8ZPC0 1-176
    42. Probable acetyltransferase SP0256 [143680]
      probable SA2161 ortholog
      1. Streptococcus pneumoniae [TaxId: 1313] [143681] (1)
        SQ Q97SR8 1-137
    43. Probable spermine/spermidine acetyltransferase EF1086 [143682]
      1. Enterococcus faecalis [TaxId: 1351] [143683] (1)
        SQ Q836M4 1-146
    44. Putative ribosomal-protein-serine acetyltransferase VC1889 [143684]
      similar to RimL and RimJ
      1. Vibrio cholerae [TaxId: 666] [143685] (1)
        SQ Q9KQV9 1-178
    45. Hypothetical protein PA3270 [143686]
      1. Pseudomonas aeruginosa [TaxId: 287] [143687] (4)
        SQ Q9HYX1 11-193
    46. Diamine acetyltransferase 2 [143688]
      1. Human (Homo sapiens) [TaxId: 9606] [143689] (4)
        SQ Q96F10 3-169
    47. Hypothetical protein MW0638 [143690]
      SA0631 ortholog
      1. Staphylococcus aureus [TaxId: 1280] [143691] (1)
        SQ Q8NXQ8 1-118
    48. Probable acetyltransferase PA4026 [143692]
      1. Pseudomonas aeruginosa [TaxId: 287] [143693] (4)
        SQ Q9HX01 1-153
    49. Hypothetical protein PA4866 [143694]
      Putative phosphinothricin acetyltransferase
      1. Pseudomonas aeruginosa [TaxId: 287] [143695] (3)
        SQ Q9HUU7 3-172! SQ Q9HUU7 4-172
    50. IAA acetyltransferase [143696]
      YvbK ortholojg
      1. Bacillus cereus [TaxId: 1396] [143697] (4)
        SQ Q81FK8 1-152
    51. Phosphinothricin acetyltransferase [143698]
      1. Agrobacterium tumefaciens [TaxId: 358] [143699] (4)
        SQ Q8UGX8 2-164
    52. Putative acetyltransferase PA4794 [143700]
      1. Pseudomonas aeruginosa [TaxId: 287] [143701] (1)
        SQ Q9HV14 1-160
    53. Histone acetyltransferase MYST3 [143702]
      ESA1 orthologue
      1. Human (Homo sapiens) [TaxId: 9606] [143703] (2)
        SQ Q92794 507-776
        solution structure of the zinc-binding motif have been determined in isolation (PDB 1m36, scop_sp 103600)
    54. Probable acetyltranferase Atu2435 [143704]
      1. Agrobacterium tumefaciens [TaxId: 358] [143705] (1)
        SQ Q8UCP8 4-167
    55. Hypothetical protein YvbK (BSu33890) [143706]
      1. Bacillus subtilis [TaxId: 1423] [143707] (4)
        SQ O32248 5-156
    56. Probable N-acetyltransferase RPA1999 [143708]
      1. Rhodopseudomonas palustris [TaxId: 1076] [143709] (1)
        SQ Q6N8A5 2-157
    57. Hypothetical protein TTHA1254 [160640]
      1. Thermus thermophilus [TaxId: 274] [160641] (2)
        SQ Q5SIW0 1-130
  2. N-myristoyl transferase, NMT [55748] (3)
    duplication: consists of two NAT-like domains swapped with the C-terminal strands
    1. N-myristoyl transferase, NMT [55749]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55750] (3)
      2. Yeast (Candida albicans) [TaxId: 5476] [55751] (3)
      3. Human (Homo sapiens) [TaxId: 9606] [143710] (8)
        SQ P30419 155-294! SQ P30419 295-496
  3. Autoinducer synthetase [75508] (2)
    Pfam 00765
    1. Acyl-homoserinelactone synthase EsaI [75509]
      1. Pantoea stewartii subsp. stewartii [TaxId: 66271] [75510] (2)
    2. Autoinducer synthesis protein LasI [111102]
      1. Pseudomonas aeruginosa [TaxId: 287] [111103] (1)
        SQ P33883
  4. FemXAB nonribosomal peptidyltransferases [82749] (3)
    duplication: consists of two NAT-like domains swapped with the C-terminal strands
    1. Methicillin resistance protein FemA [82750]
      transfer glycyl residue from tRNA-Gly
      1. Staphylococcus aureus [TaxId: 1280] [82751] (1)
    2. Peptidyltransferase FemX [103177]
      1. Weissella viridescens [TaxId: 1629] [103178] (8)
    3. Hypothetical protein BT3689 [160642]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [160643] (4)
        SQ Q8A1H2 1-134! SQ Q8A1H2 135-298
  5. Hypothetical protein cg14615-pa [103179] (1)
    duplication: consists of two NAT-like domains swapped with the C-terminal strands
    1. Hypothetical protein cg14615-pa [103180]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [103181] (1)
  6. LFTR-like [143711] (1)
    Pfam 03588; closer relative to the nonribosomal peptidyltransferases (scop_fa 82749); deletion of the N-terminal half of the N-terminal NAT-like domain after the domain duplication/swapping events
    1. Leucyl/phenylalanyl-tRNA-protein transferase, LFTR (Aat) [143712]
      1. Escherichia coli [TaxId: 562] [143713] (1)
        SQ P0A8P1 1-232
  7. Ornithine decarboxylase antizyme-like [143714] (1)
    Pfam 02100; may have evolved different function; putative active site maps to the same location in the common fold
    1. Ornithine decarboxylase antizyme [143715]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [143716] (1)
        SQ P54370 93-218
  8. AstA-like [143717] (1)
    Pfam 04958; contains extra C-terminal domain, similar to the double psi beta-barrel fold (scop_cf 50684) with missing one strand and untangled psi-loops
    1. Arginine N-succinyltransferase, alpha chain, AstA [143718]
      1. Pseudomonas aeruginosa [TaxId: 287] [143719] (1)
        SQ P80357 1-338
  9. Aq_1966-like [143720] (1)
    Pfam 06557; DUF1122; probable biological unit is homotrimeric; may have evolved different function; putative active site maps to the same location in the common fold
    1. Hypothetical protein Aq_1966 [143721]
      1. Aquifex aeolicus [TaxId: 63363] [143722] (3)
        SQ O67778 1-196
  10. EF1021-like [160644] (3)
    duplication: consists of two NAT domains swapped with the C-terminal strands; overall structural similarity to Mycothiol synthase and N-myristoyl transferase (NMT); the similarity to NMT extends to the participation of the protein C-terminus (after the SCP2-like C-terminal domain) in the active site
    1. Putative acetyltransferase EF2353 [160645]
      1. Enterococcus faecalis [TaxId: 1351] [160646] (6)
        SQ Q831Y9 10-300
    2. Putative acetyltransferase Ava4977 [160647]
      1. Anabaena variabilis [TaxId: 1172] [160648] (1)
        SQ Q3M362 8-290
    3. Hypothetical protein EF1021 [160649]
      1. Enterococcus faecalis [TaxId: 1351] [160650] (6)
        SQ Q836T6 2-286
Gelsolin-like [55752] (3)
3 layers: a/b/a; contains mixed beta-sheet
1. Actin depolymerizing proteins [55753] (2)
  uperfamily
  1. Gelsolin-like [55754] (5)
    1. Villin, domain 1 (res. 1-126) [55755]
      1. Chicken (Gallus gallus) [TaxId: 9031] [55756] (2)
    2. Severin, domain 2 [55757]
      1. Dictyostelium discoideum [TaxId: 44689] [55758] (3)
    3. Gelsolin [55759]
      consists of six similar domains
      1. Horse (Equus caballus) [TaxId: 9796] [55760] (2)
        SQ Q28372 1-346
      2. Human (Homo sapiens) [TaxId: 9606] [55761] (60)
        SQ P20065 55-179
    4. Macrophage capping protein Cap G [75511]
      1. Human (Homo sapiens) [TaxId: 9606] [75512] (2)
  2. Cofilin-like [55762] (11)
    1. Cofilin (actin depolymerizing factor, ADF) [55763]
      1. Plant (Arabidopsis thaliana), ADF1 [TaxId: 3702] [55764] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55765] (3)
      3. Acanthamoeba castellanii, actophorin [TaxId: 5755] [55766] (2)
      4. Human (Homo sapiens), non-muscle isoform [TaxId: 9606] [111104] (2)
        SQ P23528
    2. Cofilin-like domain of actin-binding protein abp1p [69793]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69794] (1)
    3. Destrin [55767]
      1. Human and pig (Homo sapiens) and (Sus scrofa) [TaxId: 9606] [55768] (2)
        identical sequence in both species
    4. Adf-H domain of twinfilin isoform-1 [82752]
      interacts only with G-actin
      1. Mouse (Mus musculus) [TaxId: 10090] [82753] (1)
    5. Coactosin-like protein Cotl1 (Clp) [111105]
      1. Mouse (Mus musculus) [TaxId: 10090] [111106] (2)
        SQ Q9CQI6
      2. Human (Homo sapiens) [TaxId: 9606] [111107] (5)
        SQ Q14019
    6. Glia maturation factor beta, GMF-beta [111108]
      1. Mouse (Mus musculus) [TaxId: 10090] [111109] (1)
        SQ Q9CQI3
    7. Glia maturation factor gamma, GMF-gamma [111110]
      1. Mouse (Mus musculus) [TaxId: 10090] [111111] (2)
        SQ Q9ERL7
2. C-terminal, gelsolin-like domain of Sec23/24 [82754] (1)
  uperfamily
  1. C-terminal, gelsolin-like domain of Sec23/24 [82755] (2)
    1. Sec23 [82756]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82757] (3)
    2. Sec24 [82758]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82759] (4)
3. FLJ32549 C-terminal domain-like [160651] (1)
  alpha-beta(2)-alpha-beta(3)-alpha; similar to the Roadblock/LC7 domain
  1. FLJ32549 C-terminal domain-like [160652] (1)
    C-terminal part of Pfam 09404; DUF2003
    1. Hypothetical protein BC048403 [160653]
      FLJ32549 ortholog
      1. Mouse (Mus musculus) [TaxId: 10090] [160654] (1)
        SQ Q6P1I3 295-440
PHP14-like [143723] (1)
beta(3)-alpha-beta(2)-alpha-beta; 3 layers, a/b/a; mixed beta-sheet, half-barrel, order: 132456; strands 2 and 5 are antiparallel to the rest
1. PHP14-like [143724] (2)
  uperfamily
  1. Janus/Ocnus [143725] (1)
    Pfam 05005
    1. Phosphohistidine phosphatase 1, PHP14 [143726]
      Janus-A homolog
      1. Human (Homo sapiens) [TaxId: 9606] [143727] (7)
        SQ Q9NRX4 1-125! SQ Q9NRX4 2-121! SQ Q9NRX4 5-122
  2. PPK middle domain-like [143728] (2)
    central part of Pfam 02503
    1. Polyphosphate kinase, PPK [143729]
      1. Porphyromonas gingivalis [TaxId: 837] [143730] (2)
        SQ Q7MTR1 113-317
      2. Escherichia coli [TaxId: 562] [143731] (4)
        SQ P0A7B1 107-314
Profilin-like [55769] (10)
core: 2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha
1. Profilin (actin-binding protein) [55770] (1)
  alpha-beta(2)-alpha-beta(5)-alpha
  uperfamily
  1. Profilin (actin-binding protein) [55771] (8)
    1. Profilin (actin-binding protein) [55772]
      1. Cow (Bos taurus) [TaxId: 9913] [55773] (3)
      2. Human (Homo sapiens), isoform I [TaxId: 9606] [55774] (9)
      3. Human (Homo sapiens), isoform II [TaxId: 9606] [55775] (1)
      4. Acanthamoeba castellanii [TaxId: 5755] [55776] (5)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55777] (2)
      6. Birch (Betula verrucosa) [TaxId: 3505] [55778] (1)
      7. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [55779] (2)
      8. Para rubber tree (Hevea brasiliensis), hevb8 [TaxId: 3981] [55780] (1)
2. GAF domain-like [55781] (4)
  alpha(2)-beta(3)-alpha-beta(3)-alpha; antiparallel beta-sheet: order 321654
  uperfamily
  1. GAF domain [55782] (8)
    1. Hypothetical protein ykl069wp [55783]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55784] (1)
    2. 3',5'-cyclic nucleotide phosphodiesterase 2A, GAF A and GAF B domains [82760]
      GAF B is the nucleotide binding domain; the two domains are connected with a long helix;
      1. Mouse (Mus musculus) [TaxId: 10090] [82761] (1)
    3. Hypothetical protein YebR [103182]
      1. Escherichia coli [TaxId: 562] [103183] (1)
    4. Sensor protein PhyB2 [160655]
      1. Rhodopseudomonas palustris [TaxId: 1076] [160656] (2)
        SQ Q6N5G2 140-333
    5. Phytochrome-like protein Cph1 [160657]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160658] (1)
        SQ Q55168 131-326
    6. Sensor protein CYB2465 [160659]
      1. Synechococcus sp. [TaxId: 1131] [160660] (1)
        SQ Q2JIZ5 31-200
    7. Bacteriophytochrome BphP [160661]
      1. Pseudomonas aeruginosa [TaxId: 287] [160662] (8)
        SQ Q9HWR3 118-309
      2. Deinococcus radiodurans [TaxId: 1299] [160663] (3)
        SQ Q9RZA4 135-321! SQ Q9RZA4 137-325
  2. IclR ligand-binding domain-like [75513] (3)
    Pfam 01614
    1. Transcriptional regulator IclR, C-terminal domain [75514]
      1. Thermotoga maritima [TaxId: 2336] [75515] (1)
      2. Escherichia coli [TaxId: 562] [111112] (9)
        SQ P16528 98-272
    2. Transcriptional regulator AllR, C-terminal domain [111113]
      1. Escherichia coli [TaxId: 562] [111114] (1)
        SQ P77734 97-269
  3. HrcA C-terminal domain-like [111115] (1)
    Pfam 01628; contains insert domain (140-229) of the Enolase N-terminal domain-like fold (scop_cf 54825)
    1. Heat-inducible transcription repressor HrcA, C-terminal domain [111116]
      1. Thermotoga maritima [TaxId: 2336] [111117] (1)
        SQ Q9WZV5
  4. Phytochrome-specific domain [160664] (2)
    Pfam 00360
    1. Bacteriophytochrome BphP [160665]
      1. Pseudomonas aeruginosa [TaxId: 287] [160666] (8)
        SQ Q9HWR3 310-494
    2. Phytochrome-like protein Cph1 [160667]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160668] (1)
        SQ Q55168 327-514
3. PYP-like sensor domain (PAS domain) [55785] (7)
  alpha-beta(2)-alpha(2)-beta(3)
  uperfamily
  1. PYP-like [55786] (2)
    1. Photoactive yellow protein, PYP [55787]
      1. Ectothiorhodospira halophila [TaxId: 1053] [55788] (43)
        SQ P16113
    2. PYP domain of sensor histidine kinase Ppr [82762]
      1. Rhodospirillum centenum [TaxId: 34018] [82763] (1)
  2. Heme-binding PAS domain [55789] (3)
    1. Histidine kinase FixL heme domain [55790]
      1. Rhizobium meliloti [TaxId: 382] [55791] (2)
      2. Bradyrhizobium japonicum [TaxId: 375] [55792] (17)
        SQ P23222 152-270
    2. Direct oxygen sensor protein, DOS [111118]
      Heme-regulated cyclic AMP phosphodiesterase; formerly hypothetical protein YddU
      1. Escherichia coli [TaxId: 562] [111119] (6)
        SQ P76129 8-126 ! SQ P76129 12-124
  3. Flavin-binding PAS domain [88853] (3)
    contains PAC motif
    1. Photoreceptor phy3 flavin-binding domain, lov2 [64354]
      1. Maidenhair fern (Adiantum capillus-veneris) [TaxId: 13818] [64355] (2)
    2. Putative blue light receptor, phot-lov1 domain [90017]
      1. Green algae (Chlamydomonas reinhardtii) [TaxId: 3055] [90018] (3)
    3. Erg potassium channel, N-terminal domain [55794]
      1. Human (Homo sapiens) [TaxId: 9606] [55795] (1)
  4. N-terminal PAS domain of Pas kinase [82764] (1)
    1. N-terminal PAS domain of Pas kinase [82765]
      1. Human (Homo sapiens) [TaxId: 9606] [82766] (1)
  5. Hypoxia-inducible factor Hif2a, C-terminal domain [103184] (1)
    contains PAC motif
    1. Hypoxia-inducible factor Hif2a, C-terminal domain [103185]
      endothelial pas domain protein 1, EPAS-1
      1. Human (Homo sapiens) [TaxId: 9606] [103186] (1)
  6. PAS domain of steroid receptor coactivator 1A, NCo-A1 [103187] (1)
    1. PAS domain of steroid receptor coactivator 1A, NCo-A1 [103188]
      1. Mouse (Mus musculus) [TaxId: 10090] [103189] (1)
  7. BphP N-terminal domain-like [160669] (4)
    Pfam 08446; PAS_2
    1. Sensor protein PhyB2 [160670]
      1. Rhodopseudomonas palustris [TaxId: 1076] [160671] (2)
        SQ Q6N5G2 26-139
    2. Bacteriophytochrome BphP [160672]
      1. Deinococcus radiodurans [TaxId: 1299] [160673] (3)
        SQ Q9RZA4 4-130! SQ Q9RZA4 5-130
      2. Pseudomonas aeruginosa [TaxId: 287] [160674] (8)
        SQ Q9HWR3 5-117
    3. Phytochrome-like protein Cph1 [160675]
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [160676] (1)
        SQ Q55168 4-130
4. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75516] (1)
  alpha(2)-beta(2)-alpha(2)-beta(3)-alpha; possibly related to the PAS domain
  uperfamily
  1. Pheromone-binding domain of LuxR-like quorum-sensing transcription factors [75517] (1)
    1. Transcription factor TraR, N-terminal domain [75518]
      1. Agrobacterium tumefaciens [TaxId: 358] [75519] (2)
5. Sensory domain-like [103190] (3)
  alpha(2)-beta(2)-alpha(2)-beta(3); possibly related to the PAS domain
  uperfamily
  1. Sensory domain of two-component sensor kinase [103191] (2)
    1. Sensor kinase CitA [103192]
      citrate-binding domain
      1. Klebsiella pneumoniae [TaxId: 573] [103193] (5)
    2. Fumarate sensor DcuS [103194]
      1. Escherichia coli [TaxId: 562] [103195] (2)
  2. YkuI C-terminal domain-like [143732] (2)
    PfamB 021678
    1. Hypothetical protein YkuI, C-terminal domain [143733]
      1. Bacillus subtilis [TaxId: 1423] [143734] (2)
        SQ O35014 263-407
    2. GGDEF family protein VP0354 [160677]
      N-terminal region, consist of two sensory domain-like domains; there is a canonical sensory (PAS) domain in the middle region
      1. Vibrio parahaemolyticus [TaxId: 670] [160678] (4)
        SQ Q87SR8 207-299! SQ Q87SR8 35-206
  3. LuxQ-periplasmic domain-like [160679] (1)
    Pfam 09308; two-domain arrangement similar to the YkuI C-terminal domain-like
    1. Autoinducer 2 sensor kinase/phosphatase LuxQ [160680]
      1. Vibrio harveyi [TaxId: 669] [160681] (4)
        SQ P54302 51-271! SQ P54302 52-270
6. SNARE-like [64356] (4)
  beta(2)-alpha-beta(3)-alpha(2)
  uperfamily
  1. Synatpobrevin N-terminal domain [64357] (2)
    1. Sec22b [64358]
      1. Mouse (Mus musculus) [TaxId: 10090] [64359] (1)
    2. Synaptobrevin homolog 1 ykt6 [64360]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64361] (2)
  2. Sedlin (SEDL) [82767] (1)
    1. Sedlin (SEDL) [82768]
      1. Mouse (Mus musculus) [TaxId: 10090] [82769] (3)
  3. Clathrin coat assembly domain [75521] (2)
    1. Mu2 adaptin (clathrin coat assembly protein AP50) [75522]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [75523] (1)
    2. Sigma2 adaptin (clathrin coat assembly protein AP17) [75524]
      1. Mouse (Mus musculus) [TaxId: 10090] [75525] (1)
  4. SRP alpha N-terminal domain-like [90019] (2)
    1. Srx domain of the signal recognition particle receptor alpha-subunit [90020]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [90021] (1)
    2. Signal recognition particle receptor alpha subunit, N-terminal domain [143735]
      1. Human (Homo sapiens) [TaxId: 9606] [143736] (2)
        SQ P08240 1-129
7. Roadblock/LC7 domain [103196] (1)
  alpha-beta(2)-alpha-beta(3)-alpha; structurally most similar to the SNARE-like superfamily with a circular permutation of the terminal helices
  uperfamily
  1. Roadblock/LC7 domain [103197] (6)
    Pfam 03259
    1. Giding protein MglB [103198]
      1. Thermus thermophilus [TaxId: 274] [103199] (1)
    2. MEK binding partner 1, MP1 [111120]
      remote homolog that forms the characteristic complex structures with other members
      1. Human (Homo sapiens) [TaxId: 9606] [111121] (2)
        SQ Q9UHA4
      2. Mouse (Mus musculus) [TaxId: 10090] [111122] (2)
        SQ O88653
    3. Late endosomal/lysosomal Mp1 interacting protein p14 [111123]
      1. Mouse (Mus musculus) [TaxId: 10090] [111124] (5)
        SQ Q9JHS3
    4. Dynein light chain 2A, cytoplasmic [118074]
      1. Human (Homo sapiens) [TaxId: 9606] [118075] (8)
        SQ Q9NP97
      2. Mouse (Mus musculus) [TaxId: 10090] [160682] (2)
        SQ P62627 1-95
8. YeeU-like [143737] (1)
  beta(2)-alpha-beta(3); 2 layers, a/b; there is an oligomerization interface instead of the 'missing' helical layer
  uperfamily
  1. YagB/YeeU/YfjZ-like [143738] (3)
    Pfam 06154
    1. Hypothetical protein YfjZ [143739]
      1. Escherichia coli [TaxId: 562] [143740] (2)
        SQ P52141 1-105
    2. Hypothetical protein YeeU [143741]
      1. Escherichia coli [TaxId: 562] [143742] (2)
        SQ P76364 16-122
      2. Shigella flexneri [TaxId: 623] [143743] (2)
        SQ Q83JN9 4-120
9. GlcG-like [143744] (1)
  alpha-beta(2)-alpha(3)-beta(2)-alpha; similar to the Roadblock/LC7 domain
  uperfamily
  1. GlcG-like [143745] (1)
    Pfam 03928; DUF336
    1. DhaI homolog [143746]
      1. Klebsiella pneumoniae [TaxId: 573] [143747] (4)
        SQ Q48422 2-143
10. YNR034W-A-like [160683] (1)
  1. YNR034W-A-like [160684] (1)
    1. Uncharacterized protein YNR034W-A [160685]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [160686] (1)
        SQ Q3E841 1-98
Ligand-binding domain in the NO signalling and Golgi transport [111125] (1)
an N-terminal helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomain enclose a ligand-binding cavity
1. Ligand-binding domain in the NO signalling and Golgi transport [111126] (3)
  uperfamily
  1. H-NOX domain [111127] (1)
    binds heme between the N-terminal 4-helical bundle and the C-terminal alpha-beta(2)-alpha-beta(2) subdomains
    1. Methyl-accepting chemotaxis protein [111128]
      1. Thermoanaerobacter tengcongensis [TaxId: 119072] [111129] (4)
        SQ Q8RBX6 1-191
  2. TRAPP components [118076] (2)
    Pfam 04051; form homo- and hetero-dimers with the first two helices of one subunit complementing the fold of the other subunit to the H-NOX domain fold
    1. Trafficking protein particle complex subunit 3, Bet3 homolog [118077]
      covalently linked long fatty acid occupies the ligand-binding cavity
      1. Mouse (Mus musculus) [TaxId: 10090] [118078] (3)
        SQ O55013 9-173
    2. TRAPPC5, similar to trafficking protein particle complex 5 [160687]
      1. Zebrafish (Brachydanio rerio) [TaxId: 7955] [160688] (2)
        SQ Q6DGL5 21-188
  3. MJ1460-like [160689] (1)
    C-terminal part corresponds to Pfam 02830; V4R (vinyl 4 reductase) domain
    1. Hypothetical protein MJ1460 [160690]
      1. Methanococcus jannaschii [TaxId: 2190] [160691] (2)
        SQ Q58855 5-156
Phage tail protein-like [143748] (1)
alpha-beta-X-beta(2)-alpha-beta(2); 2 layers: a/b; mixed beta-sheet: order 12354, strands 1 and 2 are parallel
1. Phage tail protein-like [143749] (2)
  Can form ring, tube-like oligomers, where the subunit beta-sheets are joined in a single beta-sheet (or barrel)
  uperfamily
  1. Lambda phage gpU-like [143750] (1)
    Pfam 06141
    1. Minor tail protein gpU [143751]
      1. Bacteriophage lambda [TaxId: 10710] [143752] (1)
        SQ P03732 2-130
  2. STM4215-like [143753] (1)
    1. Putative cytoplasmic protein STM4215 [143754]
      forms a ring-like hexamer; possible prophage protein
      1. Salmonella typhimurium [TaxId: 90371] [143755] (6)
        SQ Q8ZKJ0 1-134
PR-1-like [55796] (1)
alpha-beta-alpha-beta-alpha(2)-beta(2); 3 layers, alpha/beta/alpha; mixed sheet: order 1342
1. PR-1-like [55797] (1)
  uperfamily
  1. PR-1-like [55798] (4)
    Pfam 00188; groups mammalian SCP/TPX1; insects AG3/AG5; fungi SC7/SC14 and plant PR-1
    1. Pathogenesis-related protein 1 (PR1) [55799]
      1. Tomato (Lycopersicon esculentum), P14a [TaxId: 4081] [55800] (1)
    2. Insect allergen 5 (AG5) [55801]
      1. Yellow jacket (Vespula vulgaris), Ves v 5 [TaxId: 7454] [55802] (1)
    3. Golgi-associated PR-1 protein [111130]
      1. Human (Homo sapiens) [TaxId: 9606] [111131] (1)
        SQ Q9H4G4
    4. Cysteine-rich secretory protein (SteCRISP) [118079]
      1. Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] [118080] (1)
        SQ P60623 13-233
Phoshotransferase/anion transport protein [55803] (1)
beta-alpha(2)-beta(3)-alpha(3); 3 layers, alpha/beta/alpha; mixed sheet: order 1342; loop crossing
1. Phoshotransferase/anion transport protein [55804] (2)
  uperfamily
  1. IIA domain of mannitol-specific and ntr phosphotransferase EII [55805] (3)
    1. Nitrogen regulatory bacterial protein IIa-ntr [55806]
      1. Escherichia coli [TaxId: 562] [55807] (1)
    2. Phosphotransferase IIa-mannitol [55808]
      1. Escherichia coli [TaxId: 562] [55809] (2)
    3. Putative PTS protein STM3784 [118081]
      1. Salmonella typhimurium [TaxId: 90371] [118082] (1)
        SQ Q8ZL18
  2. Anion transport protein, cytoplasmic domain [64362] (1)
    elaborated with additional secondary structures
    1. Erythrocite membrane Band 3 [64363]
      1. Human (Homo sapiens) [TaxId: 9606] [64364] (1)
Nudix [55810] (1)
beta(2)-alpha-beta(3)-alpha; 3 layers: alpha/beta/alpha; mixed sheet
contains beta-grasp motif
1. Nudix [55811] (7)
  uperfamily
  1. MutT-like [55812] (20)
    1. Nucleoside triphosphate pyrophosphorylase (MutT) [55813]
      1. Escherichia coli [TaxId: 562] [55814] (6)
    2. Coenzyme A pyrophosphatase [90022]
      1. Deinococcus radiodurans [TaxId: 1299] [90023] (2)
    3. ADP-ribose pyrophosphatase [64365]
      1. Escherichia coli [TaxId: 562] [64366] (5)
      2. Mycobacterium tuberculosis [TaxId: 1773] [103200] (5)
        gene Rv1700
      3. Thermus thermophilus [TaxId: 274] [118083] (11)
        SQ Q84CU3
    4. ADP-ribose pyrophosphatase homologue YffH [103201]
      1. Escherichia coli [TaxId: 562] [103202] (1)
    5. ADP compounds hydrolase NudE [103203]
      1. Escherichia coli [TaxId: 562] [103204] (2)
    6. NUDT9 (mitochondrial ADP-ribose pyrophosphatase) [103205]
      1. Human (Homo sapiens) [TaxId: 9606] [103206] (2)
    7. 7,8-dihydro-8-oxoguanine triphosphatase Hmth1 [103207]
      1. Human (Homo sapiens) [TaxId: 9606] [103208] (1)
    8. Hypothetical protein DR1025 [103209]
      1. Deinococcus radiodurans [TaxId: 1299] [103210] (4)
    9. Diadenosine tetraphosphate hydrolase (Ap4A hydrolase) [64367]
      1. Narrow-leaved blue lupine (Lupinus angustifolius) [TaxId: 3871] [64368] (2)
      2. Caenorhabditis elegans [TaxId: 6239] [75526] (2)
      3. Human (Homo sapiens) [TaxId: 9606] [118084] (3)
        SQ P50583
    10. Hypothetical protein PAE3301 [75527]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [75528] (3)
    11. Hypothetical protein EF1141 [143756]
      1. Enterococcus faecalis [TaxId: 1351] [143757] (1)
        SQ Q836H1 2-148
    12. AP6A hydrolase Ndx1 [143758]
      1. Thermus thermophilus [TaxId: 274] [143759] (6)
        SQ Q75UV1 1-126
    13. Hypothetical protein NE0184 [143760]
      1. Nitrosomonas europaea [TaxId: 915] [143761] (1)
        SQ Q82XR9 4-149
    14. Hypothetical protein SP1235 (spr1115) [143762]
      1. Streptococcus pneumoniae [TaxId: 1313] [143763] (1)
        SQ Q97QH6 1-155
    15. U8 snorna-binding protein x29 [143764]
      nuclear decapping enzyme
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [143765] (12)
        SQ Q6TEC1 14-209
    16. Diphosphoinositol polyphosphate phosphohydrolase [143766]
      1. Human (Homo sapiens) [TaxId: 9606] [143767] (2)
        SQ O95989 8-142
  2. MutY C-terminal domain-like [103211] (2)
    1. Adenine glycosylase MutY, C-terminal domain [103212]
      1. Bacillus stearothermophilus [TaxId: 1422] [103213] (3)
    2. A/G-specific adenine DNA glycosylase [143768]
      MutY homolog
      1. Human (Homo sapiens) [TaxId: 9606] [143769] (1)
        SQ Q9UIF7 356-497
  3. NADH pyrophosphatase [103214] (1)
    duplication: consists of two structurally similar domains separated by a rubredoxin-like zinc finger; the N-terminal domain has a rudiment Nudix fold, the C-terminal, probably catalytic, domain has the canonical fold
    1. NADH pyrophosphatase [103215]
      1. Escherichia coli [TaxId: 562] [103216] (1)
  4. IPP isomerase-like [64369] (4)
    1. Isopentenyl diphosphate isomerase [64370]
      1. Escherichia coli [TaxId: 562] [64371] (25)
        SQ Q46822
    2. Hypothetical protein DR0079 [103217]
      1. Deinococcus radiodurans [TaxId: 1299] [103218] (1)
      2. Deinococcus radiodurans str. R1 (Deinococcus radiodurans R1) [TaxId: 243230] [160692] (2)
    3. Hypothetical protein YfcD [143770]
      1. Escherichia coli [TaxId: 562] [143771] (3)
        SQ P65556 8-168
  5. GDP-mannose mannosyl hydrolase NudD [111132] (1)
    1. GDP-mannose mannosyl hydrolase NudD [111133]
      1. Escherichia coli [TaxId: 562] [111134] (5)
        SQ P32056
  6. BT0354 N-terminal domain-like [143772] (2)
    accosiated with the C-terminal "winged helix" domain (scop_sf 46785)
    1. Hypothetical protein EF2700, N-terminal domain [143773]
      includes extra N-terminal alpha-hairpin, separated by a linker peptide
      1. Enterococcus faecalis [TaxId: 1351] [143774] (2)
        SQ Q830S2 3-204
    2. Hypothetical protein BT0354, N-terminal domain [143775]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [143776] (4)
        SQ Q8AAV8 3-149
  7. mRNA decapping enzyme-like [143777] (1)
    part of Pfam 00293
    1. mRNA decapping enzyme Dcp2p catalytic domain [143778]
      1. Schizosaccharomyces pombe [TaxId: 4896] [143779] (1)
        SQ O13828 95-245
5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55815] (1)
core: alpha-beta(2)-alpha-beta(2)-alpha-beta; 3 layers; mixed sheet: order 31425
1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55816] (1)
  uperfamily
  1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55817] (3)
    1. 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain [55818]
      1. Escherichia coli [TaxId: 562] [55819] (8)
        SQ P07024 26-550
      2. Candida albicans [TaxId: 5476] [160693] (2)
        SQ Q5A5Q7 338-561
      3. Thermus thermophilus [TaxId: 274] [160694] (1)
        SQ Q5SIP1 330-534
YrdC/RibB [55820] (1)
core: alpha-beta(2)-alpha-beta-alpha(2)-beta(2)-alpha-beta-alpha-beta; 3 layers; mixed twisted sheet of 7 strands; order 7126354; strands 7 and 1 are parallel to each other
1. YrdC/RibB [55821] (2)
  uperfamily
  1. YrdC-like [55822] (3)
    contains two additional strands in the C-terminal extension
    1. Hypothetical protein YrdC [55823]
      1. Escherichia coli [TaxId: 562] [55824] (1)
    2. Hypothetical protein YciO [75529]
      1. Escherichia coli [TaxId: 562] [75530] (2)
    3. Hypothetical protein MTH1692 [75531]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75532] (1)
  2. 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [64372] (4)
    contains one additional helix in the C-terminal extension
    1. 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB [64373]
      1. Escherichia coli [TaxId: 562] [64374] (3)
      2. Magnaporthe grisea [TaxId: 148305] [75533] (5)
      3. Archaeon Methanocaldococcus jannaschii [TaxId: 2190] [103219] (3)
        SQ Q60364
      4. Candida albicans [TaxId: 5476] [111135] (4)
        SQ Q5A3V6
GIY-YIG endonuclease [82770] (1)
beta(2)-alpha(2)-beta-alpha-(beta); strand 4 is very short; 3 layers; antiparallel (mixed) beta-sheet; order 312(4)
1. GIY-YIG endonuclease [82771] (1)
  uperfamily
  1. GIY-YIG endonuclease [82772] (1)
    1. Homing endonuclease I-TevI [82773]
      intron-associated endonuclease 1
      1. Bacteriophage T4 [TaxId: 10665] [82774] (2)
YbaK/ProRS associated domain [55825] (1)
core: alpha-beta-alpha-beta(2)-(alpha-beta)2-alpha-beta(2)-alpha-beta; 3 layers; bifurcated mixed sheet
1. YbaK/ProRS associated domain [55826] (1)
  uperfamily
  1. YbaK/ProRS associated domain [55827] (4)
    Pfam 04073
    1. Hypothetical protein HI1434 (YbaK homologue) [55828]
      1. Haemophilus influenzae [TaxId: 727] [55829] (2)
    2. Hypothetical protein CC0111 [103220]
      annotated as putative DNA-binding protein
      1. Caulobacter crescentus [TaxId: 155892] [103221] (1)
    3. Hypothetical protein Atu3699 [111136]
      1. Agrobacterium tumefaciens, strain C58 [TaxId: 358] [111137] (1)
        SQ Q8U9M7
    4. Hypothetical protein APE2540 [118085]
      1. Aeropyrum pernix [TaxId: 56636] [118086] (1)
        SQ Q9Y8U3
Thymidylate synthase/dCMP hydroxymethylase [55830] (1)
contains large mixed beta-sheet
1. Thymidylate synthase/dCMP hydroxymethylase [55831] (1)
  uperfamily
  1. Thymidylate synthase/dCMP hydroxymethylase [55832] (10)
    1. Thymidylate synthase [55833]
      1. Escherichia coli [TaxId: 562] [55834] (56)
      2. Lactobacillus casei [TaxId: 1582] [55835] (39)
      3. Bacillus subtilis [TaxId: 1423] [55836] (5)
      4. Bacteriophage T4 [TaxId: 10665] [55837] (1)
      5. Pneumocystis carinii [TaxId: 4754] [55838] (2)
      6. Rat (Rattus norvegicus) [TaxId: 10116] [55839] (2)
      7. Human (Homo sapiens) [TaxId: 9606] [55840] (5)
    2. Bifunctional enzyme dihydrofolate reductase-thymidylate synthase, TS domain [55841]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [88964] (2)
      2. Cryptosporidium hominis [TaxId: 237895] [100887] (8)
    3. dCMP hydroxymethylase [55843]
      1. Bacteriophage T4 [TaxId: 10665] [55844] (3)
Thymidylate synthase-complementing protein Thy1 [69795] (1)
complex alpha+beta fold; contains antiparallel 5-stranded beta-sheet: order 12354
1. Thymidylate synthase-complementing protein Thy1 [69796] (1)
  uperfamily
  1. Thymidylate synthase-complementing protein Thy1 [69797] (1)
    1. Thy1 homologue [69798]
      1. Thermotoga maritima [TaxId: 2336] [69799] (9)
        TM0449
N-acetylmuramoyl-L-alanine amidase-like [55845] (1)
contains mixed beta-sheet
1. N-acetylmuramoyl-L-alanine amidase-like [55846] (1)
  uperfamily
  1. N-acetylmuramoyl-L-alanine amidase-like [55847] (10)
    Family 2 zinc amidase;
    1. AmpD protein [82775]
      1. Citrobacter freundii [TaxId: 546] [82776] (1)
    2. Bacteriophage T7 lysozyme (Zn amidase) [55848]
      1. Bacteriophage T7 [TaxId: 10760] [55849] (2)
    3. Peptidoglycan recognition protein-lb (Cg14704) [90024]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [90025] (1)
    4. Peptidoglycan-recognition protein-SA (Cg11709) [111139]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [111140] (2)
        SQ Q9VYX7 37-203 ! SQ Q9VYX7
    5. Peptidoglycan recognition protein I-alpha [111141]
      1. Human (Homo sapiens) [TaxId: 9606] [111142] (5)
        SQ Q96LB9 177-341
    6. N-acetylmuramoyl-L-alanine amidase PlyG [143780]
      1. Bacillus anthracis [TaxId: 1392] [143781] (6)
        SQ Q81WA9 1-157
        Prophage LambdaBa02
    7. Probable N-acetylmuramoyl-L-alanine amidase YbjR, N-terminal domain [143782]
      1. Escherichia coli [TaxId: 562] [143783] (2)
        SQ P75820 22-194
    8. Peptidoglycan-recognition protein-LC [143784]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143785] (3)
        SQ Q9GNK5 335-499! SQ Q9GNK5 355-520
        Cg4432; different splicing isoforms
    9. Peptidoglycan recognition protein, PGRP-S [143786]
      1. Human (Homo sapiens) [TaxId: 9606] [143787] (1)
        SQ O75594 30-196
    10. Peptidoglycan-recognition protein-LE [143788]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [143789] (4)
        SQ Q9VXN9 174-344
Cytochrome b5-like heme/steroid binding domain [55855] (1)
beta-alpha-beta(2)-alpha(1,2)-(beta)-alpha(2)-beta; 3 layers: a/b/a; antiparallel beta-sheet, order: 1532(4)
1. Cytochrome b5-like heme/steroid binding domain [55856] (2)
  uperfamily
  1. Cytochrome b5 [55857] (7)
    1. Cytochrome b5 [55858]
      1. Cow (Bos taurus) [TaxId: 9913] [55859] (16)
        SQ P00171 7-88 ! SQ P00171 8-89
      2. Rat (Rattus norvegicus) [TaxId: 10116] [55860] (20)
      3. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55861] (1)
    2. Cytochrome b558 [55862]
      a prokaryotic homologue of cytochrome b5
      1. Ectothiorhodospira vacuolata [TaxId: 1054] [55863] (1)
    3. Flavocytochrome b2, N-terminal domain [55864]
      C-terminal domain is beta/alpha barrel
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55865] (6)
    4. Sulfite oxidase, N-terminal domain [55866]
      1. Chicken (Gallus gallus) [TaxId: 9031] [55867] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [82777] (1)
  2. Steroid-binding domain [103222] (1)
    1. Putative steroid binding protein AT2G24940 [103223]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103224] (2)
BTG domain-like [160695] (1)
alpha(2)-beta-alpha(2)-beta(3); four-helical bundle, capped at one end by an antiparallel beta-sheet, order:1234
1. BTG domain-like [160696] (1)
  1. BTG domain-like [160697] (2)
    Pfam 07742
    1. TOB1, N-terminal domain [160698]
      1. Human (Homo sapiens) [TaxId: 9606] [160699] (5)
        SQ P50616 1-115! SQ P50616 1-117
    2. NGF-inducible anti-proliferative protein PC3 (BTG2) [160700]
      1. Human (Homo sapiens) [TaxId: 9606] [160701] (1)
        SQ P78543 8-127
DUSP-like [143790] (1)
alpha-beta-alpha-X-beta-alpha-beta; three-helical bundle capped at one end by antiparallel beta-sheet, order: 213
1. DUSP-like [143791] (1)
  uperfamily
  1. DUSP, domain in ubiquitin-specific proteases [143792] (1)
    Pfam 06337 (DUF1055); SMART 00695
    1. Ubiquitin carboxyl-terminal hydrolase 15 [143793]
      1. Human (Homo sapiens) [TaxId: 9606] [143794] (1)
        SQ Q9Y4E8 1-120
DNA topoisomerase I domain [55868] (1)
beta(2)-alpha-beta-(alpha)-beta(2); left-handed crossover between strands 2 & 3
1. DNA topoisomerase I domain [55869] (1)
  uperfamily
  1. Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment [55870] (1)
    1. Vaccinia DNA topoisomerase I, 9 kDa N-terminal fragment [55871]
      1. Vaccinia virus, strain WR [TaxId: 10245] [55872] (1)
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55873] (1)
8-stranded mixed beta-sheet; 2 layers: alpha/beta
1. ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase [55874] (4)
  uperfamily
  1. Heat shock protein 90, HSP90, N-terminal domain [55875] (3)
    1. HSP90 [55876]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55877] (21)
      2. Human (Homo sapiens) [TaxId: 9606] [55878] (53)
        SQ P08238 10-220 # HSP 90-beta isoform ! SQ P07900 16-223
      3. Dog (Canis familiaris) [TaxId: 9615] [103225] (29)
        SQ P41148 76-285; Endoplasmin, GRP94
  2. DNA gyrase/MutL, N-terminal domain [55879] (7)
    1. DNA gyrase B [55880]
      1. Escherichia coli [TaxId: 562] [55881] (3)
      2. Thermus thermophilus [TaxId: 274] [75534] (1)
    2. DNA topoisomerase II [103226]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103227] (2)
    3. Topoisomerase IV subunit B [103228]
      1. Escherichia coli [TaxId: 562] [103229] (2)
    4. DNA mismatch repair protein MutL [55882]
      1. Escherichia coli [TaxId: 562] [55883] (6)
    5. DNA mismatch repair protein PMS2 [69800]
      1. Human (Homo sapiens) [TaxId: 9606] [69801] (3)
    6. Topoisomerase VI-B subunit [82778]
      contains an H2TH domain inserted after this domain and before the second family-specific domain
      1. Archaeon Sulfolobus shibatae [TaxId: 2286] [82779] (10)
  3. Histidine kinase [55884] (7)
    1. Histidine kinase domain of the osmosensor EnvZ [55885]
      1. Escherichia coli [TaxId: 562] [55886] (1)
    2. Histidine kinase CheA [55887]
      1. Thermotoga maritima [TaxId: 2336] [55888] (9)
    3. Histidine kinase PhoQ domain [69802]
      1. Escherichia coli [TaxId: 562] [69803] (1)
    4. Anti-sigma factor spoIIab [75535]
      1. Bacillus stearothermophilus [TaxId: 1422] [75536] (5)
        SQ O32727
    5. Nitrogen regulation protein NtrB, C-terminal domain [111143]
      1. Escherichia coli [TaxId: 562] [111144] (1)
        SQ P06712 194-349
    6. Sensor histidine kinase TM0853 [143795]
      1. Thermotoga maritima [TaxId: 2336] [143796] (1)
        SQ Q9WZV7 321-481
    7. Sensor-type histidine kinase PrrB [143797]
      1. Mycobacterium tuberculosis [TaxId: 1773] [143798] (6)
        SQ P0A5Z8 299-446
  4. alpha-ketoacid dehydrogenase kinase, C-terminal domain [69804] (3)
    1. Branched-chain alpha-ketoacid dehydrogenase kinase (BCK) [69805]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69806] (3)
    2. Pyruvate dehydrogenase kinase [69807]
      1. Rat (Rattus norvegicus), isozyme 2 [TaxId: 10116] [69808] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [160702] (8)
        SQ Q15120 177-301
YehR-like [160703] (1)
beta(3)-alpha-beta(2)-alpha(3)-beta; 2 layers, a/b; antiparallel beta-sheet, order: 612354
1. YehR-like [160704] (1)
  1. YehR-like [160705] (1)
    Pfam 06998; DUF1307
    1. Hypothetical lipoprotein YehR [160706]
      1. Escherichia coli [TaxId: 562] [160707] (1)
        SQ P33354 24-153
Sporulation response regulatory protein Spo0B [55889] (1)
core: alpha-beta-alpha-beta(2)-(alpha)-beta(2)
1. Sporulation response regulatory protein Spo0B [55890] (1)
  Histidine kinase-like fold lacking the kinase ATP-binding site
  uperfamily
  1. Sporulation response regulatory protein Spo0B [55891] (1)
    1. Sporulation response regulatory protein Spo0B [55892]
      1. Bacillus subtilis [TaxId: 1423] [55893] (6)
Ribonuclease Rh-like [55894] (1)
alpha+beta fold
1. Ribonuclease Rh-like [55895] (1)
  uperfamily
  1. Ribonuclease Rh-like [55896] (8)
    1. Ribonuclease Rh [55897]
      1. Rhizopus niveus [TaxId: 4844] [55898] (1)
    2. Ribonuclease MC1 [55899]
      1. Bitter gourd (Momordica charantia) [TaxId: 3673] [55900] (8)
        SQ P23540
    3. RNase LE [55901]
      1. Tomatoes (Lycopersicon esculentum) [TaxId: 4081] [55902] (1)
    4. RNase NW [103230]
      1. Nicotiana glutinosa [TaxId: 35889] [103231] (1)
    5. S3-RNase [69809]
      1. Japanese pear (Pyrus pyrifolia) [TaxId: 3767] [69810] (1)
    6. Gemetophytic self-incompatibility associated SF11-RNase [75537]
      1. Winged tobacco (Nicotiana alata) [TaxId: 4087] [75538] (1)
    7. RNase-related protein [75539]
      1. Hedge bindweed (Calystegia sepium) [TaxId: 47519] [75540] (1)
    8. Trichomaglin [111145]
      1. Gourd (Trichosanthes lepiniana) [TaxId: 282652] [111146] (1)
        SQ P84146
YlxR-like [64375] (1)
alpha+beta fold; could have evolved from a glucocorticoid receptor-like zinc finger domain
1. YlxR-like [64376] (1)
  uperfamily
  1. YlxR-like [64377] (1)
    some family sequences retain zinc-binding residues
    1. Hypothetical cytosolic protein SP0554 [64378]
      1. Streptococcus pneumoniae [TaxId: 1313] [64379] (1)
YggX-like [111147] (1)
beta(2)-alpha(3); contains zinc-less 'zinc finger'-like fold (scop_cf 57715; see also scop_cf 64375)
1. YggX-like [111148] (1)
  uperfamily
  1. YggX-like [111149] (2)
    Pfam 04362
    1. Hypothetical protein PA5148 [111150]
      1. Pseudomonas aeruginosa [TaxId: 287] [111151] (1)
        SQ Q9HU36
    2. Hypothetical protein YggX [118087]
      1. Salmonella typhimurium [TaxId: 90371] [118088] (1)
        SQ P67617
L28p-like [143799] (1)
unusual fold consisting of three beta-hairpins, that form a paper clip-like structure, and two helices; could have evolved from a glucocorticoid receptor-like zinc finger domain (scop_cf 57715)
1. L28p-like [143800] (2)
  In early ribosomal structures, L28p has been misinterpreted as L31p. in the Ribosomal protein L28p family, there are sequences containing two CxxC pairs. Threading these sequences into this fold brings the four cysteines in a similar site to the zinc-binding site of glucocorticoid receptor-like zinc fingers. In the Ribosomal protein L31p, there are also members with two CxxC pairs. However, these won't form a putative zinc-binding site in this fold. The L31p family are classified here temporarily, until its true fold is known
  uperfamily
  1. Ribosomal protein L28 [143801] (4)
    1. Ribosomal protein L28 (L28p) [143802]
      1. Thermus thermophilus [TaxId: 274] [143803] (2)
        SQ P60494 7-95
      2. Deinococcus radiodurans [TaxId: 1299] [160708] (5)
        SQ Q9RRG8 8-79
      3. Escherichia coli [TaxId: 562] [160709] (18)
        SQ P0A7M2 1-77
      4. Thermotoga maritima [TaxId: 2336] [160710] (1)
        SQ Q9WY96 1-70
  2. Ribosomal protein L31p [143804] (2)
    Pfam 01197
    1. Ribosomal protein L31p [143805]
      1. Escherichia coli [TaxId: 562] [143806] (9)
        SQ P0A7M9 1-70
      2. Thermus thermophilus [TaxId: 274] [160711] (7)
        SQ Q5SJE1 1-50
YqaI-like [160712] (1)
dimeric zinc-less 'zinc finger'-like fold; similar to the C-terminal strand-swapped B-box domain (scop_cf 57844)
1. YqaI-like [160713] (1)
  1. YqaI-like [160714] (1)
    Pfam 09466
    1. Hypothetical protein YqaI [160715]
      1. Bacillus subtilis [TaxId: 1423] [160716] (2)
        SQ P45906 1-64
Ornithine decarboxylase C-terminal domain [55903] (1)
complex alpha+beta motif
1. Ornithine decarboxylase C-terminal domain [55904] (1)
  uperfamily
  1. Ornithine decarboxylase C-terminal domain [55905] (1)
    1. Ornithine decarboxylase C-terminal domain [55906]
      1. Lactobacillus sp., strain 30a [TaxId: 1591] [55907] (2)
Pentein, beta/alpha-propeller [55908] (1)
duplication: composed of 5 alpha-beta(2)-alpha-beta units arranged around pseudo fivefold axis
1. Pentein [55909] (7)
  uperfamily
  1. Ribosome anti-association factor eIF6 (aIF6) [55910] (2)
    1. Ribosome anti-association factor eIF6 (aIF6) [55911]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [55912] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55913] (1)
  2. Amidinotransferase [55914] (2)
    common fold is elaborated with many active site-forming insertions
    1. L-arginine: glycine amidinotransferase [55915]
      1. Human (Homo sapiens) [TaxId: 9606] [55916] (11)
    2. L-arginine: inosamine-phosphate amidinotransferase [55917]
      1. Streptomyces griseus [TaxId: 1911] [55918] (1)
  3. Dimethylarginine dimethylaminohydrolase DDAH [64380] (1)
    functionally related to the amidinotransferase, similar active sites
    1. Dimethylarginine dimethylaminohydrolase DDAH [64381]
      1. Pseudomonas aeruginosa [TaxId: 287] [64382] (1)
  4. Arginine deiminase [103232] (2)
    functionally related to the amidinotransferase, similar active sites
    1. Arginine deiminase [103233]
      1. Pseudomonas aeruginosa [TaxId: 287] [103234] (17)
      2. Mycoplasma arginini [TaxId: 2094] [103235] (2)
  5. Peptidylarginine deiminase Pad4, catalytic C-terminal domain [111152] (1)
    # functionally related to the amidinotransferase, similar active sites
    1. Peptidylarginine deiminase Pad4, catalytic C-terminal domain [111153]
      1. Human (Homo sapiens) [TaxId: 9606] [111154] (7)
        SQ Q9UM07
  6. Porphyromonas-type peptidylarginine deiminase [111155] (6)
    Pfam 04371; functionally related to the amidinotransferase, similar active site
    1. Agmatine iminohydrolase [111156]
      1. Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [111157] (3)
        SQ Q8GWW7
      2. Streptococcus mutans [TaxId: 1309] [143807] (12)
        SQ Q8DW17 2-370
      3. Enterococcus faecalis [TaxId: 1351] [160717] (6)
        SQ Q837U5 2-365
    2. Putative peptidyl-arginine deiminase [111158]
      1. Helicobacter pylori J99 [TaxId: 85963] [111159] (1)
        SQ Q9ZN18
      2. Chlorobium tepidum [TaxId: 1097] [118089] (1)
        SQ Q8KCB6
      3. Porphyromonas gingivalis [TaxId: 837] [143808] (2)
        SQ Q7MXM8 3-341
  7. Succinylarginine dihydrolase-like [143809] (1)
    Pfam 04996
    1. Succinylarginine dihydrolase [143810]
      1. Escherichia coli [TaxId: 562] [143811] (14)
        SQ P76216 2-441
Creatinase/aminopeptidase [55919] (1)
duplication: composed of two very similar alpha+beta folds
1. Creatinase/aminopeptidase [55920] (1)
  uperfamily
  1. Creatinase/aminopeptidase [55921] (9)
    1. Creatinase, catalytic (C-terminal) domain [55922]
      1. Pseudomonas putida [TaxId: 303] [55923] (1)
      2. Actinobacillus sp. [TaxId: 41114] [75541] (1)
    2. Methionine aminopeptidase [55924]
      1. Escherichia coli [TaxId: 562] [55925] (44)
        SQ P07906
      2. Thermotoga maritima [TaxId: 2336] [82780] (1)
      3. Staphylococcus aureus [TaxId: 1280] [103236] (3)
      4. Archaeon Pyrococcus furiosus [TaxId: 2261] [55926] (4)
        contains insert domain with a circularly permuted "winged helix" fold
      5. Human (Homo sapiens) [TaxId: 9606] [55927] (18)
        SQ P50579 110-478
        methionine aminopeptidase 2 contains insert domain with a circularly permuted "winged helix" fold
    3. Aminopeptidase P, C-terminal domain [55928]
      1. Escherichia coli [TaxId: 562] [55929] (37)
      2. Archaeon Pyrococcus furiosus [TaxId: 2261] [103237] (1)
gpW/gp25-like [160718] (1)
alpha(2)-beta(3); similar to one structural repeat of the Creatinase/aminopeptidase family and the C-terminal subdomain of PanC
1. gpW/gp25-like [160719] (1)
  Contains phage tail lysozyme
  1. gpW/gp25-like [160720] (1)
    Pfam 04965; T4 gene 25-like lysozyme
    1. Uncharacterized protein GSU0986 [160721]
      1. Geobacter sulfurreducens [TaxId: 35554] [160722] (1)
        SQ Q74EH6 23-133
Glutamine synthetase/guanido kinase [55930] (1)
duplication: common core consists of two beta-alpha-beta2-alpha repeats
1. Glutamine synthetase/guanido kinase [55931] (5)
  uperfamily
  1. Glutamine synthetase catalytic domain [55932] (2)
    1. Glutamine synthetase, C-terminal domain [55933]
      1. Salmonella typhimurium [TaxId: 90371] [55934] (18)
      2. Mycobacterium tuberculosis [TaxId: 1773] [75542] (8)
  2. Guanido kinase catalytic domain [55935] (8)
    1. Creatine kinase, C-terminal domain [55936]
      1. Chicken (Gallus gallus), mitochondria [TaxId: 9031] [55937] (1)
      2. Chicken (Gallus gallus), brain-type [TaxId: 9031] [55938] (1)
      3. Human (Homo sapiens), muscle isoform [TaxId: 9606] [90026] (1)
      4. Human (Homo sapiens), mitochondria [TaxId: 9606] [55939] (1)
      5. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55940] (3)
      6. Cow (Bos taurus), retinal isoform [TaxId: 9913] [55941] (1)
      7. Pacific electric ray (Torpedo californica) [TaxId: 7787] [82781] (2)
    2. Arginine kinase, C-terminal domain [55942]
      1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [55943] (7)
        SQ P51541
  3. Glutamate-cysteine ligase family 2 (GCS2) [111160] (2)
    Pfam 04107; structural and functional relationships to Glutamine synthetase
    1. Carboxylate-amine ligase YbdK [111161]
      1. Escherichia coli [TaxId: 562] [111162] (1)
        SQ P77213
      2. Salmonella typhimurium [TaxId: 90371] [111163] (1)
        SQ Q8ZR41
  4. Glutamate-cysteine ligase [118090] (1)
    Pfam 04262
    1. Gamma-glutamylcysteine synthetase GshA [118091]
      1. Escherichia coli [TaxId: 562] [118092] (10)
        SQ P0A6W9
  5. GatB/GatE catalytic domain-like [143812] (3)
    N-terminal and C-terminal parts correspond to Pfam 02934 (GatB_N) and Pfam 01162 (GatB), respectively
    1. Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, GatB, N-terminal domain [143813]
      1. Staphylococcus aureus [TaxId: 1280] [143814] (5)
        SQ P64201 2-293
    2. Glutamyl-tRNA(Gln) amidotransferase subunit E, GatE [143815]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [143816] (2)
        SQ O26803 1-270,396-444
      2. Pyrococcus abyssi [TaxId: 29292] [143817] (2)
        SQ Q9V0U0 5-276,408-456
TBP-like [55944] (11)
beta-alpha-beta(4)-alpha
1. TATA-box binding protein-like [55945] (2)
  uperfamily
  1. TATA-box binding protein (TBP), C-terminal domain [55946] (5)
    duplication: consists of two clear structural repeats
    1. TATA-box binding protein (TBP), C-terminal domain [55947]
      structure of the N-terminal domain is not known yet
      1. Human (Homo sapiens) [TaxId: 9606] [55948] (5)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [55949] (13)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55950] (8)
      4. Archaeon Pyrococcus woesei [TaxId: 2262] [55951] (3)
      5. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [103238] (1)
  2. DNA repair glycosylase, N-terminal domain [55952] (2)
    contains a single copy of this fold
    1. 3-Methyladenine DNA glycosylase II (gene alkA or aidA) [55953]
      1. Escherichia coli [TaxId: 562] [55954] (35)
        SQ P04395
    2. 8-oxoguanine glycosylase [55955]
      1. Human (Homo sapiens) [TaxId: 9606] [55956] (23)
2. MoaD-related protein, C-terminal domain [103239] (1)
  contains a single copy of this fold
  uperfamily
  1. MoaD-related protein, C-terminal domain [103240] (1)
    1. MoaD-related protein, C-terminal domain [103241]
      1. Thermus thermophilus [TaxId: 274] [103242] (1)
3. KA1-like [103243] (2)
  contains a single copy of this fold
  uperfamily
  1. Kinase associated domain 1, KA1 [103244] (1)
    Pfam 02149
    1. Map/microtubule affinity-regulating kinase 3 [103245]
      1. Mouse (Mus musculus) [TaxId: 10090] [103246] (2)
        SQ Q8C6G9 373-452
  2. Ssp2 C-terminal domain-like [160723] (3)
    PfamB 166430
    1. Carbon catabolite-derepressing protein kinase SNF1 [160724]
      1. Saccharomyces cerevisiae [TaxId: 4932] [160725] (2)
        SQ P06782 460-630
    2. Snf1-like protein kinase ssp2 [160726]
      1. Schizosaccharomyces pombe [TaxId: 4896] [160727] (12)
        SQ O74536 449-576
    3. 5'-AMP-activated protein kinase catalytic subunit alpha-1, AMPK1 [160728]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [160729] (3)
        SQ P54645 396-548
4. TT1751-like [103247] (1)
  contains a single copy of this fold decorated with additional structures; forms dimer
  uperfamily
  1. TT1751-like [103248] (2)
    Pfam 03625; DUF302
    1. Unnamed hypothetical protein [103249]
      1. Bacillus stearothermophilus [TaxId: 1422] [103250] (1)
    2. Hypothetical protein TT1751 (TTHA1732) [111164]
      1. Thermus thermophilus HB8 [TaxId: 300852] [111165] (1)
        SQ Q84BQ8
5. Cell-division protein ZipA, C-terminal domain [64383] (1)
  contains a single copy of this fold
  uperfamily
  1. Cell-division protein ZipA, C-terminal domain [64384] (1)
    1. Cell-division protein ZipA, C-terminal domain [64385]
      1. Escherichia coli [TaxId: 562] [64386] (10)
6. Phosphoglucomutase, C-terminal domain [55957] (1)
  contains a single copy of this fold and an extra beta-strand at the C-terminus
  uperfamily
  1. Phosphoglucomutase, C-terminal domain [55958] (4)
    Pfam 00408
    1. Phosphoglucomutase [55959]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [55960] (6)
    2. Exocytosis-sensitive phosphoprotein, pp63/parafusin [69811]
      1. Paramecium tetraurelia [TaxId: 5888] [69812] (2)
    3. Phosphomannomutase/phosphoglucomutase [81375]
      1. Pseudomonas aeruginosa [TaxId: 287] [81374] (12)
    4. Phosphoacetylglucosamine mutase [118093]
      1. Mouse (Mus musculus) [TaxId: 10090] [118094] (1)
        SQ Q9CYR6 442-540
7. Bet v1-like [55961] (10)
  contains a single copy of this fold with a alpha-beta2 insertion after the first helix; there is a cavity between the beta-sheet and the long C-terminal helix
  uperfamily
  1. Pathogenesis-related protein 10 (PR10)-like [55962] (8)
    1. Major tree pollen allergen [55963]
      1. White birch (Betula verrucosa), Bet v 1 [TaxId: 3505] [55964] (5)
      2. European white birch (Betula pendula), Bet v I-a [TaxId: 3505] [55965] (1)
      3. European white birch (Betula pendula), Bet v 1-l [TaxId: 3505] [82782] (1)
      4. Sweet cherry (Prunus avium), pru av 1 [TaxId: 42229] [64387] (2)
    2. Plant pathogenesis-related protein PR10 [75543]
      1. Yellow lupine (Lupinus luteus) [TaxId: 3873] [75544] (4)
      2. Jicama (Pachyrhizus erosus), SPE-16 [TaxId: 109171] [143818] (4)
        SQ Q6T6J0 2-148
    3. Hypothetical protein At1G24000 [103251]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [103252] (3)
    4. Major allergen api g 1 [143819]
      1. Celery (Apium graveolens) [TaxId: 4045] [143820] (2)
        SQ P49372 2-154
  2. STAR domain [55966] (4)
    1. Lipid transport domain of Mln64 [55967]
      1. Human (Homo sapiens) [TaxId: 9606] [55968] (1)
    2. Cholesterol-regulated Start protein 4 (Stard4). [75545]
      1. Mouse (Mus musculus) [TaxId: 10090] [75546] (1)
    3. Phosphatidylcholine transfer protein [75547]
      1. Human (Homo sapiens) [TaxId: 9606] [75548] (3)
    4. Star-related lipid transfer protein 13 [160730]
      1. Human (Homo sapiens) [TaxId: 9606] [160731] (3)
        SQ Q9Y3M8 908-1104
  3. Phoshatidylinositol transfer protein, PITP [64388] (4)
    1. Phoshatidylinositol transfer protein, PITP [64389]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [64390] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [75549] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [103253] (1)
      4. Rat (Rattus norvegicus), beta isoform [TaxId: 10116] [143821] (1)
        SQ P53812 1-270
  4. Ring hydroxylating alpha subunit catalytic domain [55969] (7)
    Pfam 00848; contains a few insertion and C-terminal extension compared with Bet v1
    1. Naphthalene 1,2-dioxygenase alpha subunit, C-domain [55970]
      1. Pseudomonas putida [TaxId: 303] [55971] (16)
      2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [143822] (6)
        SQ Q9X3R9 163-441
    2. Biphenyl dioxygenase large subunit BphA1, C-terminal domain [111166]
      1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [111167] (2)
        SQ Q53122 17-451
    3. 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO [143823]
      1. Pseudomonas putida [TaxId: 303] [143824] (1)
        SQ O05935 164-442
    4. Large subunit of cumene dioxygenase cumA1 [143825]
      1. Pseudomonas fluorescens [TaxId: 294] [143826] (1)
        SQ Q51743 181-459
    5. Terminal oxygenase component of carbazole CarAa [143827]
      1. Janthinobacterium sp. j3 [TaxId: 213804] [143828] (10)
        SQ Q84II6 143-384
    6. Nitrobenzene dioxygenase alpha subunit, NBDO-alpha [143829]
      1. Comamonas sp. JS765 [TaxId: 58226] [143830] (3)
        SQ Q8RTL4 153-439
  5. AHSA1 domain [111168] (11)
    Pfam 05146
    1. Hypothetical protein NE0264 [111169]
      1. Nitrosomonas europaea [TaxId: 915] [111170] (1)
        SQ Q82XK1
    2. Hypothetical protein MM0500 [118095]
      1. Methanosarcina mazei [TaxId: 2209] [118096] (1)
        SQ Q8PZJ2
    3. Hypothetical protein BH1534 [118097]
      1. Bacillus halodurans [TaxId: 86665] [118098] (1)
        SQ Q9KCN5
    4. Hypothetical protein BC4709 [118099]
      1. Bacillus cereus [TaxId: 1396] [118100] (1)
        SQ Q816V6
    5. Calicheamicin gene cluster protein CalC [143831]
      possible link between the AHSA1 (Pfam 08327) and oligoketide cyclase/dehydrase-like (new Pfam 03364) families
      1. Micromonospora echinospora [TaxId: 1877] [143832] (3)
        SQ Q8KNF0 27-181
    6. Activator of 90 kda heat shock protein ATPase homolog 1, AHSA1 [143833]
      1. Human (Homo sapiens) [TaxId: 9606] [143834] (1)
        SQ O95433 204-335
    7. Hypothetical protein CV1439 [143835]
      1. Chromobacterium violaceum [TaxId: 536] [143836] (6)
        SQ Q7NY36 2-144
    8. Hypothetical protein EF2215 [160732]
      1. Enterococcus faecalis [TaxId: 1351] [160733] (1)
        SQ Q832L1 1-160
    9. Uncharacterized protein SPO3351 [160734]
      1. Silicibacter pomeroyi [TaxId: 89184] [160735] (1)
        SQ Q5LN61 2-144
    10. Hypothetical protein SA2116 [160736]
      1. Staphylococcus aureus [TaxId: 1280] [160737] (1)
        SQ Q2FEH1 5-168
    11. Uncharacterized protein BPP1335 [160738]
      1. Bordetella parapertussis [TaxId: 519] [160739] (1)
        SQ Q7WAN9 1-183
  6. oligoketide cyclase/dehydrase-like [118101] (3)
    Pfam 03654
    1. Hypothetical protein CC1736 [118102]
      1. Caulobacter crescentus [TaxId: 155892] [118103] (1)
        SQ Q9A7I7
    2. Hypothetical protein TTHA0849 [143837]
      1. Thermus thermophilus [TaxId: 274] [143838] (4)
        SQ Q5SK03 2-147
    3. Multifunctional enzyme TcmN, cyclase/aromatase domain [160740]
      1. Streptomyces glaucescens [TaxId: 1907] [160741] (3)
        SQ P16559 1-152! SQ P16559 1-155
  7. PA1206-like [143839] (1)
    1. Hypothetical protein PA1206 [143840]
      1. Pseudomonas aeruginosa [TaxId: 287] [143841] (2)
        SQ Q9I4D2 1-151
  8. Atu1531-like [160742] (2)
    Pfam 10604; Polyketide cyclase/dehydrase and lipid transport
    1. Uncharacterized protein XoxI [160743]
      1. Bacillus cereus [TaxId: 1396] [160744] (2)
        SQ Q81AY6 3-140
    2. Uncharacterized protein Atu1531 [160745]
      1. Agrobacterium tumefaciens [TaxId: 358] [160746] (2)
        SQ Q7CZ16 1-133
  9. Smu440-like [160747] (1)
    PfamB 094079
    1. Hypothetical protein SMU440 [160748]
      1. Streptococcus mutans [TaxId: 1309] [160749] (2)
        SQ Q8DVN6 1-137
  10. CoxG-like [160750] (2)
    Pfam 06240
    1. Hypothetical protein APE2225 [160751]
      1. Aeropyrum pernix [TaxId: 56636] [160752] (2)
        SQ Q9Y9R3 1-147
    2. Hypothetical protein GKP20 [160753]
      1. Geobacillus kaustophilus [TaxId: 1462] [160754] (1)
        SQ Q5QL47 1-147
8. Rbstp2229 protein [111171] (1)
  forms segment-swapped dimers further organized in hexamers
  uperfamily
  1. Rbstp2229 protein [111172] (1)
    1. Rbstp2229 protein [111173]
      1. Bacillus stearothermophilus [TaxId: 1422] [111174] (1)
        SQ P84137
9. RalF, C-terminal domain [118104] (1)
  contains a single copy of this fold decorated with additional structures
  uperfamily
  1. RalF, C-terminal domain [118105] (1)
    1. RalF, C-terminal domain [118106]
      1. Legionella pneumophila [TaxId: 446] [118107] (1)
        SQ Q8RT31 2-353
10. YwmB-like [143842] (1)
  duplication: tandem repeat of two circularly permuted motifs, alpha-beta-alpha-beta(4), assembled as in the TATA-box binding domain; forms a swapped dimer by exchanging the equivalent parts of the C-terminal motifs
  uperfamily
  1. YwmB-like [143843] (1)
    1. Hypothetical protein YwmB [143844]
      1. Bacillus subtilis [TaxId: 1423] [143845] (1)
        SQ O32277 31-244
11. YugN-like [160755] (1)
  1. YugN-like [160756] (1)
    Pfam 08868
    1. Uncharacterized protein ABC2387 [160757]
      YugN homologue
      1. Bacillus clausii [TaxId: 79880] [160758] (1)
        SQ Q5WFD8 1-114
XisI-like [143846] (1)
alpha-beta(4)-alpha-beta-alpha; 2 layers, a/b; antiparallel beta-sheet, order 1234, meander; the open side of beta-sheet provides dimerization interface
1. XisI-like [143847] (1)
  uperfamily
  1. XisI-like [143848] (3)
    Pfam 08869
    1. Hypothetical protein Ava3825 [143849]
      1. Anabaena variabilis [TaxId: 1172] [143850] (2)
        SQ Q3M6F6 1-111
    2. XisI [143851]
      the fdxN element excision controlling factor
      1. Anabaena variabilis [TaxId: 1172] [143852] (2)
        SQ Q3MD55 2-118
        Ava1458
    3. Hypothetical protein Ava3320 [143853]
      1. Anabaena variabilis [TaxId: 1172] [143854] (1)
        SQ Q3M7V9 2-113
S-adenosylmethionine synthetase [55972] (1)
duplication: consists of 3 similar intertwined domains
structural repeat: beta-alpha-beta(2)-alpha-beta; two layers, alpha/beta
1. S-adenosylmethionine synthetase [55973] (1)
  uperfamily
  1. S-adenosylmethionine synthetase [55974] (3)
    1. S-adenosylmethionine synthetase [55975]
      synonym: methionine adenosyltransferase, MAT
      1. Escherichia coli [TaxId: 562] [55976] (9)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [55977] (5)
      3. Human (Homo sapiens), isoform type-2 [TaxId: 9606] [160759] (3)
        SQ P31153 126-251! SQ P31153 16-125! SQ P31153 252-395
        MAT2A
DNA clamp [55978] (1)
contains two helices and two beta sheets
duplication: fold has internal pseudo two-fold symmetry
1. DNA clamp [55979] (2)
  uperfamily
  1. DNA polymerase III, beta subunit [55980] (2)
    duplication: consists of three domains of this fold
    1. DNA polymerase III, beta subunit [55981]
      1. Escherichia coli [TaxId: 562] [55982] (30)
        SQ P00583
      2. Thermotoga maritima [TaxId: 2336] [118108] (1)
        SQ Q9WYA0
  2. DNA polymerase processivity factor [55983] (9)
    duplication: consists of two domains of this fold
    1. gp45 sliding clamp [55984]
      1. Bacteriophage RB69 [TaxId: 12353] [55985] (2)
      2. Bacteriophage T4 [TaxId: 10665] [55986] (1)
    2. UL42 [55987]
      1. Human herpesvirus type 1 [TaxId: 10298] [55988] (1)
    3. Proliferating cell nuclear antigen (PCNA) [55989]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [55990] (5)
        SQ P15873
      2. Human (Homo sapiens) [TaxId: 9606] [55991] (31)
        SQ P12004
      3. Archaeon Pyrococcus furiosus [TaxId: 2261] [55992] (4)
      4. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [103254] (3)
      5. Archaeon Sulfolobus tokodaii [TaxId: 111955] [111175] (1)
        SQ Q975N2
    4. UL44 [111176]
      1. Human cytomegalovirus, HHV-5 [TaxId: 10359] [111177] (3)
        SQ P16790 1-290
Hypothetical protein TM0160 [103255] (1)
duplication: consists of two beta(3)-alpha(2) structural repeats; single barrel-like beta-sheet
1. Hypothetical protein TM0160 [103256] (1)
  uperfamily
  1. Hypothetical protein TM0160 [103257] (1)
    1. Hypothetical protein TM0160 [103258]
      1. Thermotoga maritima [TaxId: 2336] [103259] (1)
TTHC002-like [160760] (1)
alpha-beta-alpha-beta(3); forms dimer with a single beta-sheet, folded in a barrel-like shape
1. TTHC002-like [160761] (1)
  1. TTHC002-like [160762] (1)
    1. Hypothetical protein TTHC002 [160763]
      1. Thermus thermophilus [TaxId: 274] [160764] (2)
        SQ Q5SGN2 7-86
Molybdenum cofactor-binding domain [56002] (1)
beta(2)-alpha-beta-alpha-beta; 2 layers: a/b; mixed sheet: order 1243: crossing loops
1. Molybdenum cofactor-binding domain [56003] (1)
  duplication: consists of 4 structural repeats arranged in 2 lobes
  contains one left-hand beta-alpha-beta unit per lobe
  uperfamily
  1. Molybdenum cofactor-binding domain [56004] (8)
    1. Aldehyde oxidoreductase [56005]
      1. Desulfovibrio gigas [TaxId: 879] [56006] (3)
        SQ Q46509
      2. Desulfovibrio desulfuricans [TaxId: 876] [56007] (1)
    2. Xanthine oxidase, C-terminal domain [56008]
      1. Cow (Bos taurus) [TaxId: 9913] [56009] (6)
        SQ P80457
    3. Xanthine dehydrogenase chain B, C-terminal domain [69813]
      1. Rhodobacter capsulatus [TaxId: 1061] [69814] (2)
    4. Carbon monoxide (CO) dehydrogenase molybdoprotein [56010]
      1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [56011] (6)
      2. Hydrogenophaga pseudoflava [TaxId: 47421] [56012] (2)
    5. Quinoline 2-oxidoreductase large subunit QorL [111178]
      1. Pseudomonas putida [TaxId: 303] [111179] (1)
        SQ P72224
    6. 4-hydroxybenzoyl-CoA reductase alpha subunit HrcA, C-terminal domain [118109]
      1. Thauera aromatica [TaxId: 59405] [118110] (2)
        SQ O33819
NE1680-like [160765] (1)
beta(2)-alpha-beta-alpha-beta; 2 layers, a/b; antiparallel sheet, order 3124
1. NE1680-like [160766] (1)
  1. NE1680-like [160767] (1)
    Pfam 09630; DUF2024
    1. Hypothetical protein NE1680 [160768]
      1. Nitrosomonas europaea [TaxId: 915] [160769] (1)
        SQ Q82U33 1-85
Nitrite and sulphite reductase 4Fe-4S domain-like [56013] (1)
beta-alpha-beta-alpha-beta(3)-alpha(2,3); mixed sheet: order 12345; left-handed crossover connection between strands 1 and 2
1. Nitrite and sulphite reductase 4Fe-4S domain-like [56014] (1)
  duplication: contains two domains of this fold
  uperfamily
  1. Nitrite and sulphite reductase 4Fe-4S domain-like [56015] (7)
    1. Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 [56016]
      1. Escherichia coli [TaxId: 562] [56017] (12)
    2. Sulfite reductase NirA [160770]
      1. Mycobacterium tuberculosis [TaxId: 1773] [160771] (8)
        SQ P71753 162-326! SQ P71753 407-555
    3. Dissimilatory sulfite reductase subunit beta, DsrB [160772]
      1. Desulfovibrio vulgaris [TaxId: 881] [160773] (2)
        SQ P45575 136-208,278-381
      2. Archaeoglobus fulgidus [TaxId: 2234] [160774] (2)
        SQ Q59110 123-196,262-366
    4. Ferredoxin--nitrite reductase, NIR [160775]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [160776] (2)
        SQ P05314 207-377! SQ P05314 463-588
        chloroplastic
    5. Dissimilatory sulfite reductase subunit alpha, DsrA [160777]
      1. Desulfovibrio vulgaris [TaxId: 881] [160778] (2)
        SQ P45574 168-241,323-437
      2. Archaeoglobus fulgidus [TaxId: 2234] [160779] (2)
        SQ Q59109 168-239,306-418
DeoB insert domain-like [143855] (1)
alpha-beta-X-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet of 5 strands, order 12345; strands 2 and 5 are antiparallel to the rest
1. DeoB insert domain-like [143856] (1)
  uperfamily
  1. DeoB insert domain-like [143857] (1)
    1. Phosphopentomutase DeoB [143858]
      1. Streptococcus mutans [TaxId: 1309] [143859] (2)
        SQ Q8DTU0 108-226
The spindle assembly checkpoint protein mad2 [56018] (1)
core: alpha(2)-beta(2)-alpha-beta; mixed sheet: order 213
1. The spindle assembly checkpoint protein mad2 [56019] (1)
  N- and C-termini undergo large conformational rearrangement upon ligand binding
  uperfamily
  1. The spindle assembly checkpoint protein mad2 [56020] (1)
    1. The spindle assembly checkpoint protein mad2 [56021]
      1. Human (Homo sapiens) [TaxId: 9606] [56022] (7)
Phospholipase D/nuclease [56023] (1)
beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
1. Phospholipase D/nuclease [56024] (5)
  uperfamily
  1. Nuclease [56025] (1)
    1. Nuclease Nuc [56026]
      1. Salmonella typhimurium [TaxId: 90371] [56027] (2)
  2. Phospholipase D [64391] (1)
    duplication: contains two domains of this fold arranged as in the Nuc dimer
    1. Phospholipase D [64392]
      1. Streptomyces sp. [TaxId: 1931] [64393] (8)
        SQ P84147
  3. Tyrosyl-DNA phosphodiesterase TDP1 [69815] (2)
    1. Tyrosyl-DNA phosphodiesterase TDP1 [69816]
      1. Human (Homo sapiens) [TaxId: 9606] [69817] (12)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111180] (1)
        SQ P38319 79-538
  4. Polyphosphate kinase C-terminal domain [143860] (2)
    C-terminal part of Pfam 02503; similar to PLD; contains two domains of this fold arranged as in the Nuc dimer
    1. Polyphosphate kinase, PPK [143861]
      1. Porphyromonas gingivalis [TaxId: 837] [143862] (4)
        SQ Q7MTR1 318-505! SQ Q7MTR1 506-691
      2. Escherichia coli [TaxId: 562] [143863] (8)
        SQ P0A7B1 315-501! SQ P0A7B1 502-688
  5. TrmB middle domain-like [160780] (1)
    N-terminal part of PfamB 004822
    1. Transcriptional regulator TrmB [160781]
      1. Thermococcus litoralis [TaxId: 2265] [160782] (1)
        SQ Q7LYW4 110-246
CorA soluble domain-like [143864] (1)
beta(2)-alpha-beta-alpha(2)-beta(4)-alpha(3); 3 layers: a/b/a; mixed beta-sheet, order 2137654; strands 3 and 7 are parallel
1. CorA soluble domain-like [143865] (1)
  uperfamily
  1. CorA soluble domain-like [143866] (1)
    N-terminal part of Pfam 01544
    1. Magnesium transport protein CorA, soluble domain [143867]
      1. Thermotoga maritima [TaxId: 2336] [143868] (21)
        SQ Q9WZ31 13-244! SQ Q9WZ31 9-285
Monooxygenase (hydroxylase) regulatory protein [56028] (1)
corner-like structure formed by two sheets and filled in with 2-3 helices
1. Monooxygenase (hydroxylase) regulatory protein [56029] (1)
  duplication: consists of two beta-alpha-(beta)-beta(2) motifs; some topological similarity to the ferredoxin-like fold
  uperfamily
  1. Monooxygenase (hydroxylase) regulatory protein [56030] (4)
    note: the solution structure determinations disagree in the relative orientations of two motifs
    1. Soluble methane monooxygenase regulatory protein B [56031]
      1. Escherichia coli [TaxId: 562] [56032] (1)
      2. Methylosinus trichosporium [TaxId: 426] [56033] (1)
    2. Toluene-4-monooxygenase catalytic effector protein [64394]
      1. Pseudomonas mendocina [TaxId: 300] [64395] (6)
    3. Phenol hydroxylase P2 protein [56034]
      1. Pseudomonas sp., CF600 [TaxId: 306] [56035] (1)
PurM C-terminal domain-like [56041] (1)
3 layers: alpha/beta/alpha; partial topological similarity to the ferredoxin-like fold
1. PurM C-terminal domain-like [56042] (1)
  uperfamily
  1. PurM C-terminal domain-like [56043] (6)
    1. Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain [56044]
      1. Escherichia coli [TaxId: 562] [56045] (1)
    2. Phosphoribosylformylglycinamidine synthase II, domains 2 and 4 [103260]
      duplication: tandem repeats of two PurM-like units arranged like the PurM subunits in the dimer
      1. Thermotoga maritima [TaxId: 2336] [103261] (17)
        TM1246
    3. FGAM synthase PurL, PurM-like module, C1 and C2 domains [111181]
      1. Salmonella typhimurium [TaxId: 90371] [111182] (1)
        SQ P74881
    4. Thiamine monophosphate kinase (ThiL) C-terminal domain [118111]
      1. Aquifex aeolicus [TaxId: 63363] [118112] (9)
        SQ O67883
    5. Hydrogenase expression/formation protein HypE [160783]
      1. Thermococcus kodakaraensis [TaxId: 311400] [160784] (2)
        SQ Q5JII7 156-334
    6. Selenide, water dikinase SelD [160785]
      1. Aquifex aeolicus [TaxId: 63363] [160786] (7)
        SQ O67139 155-336
PF0523-like [143869] (1)
beta-alpha-beta-alpha(3)-beta-alpha-beta-alpha; 3 layers, a/b/a; antiparallel beta-sheet, order 4132; some similarity to the PurM C-terminal domain-like fold (scop_cf 56041)
1. PF0523-like [143870] (1)
  uperfamily
  1. PF0523-like [143871] (1)
    Pfam 04416; DUF509
    1. Hypothetical protein PF0523 [143872]
      1. Pyrococcus furiosus [TaxId: 2261] [143873] (1)
        SQ Q8U3E5 2-137
Chorismate synthase, AroC [103262] (1)
duplication: consists of two DCoH-like beta(2)-alpha-beta(2)-alpha structural repeats; 3 layers, beta/alpha/beta
1. Chorismate synthase, AroC [103263] (1)
  uperfamily
  1. Chorismate synthase, AroC [103264] (5)
    1. Chorismate synthase, AroC [103265]
      1. Streptococcus pneumoniae [TaxId: 1313] [103266] (1)
      2. Aquifex aeolicus [TaxId: 63363] [103267] (1)
      3. Campylobacter jejuni [TaxId: 197] [103268] (1)
      4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [103269] (2)
      5. Helicobacter pylori [TaxId: 210] [111183] (2)
        SQ P56122
Hsp33 domain [64396] (1)
3 layers: beta/alpha/beta; buried helix
1. Hsp33 domain [64397] (1)
  uperfamily
  1. Hsp33 domain [64398] (3)
    forms strand-swapped dimer
    1. Heat shock protein 33, Hsp33 [64399]
      1. Escherichia coli [TaxId: 562] [64400] (2)
      2. Bacillus subtilis [TaxId: 1423] [118113] (1)
        SQ P37565
      3. Thermotoga maritima [TaxId: 2336] [118114] (1)
        SQ Q9X1B4
MTH1598-like [69818] (1)
beta(2)-alpha-beta-alpha-beta(4); 3 layers: beta/alpha/beta; some similarity to the Hsp33 fold
1. MTH1598-like [69819] (1)
  uperfamily
  1. MTH1598-like [69820] (2)
    1. Hypothetical protein MTH1598 [69821]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [69822] (1)
    2. Hypothetical protein TM1083 [75550]
      1. Thermotoga maritima [TaxId: 2336] [75551] (1)
Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68929] (1)
beta-alpha-beta(4)-alpha-beta(2); 3 layers: beta/alpha/beta; buried helix
1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68930] (1)
  uperfamily
  1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68931] (1)
    1. Protein-L-isoaspartyl O-methyltransferase, C-terminal domain [68932]
      1. Thermotoga maritima [TaxId: 2336] [53356] (1)
OsmC-like [82783] (1)
swapped dimer of beta(3)-alpha-beta(2)-alpha(2)-beta subunits; mixed beta-sheet; order: 321[4][5][6]; buried helix
1. OsmC-like [82784] (2)
  uperfamily
  1. Ohr/OsmC resistance proteins [82785] (9)
    1. Organic hydroperoxide resistance protein Ohr [82786]
      1. Pseudomonas aeruginosa, pa01 [TaxId: 287] [82787] (1)
      2. Deinococcus radiodurans [TaxId: 1299] [103270] (1)
    2. Osmotically inducible protein OsmC [103271]
      1. Escherichia coli [TaxId: 562] [103272] (2)
    3. Hypothetical protein MPN625 [103273]
      1. Mycoplasma pneumoniae [TaxId: 2104] [103274] (1)
      2. Thermus thermophilus [TaxId: 274] [103275] (1)
    4. Hypothetical protein VCA0330 [160787]
      1. Vibrio cholerae [TaxId: 666] [160788] (2)
        SQ Q9KMK9 7-161
    5. Hypothetical protein GSU2788 [160789]
      1. Geobacter sulfurreducens [TaxId: 35554] [160790] (2)
        SQ Q749F5 4-185! SQ Q749F5 5-186
    6. Uncharacterized protein Psyc0566 [160791]
      1. Psychrobacter arcticus 273-4 [TaxId: 259536] [160792] (1)
        SQ Q4FU81 1-132
    7. Hypothetical protein Ta0195 [160793]
      1. Thermoplasma acidophilum [TaxId: 2303] [160794] (2)
        SQ Q9HLN2 1-139
  2. YhfA-like [90027] (2)
    1. Hypothetical protein in CRP region [90028]
      probably the same as YhfA
      1. Escherichia coli [TaxId: 562] [90029] (1)
    2. Hypothetical protein TM0919 [111184]
      1. Thermotoga maritima [TaxId: 2336] [111185] (1)
        SQ Q9X021
Hypothetical protein HI1480 [103276] (1)
beta-alpha(4)-beta-alpha-beta; segregated alpha-helical and beta-sheet subdomains; dimeric beta-sheet barrel: n=6, S=10
1. Hypothetical protein HI1480 [103277] (1)
  uperfamily
  1. Hypothetical protein HI1480 [103278] (1)
    1. Hypothetical protein HI1480 [103279]
      1. Haemophilus influenzae [TaxId: 727] [103280] (1)
        structural genomics
ERH-like [143874] (1)
beta(2)-alpha(2)-beta(2)-alpha; antiparallel beta-sheet, order:2134; helices are arranged in a bundle rather than packed agains beta-sheet; dimerises via with the formation of a flattened beta-barel: closed n=8, S=10
1. ERH-like [143875] (1)
  uperfamily
  1. ERH-like [143876] (1)
    Pfam 01133
    1. Enhancer of rudimentary homolog, ERH [143877]
      1. Mouse (Mus musculus) [TaxId: 10090] [143878] (7)
        SQ P84089 1-104! SQ P84090 2-101
        also includes 100% identical human protein P84090 (1W9G)
Ribosomal protein S8 [56046] (1)
consists of 2 different alpha+beta subdomains arranged in a 4-layer structure: b/a/b/a
1. Ribosomal protein S8 [56047] (1)
  uperfamily
  1. Ribosomal protein S8 [56048] (4)
    1. Ribosomal protein S8 [56049]
      1. Bacillus stearothermophilus [TaxId: 1422] [56050] (1)
      2. Thermus thermophilus [TaxId: 274] [56051] (46)
        SQ P24319
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [64401] (1)
      4. Escherichia coli [TaxId: 562] [111186] (9)
        SQ P02361
Ribosomal protein L6 [56052] (1)
consists of two beta-sheets and one alpha-helix packed around single core
1. Ribosomal protein L6 [56053] (1)
  uperfamily
  1. Ribosomal protein L6 [56054] (6)
    1. Ribosomal protein L6 [56055]
      duplication: consists of two domains of this fold
      1. Bacillus stearothermophilus [TaxId: 1422] [56056] (9)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [56057] (61)
        SQ P14135
      3. Human (Homo sapiens) [TaxId: 9606] [160795] (1)
        SQ P32969 1-87
      4. Escherichia coli [TaxId: 562] [160796] (54)
        SQ P02390 1-81! SQ P02390 82-176
      5. Thermus thermophilus [TaxId: 274] [160797] (22)
        SQ Q72I19 11-81! SQ Q72I19 82-170
      6. Deinococcus radiodurans [TaxId: 1299] [160798] (12)
        SQ Q9RSL3 8-82! SQ Q9RSL3 83-172
NE0471 N-terminal domain-like [143879] (1)
beta(3)-alpha(n)-beta(3)-alpha; the two meander beta-sheets and helices are packed against the same core
1. NE0471 N-terminal domain-like [143880] (1)
  uperfamily
  1. NE0471 N-terminal domain-like [143881] (1)
    1. Hypothetical protein NE0471 N-terminal domain [143882]
      1. Nitrosomonas europaea [TaxId: 915] [143883] (2)
        SQ Q82X29 4-87
Lp2179-like [160799] (1)
beta(2)-alpha-beta(4)-alpha-beta; contains two antiparallel beta-sheets (orders: 127 and 3456) packed against the longer C-terminal helix
1. Lp2179-like [160800] (1)
  1. Lp2179-like [160801] (1)
    Pfam 08866, DUF1831
    1. Hypothetical protein Lp2179 [160802]
      1. Lactobacillus plantarum [TaxId: 1590] [160803] (1)
        SQ Q88V95 1-113
RGC domain-like [143884] (1)
consists of two beta-sheets and four helices eclosing a cental cavity
1. RGC domain-like [143885] (1)
  uperfamily
  1. RGC domain [143886] (1)
    Pfam 03836; RasGAP C-terminus
    1. Ras GTPase-activating-like protein IQGAP1 [143887]
      1. Human (Homo sapiens) [TaxId: 9606] [143888] (1)
        SQ P46940 1559-1657
Smc hinge domain [75552] (1)
consists of 2 different alpha+beta subdomains; forms subdomain-swapped dimers
1. Smc hinge domain [75553] (1)
  uperfamily
  1. Smc hinge domain [75554] (1)
    1. Smc hinge domain [75555]
      1. Thermotoga maritima [TaxId: 2336] [75556] (3)
DNA mismatch repair protein MutL [118115] (1)
consists of two different alpha+beta (sub)domains; d1: [beta(3)-alpha-(insert of d2)-alpha(2)-beta; 2 layers, a/b; antiparallel sheet, order: 1234]; d2: [beta-alpha-beta(2)-alpha(2); 2 layers, a/b; antiparallel sheet, order: 132]
1. DNA mismatch repair protein MutL [118116] (1)
  uperfamily
  1. DNA mismatch repair protein MutL [118117] (1)
    1. DNA mismatch repair protein MutL [118118]
      1. Escherichia coli [TaxId: 562] [118119] (1)
        SQ P23367 433-614 # structure of the N-terminal domains (1-349) is also known, scop_sp 55883 and 54226
ATP-grasp [56058] (2)
Consists of two subdomains with different alpha+beta folds
shares functional and structural similarities with the PIPK and protein kinase superfamilies
1. Glutathione synthetase ATP-binding domain-like [56059] (9)
  uperfamily
  1. ATP-binding domain of peptide synthetases [56060] (4)
    1. Prokaryotic glutathione synthetase, C-domain [56061]
      1. Escherichia coli [TaxId: 562] [56062] (4)
    2. D-ala-D-ala ligase, C-domain [56063]
      1. Escherichia coli, gene ddlB [TaxId: 562] [56064] (3)
    3. D-alanine:D-lactate ligase VanA, C-domain [56065]
      1. Leuconostoc mesenteroides, Ddl2 [TaxId: 1245] [56066] (1)
      2. Enterococcus faecium [TaxId: 1352] [64402] (1)
  2. Lysine biosynthesis enzyme LysX ATP-binding domain [103281] (1)
    1. Lysine biosynthesis enzyme LysX ATP-binding domain [103282]
      1. Thermus thermophilus [TaxId: 274] [103283] (2)
  3. BC ATP-binding domain-like [56067] (8)
    1. Biotin carboxylase (BC), domain 2 [56068]
      subunit of acetyl-CoA and pyruvate carboxylases
      1. Escherichia coli [TaxId: 562] [56069] (13)
      2. Aquifex aeolicus [TaxId: 63363] [103284] (1)
    2. Glycinamide ribonucleotide synthetase (GAR-syn), domain 2 [56070]
      1. Escherichia coli [TaxId: 562] [56071] (1)
      2. Thermotoga maritima [TaxId: 2336] [111187] (1)
        SQ Q9X0X7
    3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), domain 2 [56072]
      1. Escherichia coli [TaxId: 562] [56073] (6)
    4. Glycinamide ribonucleotide transformylase PurT, domain 2 [56074]
      1. Escherichia coli [TaxId: 562] [56075] (7)
    5. Carbamoyl phosphate synthetase (CPS), large subunit ATP-binding domains [56076]
      duplication: CPS large subunit contains two full BC-like lobes: carboxyphosphate and carbamoyl phosphate domains
      1. Escherichia coli [TaxId: 562] [56077] (10)
        SQ P00968
    6. Acetyl-CoA carboxylase, BC-M subdomain [118120]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [118121] (2)
        SQ Q00955 13-566
  4. Synapsin C-terminal domain [56078] (3)
    1. Synapsin [56079]
      1. Cow (Bos taurus) [TaxId: 9913] [56080] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [103285] (2)
    2. Synapsin II [90030]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [90031] (2)
  5. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56081] (2)
    1. Succinyl-CoA synthetase, beta-chain, N-terminal domain [56082]
      1. Escherichia coli [TaxId: 562] [56083] (18)
      2. Pig (Sus scrofa) [TaxId: 9823] [56084] (6)
        GTP-specific enzyme
  6. Pyruvate phosphate dikinase, N-terminal domain [56085] (3)
    1. Pyruvate phosphate dikinase, N-terminal domain [56086]
      the common fold is interrupted by a 4-helical subdomain (residues 112-198)
      1. Clostridium symbiosum [TaxId: 1512] [56087] (7)
      2. Trypanosoma brucei [TaxId: 5691] [75557] (1)
      3. Maize (Zea mays) [TaxId: 4577] [143889] (2)
        SQ P11155 74-453
  7. Eukaryotic glutathione synthetase ATP-binding domain [56088] (2)
    circularly permuted version of prokaryotic enzyme
    1. Eukaryotic glutathione synthetase ATP-binding domain [56089]
      1. Human (Homo sapiens) [TaxId: 9606] [56090] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82788] (2)
  8. Glutathionylspermidine synthase ATP-binding domain-like [143890] (1)
    both terminal parts of Pfam 03738; GSP; overal similarity of the Pfam domain to the Eukaryotic glutathione synthetase
    1. Glutathionylspermidine synthase, synthetase domain [143891]
      1. Escherichia coli [TaxId: 562] [143892] (10)
        SQ P0AES0 201-378,497-615
  9. PurP ATP-binding domain-like [160804] (3)
    Pfam 06973; DUF1297
    1. 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase PurP [160805]
      1. Thermococcus kodakaraensis [TaxId: 311400] [160806] (3)
        SQ Q5JD28 98-310
      2. Methanocaldococcus jannaschii [TaxId: 2190] [160807] (4)
        SQ Q57600 124-361
      3. Pyrococcus furiosus [TaxId: 2261] [160808] (12)
        SQ Q8U0R7 100-334
2. DNA ligase/mRNA capping enzyme, catalytic domain [56091] (4)
  has a circularly permuted topology
  uperfamily
  1. ATP-dependent DNA ligase catalytic domain [56092] (3)
    1. ATP-dependent DNA ligase, N-terminal domain [56093]
      1. Bacteriophage T7 [TaxId: 10760] [56094] (1)
      2. Chlorella virus PBCV-1 [TaxId: 10506] [56095] (7)
    2. DNA ligase I (LIG1) [118122]
      1. Human (Homo sapiens) [TaxId: 9606] [118123] (1)
        SQ P18858 262-901
  2. Adenylation domain of NAD+-dependent DNA ligase [56096] (3)
    1. Adenylation domain of NAD+-dependent DNA ligase [56097]
      contains additional, N-terminal all-alpha subdomain
      1. Bacillus stearothermophilus [TaxId: 1422] [56098] (1)
      2. Thermus filiformis [TaxId: 276] [56099] (2)
      3. Enterococcus faecalis [TaxId: 1351] [118124] (2)
        SQ Q837V6 5-317
  3. mRNA capping enzyme [56100] (2)
    1. RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain [56101]
      1. Chlorella virus PBCV-1 [TaxId: 10506] [56102] (3)
    2. mRNA capping enzyme alpha subunit [90032]
      1. Yeast (Candida albicans) [TaxId: 5476] [90033] (1)
  4. RNA ligase [103286] (2)
    1. RNA ligase 2, N-terminal domain [103287]
      1. Bacteriophage T4 [TaxId: 10665] [103288] (1)
    2. RNA editing ligase MP52 [118125]
      1. Trypanosoma brucei [TaxId: 5691] [118126] (1)
        SQ P82863 52-316
SAICAR synthase-like [56103] (1)
consists of two alpha+beta subdomains
1. SAICAR synthase-like [56104] (3)
  shares functional and structural similarities with the ATP-grasp fold and protein kinase superfamilies
  uperfamily
  1. SAICAR synthase [56105] (2)
    1. SAICAR synthase [56106]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56107] (6)
      2. Thermotoga maritima [TaxId: 2336] [75558] (1)
        TM1243
  2. Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta [56108] (1)
    1. Phosphatidylinositol phosphate kinase IIbeta, PIPK IIbeta [56109]
      1. Human (Homo sapiens) [TaxId: 9606] [56110] (1)
  3. Inositol polyphosphate kinase (IPK) [111188] (2)
    Pfam 03770
    1. Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A [111189]
      1. Human (Homo sapiens) [TaxId: 9606] [111190] (3)
        SQ P23677 187-461
      2. Rat (Rattus norvegicus) [TaxId: 10116] [111191] (1)
        SQ P17105 203-458
Protein kinase-like (PK-like) [56111] (1)
consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
1. Protein kinase-like (PK-like) [56112] (7)
  shares functional and structural similarities with the ATP-grasp fold and PIPK
  uperfamily
  1. Protein kinases, catalytic subunit [88854] (74)
    members organized in the groups and subfamiles specified by the comments
    1. Cyclin-dependent PK, CDK2 [88855]
      CMGC group; CDKs subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [88856] (146)
        SQ P24941
      2. (Plasmodium falciparum) [TaxId: 5833] [103289] (4)
        CDK2 homologue Pfpk5
    2. Cyclin-dependent PK, CDK5 [88857]
      CMGC group; CDKs subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [88858] (4)
        SQ Q00535
    3. Cyclin-dependent PK, CDK6 [88859]
      CMGC group; CDKs subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [88860] (8)
    4. MAP kinase p38 [56129]
      CMGC group; ERK/MAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56130] (65)
      2. Mouse (Mus musculus) [TaxId: 10090] [56131] (3)
    5. MAP kinase p38-gamma [56132]
      CMGC group; ERK/MAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56133] (1)
    6. MAP kinase Erk2 [56134]
      CMGC group; ERK/MAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56135] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [56136] (10)
    7. c-jun N-terminal kinase (jnk3s) [56137]
      CMGC group; ERK/MAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56138] (17)
    8. Glycogen synthase kinase-3 beta (Gsk3b) [69823]
      CMGC group; GSK3 subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [69824] (17)
        SQ P49841 35-383 ! SQ P49841 35-384
    9. Protein kinase CK2, alpha subunit [56142]
      CMGC group; CK2 subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [75559] (4)
      2. Maize (Zea mays) [TaxId: 4577] [56143] (21)
      3. Rattus norvegicus [TaxId: 10116] [160809] (8)
    10. Sky1p [56148]
      CMGC group; Clk subfamily; serine/threonine kinase
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56149] (5)
    11. cAMP-dependent PK, catalytic subunit [56116]
      AGC group; PKA subfamily; serine/threonine kinase
      1. Pig (Sus scrofa) [TaxId: 9823] [56117] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [56118] (32)
        SQ P00517
      3. Mouse (Mus musculus) [TaxId: 10090] [56119] (17)
      4. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64403] (1)
    12. Pkb kinase (Akt-2) [82791]
      AGC group; RAC/Akt subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [82792] (18)
    13. G-protein coupled receptor kinase 2 [90034]
      AGC group; GRKs subfamily; serine/threonine kinase
      1. Cow (Bos taurus) [TaxId: 9913] [90035] (6)
    14. 3-phosphoinositide dependent protein kinase-1 Pdk1 [90036]
      AGC group; PBK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [90037] (13)
        SQ O15530 75-363
    15. Calmodulin-dependent protein kinase [56120]
      CaMK group; CAMKI subfamily; serine/threonine kinase
      1. Rat (Rattus norvegicus) [TaxId: 10116] [56121] (1)
    16. Titin, kinase domain [56124]
      CaMK group; CAMKI subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56125] (1)
    17. Twitchin, kinase domain [56126]
      CaMK group; CAMKI subfamily; serine/threonine kinase
      1. California sea hare (Aplysia californica), twk43 [TaxId: 6500] [56127] (1)
      2. Caenorhabditis elegans, pjk4 [TaxId: 6239] [56128] (1)
    18. Death-associated protein kinase, Dap [75560]
      CaMK group; CAMKI subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [75561] (6)
        SQ P53355 2-285
    19. gamma-subunit of glycogen phosphorylase kinase (Phk) [56122]
      CaMK group; CAMKI subfamily; serine/threonine kinase
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [56123] (3)
    20. MAP kinase activated protein kinase 2, mapkap2 [82789]
      CaMK group; MAPKAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [82790] (6)
    21. Cell cycle checkpoint kinase chk1 [64404]
      CaMK group; CAMKL subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [64405] (36)
    22. pak1 [56146]
      OPK group; PAK/STE20 subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56147] (2)
    23. Mycobacterial protein kinase PknB, catalytic domain [82793]
      OPK group; PKN subfamily; serine/threonine kinase
      1. Mycobacterium tuberculosis [TaxId: 1773] [82794] (6)
    24. Casein kinase-1, CK1 [56139]
      OPK group; CKI subfamily; serine/threonine kinase
      1. Rat (Rattus norvegicus) [TaxId: 10116] [56140] (2)
      2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [56141] (3)
    25. Aurora-related kinase 1 (aurora-2) [90038]
      OPK group; AIRK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [90039] (10)
    26. B-Raf kinase [103290]
      OPK group; RAF subfamily; serine/threonine kinase; possible evolutionary link to tyrosine kinases
      1. Human (Homo sapiens) [TaxId: 9606] [103291] (2)
    27. Type I TGF-beta receptor R4 [56144]
      TKL group; STKR subfamily; serine/threonine kinase; possible evolutionary link to tyrosine kinases
      1. Human (Homo sapiens) [TaxId: 9606] [56145] (4)
        SQ P36897 200-500 ! SQ P36897 201-503
    28. c-src tyrosine kinase [56155]
      PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56156] (10)
      2. Chicken (Gallus gallus) [TaxId: 9031] [56157] (1)
    29. Haemopoetic cell kinase Hck [56151]
      PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56152] (4)
    30. Lymphocyte kinase (lck) [56153]
      PTK group; Src subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56154] (19)
    31. Bruton's tyrosine kinase (Btk) [75564]
      PTK group; Tec/Atk subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [75565] (1)
    32. Carboxyl-terminal src kinase (csk) [56164]
      PTK group; CSK subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56165] (4)
    33. Abelsone tyrosine kinase (abl) [56166]
      PTK group; Abl subfamily; non-membrane spanning protein tyrosine kinase
      1. Mouse (Mus musculus) [TaxId: 10090] [56167] (10)
    34. Musk tyrosine kinase [82797]
      PTK group; MUSK subfamily; non-membrane spanning protein tyrosine kinase
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82798] (1)
    35. Focal adhesion kinase 1 (fak) [103292]
      PTK group; FAK subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [103293] (6)
    36. EGF receptor tyrosine kinase, Erbb-1 [82795]
      PTK group; EGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [82796] (10)
        SQ P00533 702-1018
    37. ephb2 receptor tyrosine kinase [69827]
      PTK group; Eph/Elk/Eck subfamily; membrane spanning protein tyrosine kinase
      1. Mouse (Mus musculus) [TaxId: 10090] [69828] (1)
    38. epha2 receptor tyrosine kinase [103294]
      PTK group; Eph/Elk/Eck subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [103295] (1)
    39. Tie2 kinase [64406]
      PTK group; Tie/Tck subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [64407] (1)
    40. Fibroblast growth factor receptor 1 [56158]
      PTK group; FGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56159] (4)
    41. Fibroblast growth factor receptor 2 [75562]
      PTK group; FGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [75563] (4)
        SQ P21802 467-765
    42. Vascular endothelial growth factor receptor 2 (kdr) [56160]
      PTK group; PDGFR/VEGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56161] (4)
    43. c-KIT receptor [103296]
      PTK group; PDGFR/VEGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [103297] (3)
        SQ P10721 547-935
    44. Fl cytokine receptor [103298]
      PTK group; CSF-1/PDGF receptor subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [103299] (1)
    45. Insulin receptor [56162]
      PTK group; InsR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [56163] (13)
    46. Insulin-like growth factor 1 receptor [69825]
      PTK group; InsR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [69826] (9)
    47. Hepatocyte growth factor receptor, c-MET [103300]
      PTK group; HGFR subfamily; membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [103301] (6)
    48. Ribosomal protein S6 kinase alpha 5, Msk1 [111192]
      AGC group (?); S6 kinase subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111193] (1)
        SQ O75582 24-345
    49. Tyrosine-protein kinase Itk/Tsk [111194]
      PTK group; Tec/Atk subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111195] (3)
        SQ Q08881 357-619
    50. Protein kinase wnk1 [111196]
      OPK group; WNK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111197] (1)
        SQ Q9JIH7 211-480
    51. Tyrosine-protein kinase ZAP-70 [111198]
      PTK group; SYK/ZAP-70 subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111199] (1)
        SQ P43403 328-606 # structure of the N-terminal SH2 domains (1-132;133-256) is also known: 1m61 (scop_sp 89997)
    52. Activated CDC42 kinase 1, ACK1 [111200]
      PTK group; Tck subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111201] (3)
        SQ Q07912 117-389
    53. Mitogen-activated protein kinase 8 (jnk1) [111202]
      CMGC group; ERK/MAPK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [111203] (2)
        SQ P45983 9-363
    54. Serine/threonine protein kinase TAO2 [118127]
      OPK group; serine/threonine kinase
      1. Rat (Rattus norvegicus) [TaxId: 10116] [118128] (4)
        SQ Q9JLS3 12-320
    55. Protein kinase C, theta type [118129]
      AGC group; PKC subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118130] (1)
        SQ Q04759 377-696
    56. Tyrosine-protein kinase SYK [118131]
      PTK group; SYK/ZAP-70 subfamily; non-membrane spanning protein tyrosine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118132] (3)
        SQ P43405 363-635 # structure of the SH2 domain tandem region (9-265) is also known (scop_sp 55576)
    57. Proto-oncogene serine/threonine-protein kinase Pim-1 [118133]
      OPK group(?); PIM subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118134] (8)
        SQ P11309 33-305 ! SQ P11309 32-308
    58. Dual specificity mitogen-activated protein kinase kinase 2, Mek2 [118135]
      OPK group (?); MAPKK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118136] (1)
        SQ P36507 60-393
    59. Dual specificity mitogen-activated protein kinase kinase 1, Mek1 [118137]
      OPK group (?); MAPKK subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118138] (2)
        SQ Q02750 61-381
    60. Cell division protein kinase 7, CDK7 [118139]
      CMGC group; CDKs subfamily; serine/threonine kinase
      1. Human (Homo sapiens) [TaxId: 9606] [118140] (1)
        SQ P50613 13-311
    61. Serine/threonine-protein kinase Nek2 [143893]
      NIMA subfamily (NimA-related protein kinase 2)
      1. Human (Homo sapiens) [TaxId: 9606] [143894] (1)
        SQ P51955 3-271
    62. Cell division protein kinase 9, CDK9 [160810]
      1. Human (Homo sapiens) [TaxId: 9606] [160811] (3)
        SQ P50750 8-325
    63. STE20-like serine/threonine-protein kinase, SLK [160812]
      1. Human (Homo sapiens) [TaxId: 9606] [160813] (3)
        SQ Q9H2G2 21-308
  2. Actin-fragmin kinase, catalytic domain [56168] (1)
    Atypical protein kinases
    1. Actin-fragmin kinase, catalytic domain [56169]
      1. Physarum polycephalum [TaxId: 5791] [56170] (1)
  3. MHCK/EF2 kinase [64408] (1)
    Atypical protein kinases
    1. Trp Ca-channel kinase domain [64409]
      contains closed beta-barrel (n=6; S=10) in the N-terminal subdomain
      1. Mouse (Mus musculus) [TaxId: 10090] [64410] (3)
  4. Phoshoinositide 3-kinase (PI3K), catalytic domain [56171] (2)
    1. Phoshoinositide 3-kinase (PI3K), catalytic domain [56172]
      1. Pig (Sus scrofa) [TaxId: 9823] [56173] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [56174] (3)
  5. Choline kinase [90040] (1)
    1. Choline kinase [90041]
      1. Caenorhabditis elegans [TaxId: 6239] [90042] (1)
  6. APH phosphotransferases [64411] (5)
    1. Type IIIa 3',5"-aminoglycoside phosphotransferase [64412]
      1. Enterococcus faecalis [TaxId: 1351] [64413] (5)
    2. Aminoglycoside 3'-phosphotransferase IIa (Kanamycin kinase) [103302]
      1. Bacteria (Klebsiella pneumoniae) [TaxId: 573] [103303] (1)
    3. Methylthioribose kinase MtnK [160814]
      1. Bacillus subtilis [TaxId: 1423] [160815] (12)
        SQ O31663 5-396
    4. Homoserine kinase ThrB [160816]
      1. Agrobacterium tumefaciens [TaxId: 358] [160817] (1)
        SQ Q8UHA8 5-320
    5. RdoA [160818]
      Hypothetical protein YihE
      1. Escherichia coli [TaxId: 562] [160819] (1)
        SQ P0C0K3 4-328
  7. RIO1-like kinases [111204] (1)
    Pfam 01163
    1. Rio2 serine protein kinase C-terminal domain [111205]
      1. Archaeoglobus fulgidus [TaxId: 2234] [111206] (5)
        SQ O30245 # AF2426
FAD-binding/transporter-associated domain-like [56175] (1)
consists of two alpha+beta subdomains
1. FAD-binding/transporter-associated domain-like [56176] (4)
  uperfamily
  1. FAD-linked oxidases, N-terminal domain [56177] (5)
    1. Vanillyl-alcohol oxidase [56178]
      1. Fungus (Penicillium simplicissimum) [TaxId: 69488] [56179] (16)
        SQ P56216
    2. Flavoprotein subunit of p-cresol methylhydroxylase [56180]
      the other subunit is a short-chain cytochrome c
      1. Pseudomonas putida [TaxId: 303] [56181] (5)
    3. D-lactate dehydrogenase [56182]
      1. Escherichia coli [TaxId: 562] [56183] (1)
    4. Cholesterol oxidase [64414]
      1. Brevibacterium sterolicum [TaxId: 1702] [64415] (2)
    5. Cytokinin dehydrogenase 1 [111207]
      1. Maize (Zea mays) [TaxId: 4577] [111208] (4)
        SQ Q9T0N8
  2. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain [56184] (2)
    1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain [56185]
      1. Escherichia coli [TaxId: 562] [56186] (5)
      2. Staphylococcus aureus [TaxId: 1280] [64416] (1)
  3. CO dehydrogenase flavoprotein N-terminal domain-like [56187] (6)
    1. Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain [56188]
      1. Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137] [56189] (7)
      2. Hydrogenophaga pseudoflava [TaxId: 47421] [56190] (2)
    2. Xanthine oxidase, domain 3 (?) [56191]
      1. Cow (Bos taurus) [TaxId: 9913] [56192] (7)
        SQ P80457
    3. Xanthine dehydrogenase chain A, domain 3 [69829]
      1. Rhodobacter capsulatus [TaxId: 1061] [69830] (2)
    4. Quinoline 2-oxidoreductase medium subunit QorM [111209]
      1. Pseudomonas putida [TaxId: 303] [111210] (1)
        SQ P72222
    5. 4-hydroxybenzoyl-CoA reductase beta subunit HrcB, N-terminal domain [118141]
      1. Thauera aromatica [TaxId: 59405] [118142] (2)
        SQ O33820
  4. CorC/HlyC domain-like [160820] (12)
    Pfam 03471; similar to the C-terminal subdomain of FAD-binding domain with transposition of strands 3 and 4; possible adenosine cofactor-binding domain
    1. Putative hemolysin SMU1693 [160821]
      HlyX
      1. Streptococcus mutans [TaxId: 1309] [160822] (1)
        SQ O68574 352-435
    2. Hypothetical protein CT0541 [160823]
      1. Chlorobium tepidum [TaxId: 1097] [160824] (12)
        SQ Q8KEZ1 345-428
    3. Uncharacterized protein NE2227 [160825]
      1. Nitrosomonas europaea [TaxId: 915] [160826] (2)
        SQ Q82SS8 431-515
    4. Hypothetical protein HI0107 [160827]
      1. Haemophilus influenzae [TaxId: 727] [160828] (1)
        SQ Q57017 343-420
    5. Putative protein NMB1485 [160829]
      1. Neisseria meningitidis [TaxId: 487] [160830] (1)
        SQ Q9JYP7 441-516
    6. Putative hemolysin EF0700 [160831]
      1. Enterococcus faecalis [TaxId: 1351] [160832] (1)
        SQ Q837X5 350-433
    7. Hypothetical protein PG0272 [160833]
      1. Porphyromonas gingivalis [TaxId: 837] [160834] (1)
        SQ Q7MXD1 327-413
    8. Uncharacterized protein NMB0537 [160835]
      1. Neisseria meningitidis [TaxId: 487] [160836] (4)
        SQ Q9K0P8 191-274
    9. Hypothetical protein HD1797 [160837]
      1. Haemophilus ducreyi [TaxId: 730] [160838] (2)
        SQ Q7VKS4 347-428
    10. Hemolysin TlyC [160839]
      1. Xylella fastidiosa [TaxId: 2371] [160840] (2)
        SQ Q87DZ3 353-439! SQ Q87DZ3 355-439
    11. Probable hemolysin CV0231 [160841]
      1. Chromobacterium violaceum [TaxId: 536] [160842] (6)
        SQ Q7P1I2 341-427
    12. Uncharacterized protein Cgl1194/Cg1349 [160843]
      1. Corynebacterium glutamicum [TaxId: 1718] [160844] (1)
        SQ Q8NR63 356-453
Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56193] (1)
consists of two alpha+beta subdomains
1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56194] (1)
  uperfamily
  1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56195] (2)
    1. Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain [56196]
      N-terminal domain is a FAD-binding domain
      1. Escherichia coli [TaxId: 562] [56197] (5)
      2. Staphylococcus aureus [TaxId: 1280] [64417] (1)
Methenyltetrahydromethanopterin cyclohydrolase [56198] (1)
consists of two alpha+beta subdomains
1. Methenyltetrahydromethanopterin cyclohydrolase [56199] (1)
  uperfamily
  1. Methenyltetrahydromethanopterin cyclohydrolase [56200] (1)
    1. Methenyltetrahydromethanopterin cyclohydrolase [56201]
      1. Archaeon Methanopyrus kandleri [TaxId: 2320] [56202] (1)
Prim-pol domain [56746] (1)
consists of two alpha+beta domains
1. Prim-pol domain [56747] (3)
  uperfamily
  1. PriA-like [56748] (3)
    contains additional insert all-alpha subdomain
    1. DNA primase [56749]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56750] (1)
      2. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103304] (2)
    2. DNA primase small subunit PriA [143895]
      includes insert zinc-finger domain and extra C-terminal alpha+beta subdomain
      1. Sulfolobus solfataricus [TaxId: 2287] [143896] (1)
        SQ Q97Z83 3-329
  2. Bifunctional DNA primase/polymerase N-terminal domain [103305] (1)
    1. Bifunctional DNA primase/polymerase N-terminal domain [103306]
      1. Archaeon Sulfolobus islandicus [TaxId: 43080] [103307] (3)
  3. HP0184-like [143897] (1)
    stand-alone domain with the least decorated Prim-pol fold
    1. Hypothetical protein HP0184 [143898]
      1. Helicobacter pylori [TaxId: 210] [143899] (1)
        SQ O24984 3-178
Hect, E3 ligase catalytic domain [56203] (1)
consists of two alpha+beta domains; the N-terminal domain is array of helices and beta-hairpins; the C-terminal domain is an a/b sandwich with one left-handed beta-alpha(n)-beta unit; conformational flexibility of domain orientation
1. Hect, E3 ligase catalytic domain [56204] (1)
  uperfamily
  1. Hect, E3 ligase catalytic domain [56205] (2)
    1. Ubiquitin-protein ligase E3a (E6ap) [56206]
      1. Human (Homo sapiens) [TaxId: 9606] [56207] (2)
    2. WW domain-containing protein 1, WWP1 [103308]
      1. Human (Homo sapiens) [TaxId: 9606] [103309] (1)
Nitrile hydratase alpha chain [56208] (1)
4 layers a/b/b/a; inside is a sandwich of two 2-stranded beta-sheets
1. Nitrile hydratase alpha chain [56209] (1)
  duplication: contains two structural repeats
  uperfamily
  1. Nitrile hydratase alpha chain [56210] (3)
    1. Iron-containing nitrile hydratase [56211]
      1. Rhodococcus erythropolis [TaxId: 1833] [56212] (9)
        also Rhodococcus sp. R312
    2. Cobalt-containing nitrile hydratase [82799]
      1. Pseudonocardia thermophila [TaxId: 1848] [82800] (5)
        SQ Q7SID2
      2. Bacillus smithii [TaxId: 1479] [118143] (1)
        SQ Q84FS5 # 93% sequence identity; Bacillus sp. RAPc8 TaxID: 218609
4'-phosphopantetheinyl transferase [56213] (1)
beta-alpha(3)-beta(2) motif
1. 4'-phosphopantetheinyl transferase [56214] (2)
  possibly related to the IspF (d.79.5) and YjgF-like superfamilies (d.79.1)
  uperfamily
  1. Holo-(acyl carrier protein) synthase ACPS [64418] (2)
    forms trimers with three closely packed beta-sheets similar to the IspF trimers
    1. Holo-(acyl carrier protein) synthase ACPS [64419]
      1. Bacillus subtilis [TaxId: 1423] [64420] (3)
      2. Streptococcus pneumoniae [TaxId: 1313] [64421] (3)
  2. 4'-Phosphopantetheinyl transferase SFP [56215] (1)
    monomeric; tandem duplication of beta-alpha(3)-beta(2) motif
    1. 4'-Phosphopantetheinyl transferase SFP [63407]
      1. Bacillus subtilis [TaxId: 1423] [56217] (1)
DNase I-like [56218] (1)
contains beta-sandwich; duplication of alpha+beta motif
1. DNase I-like [56219] (3)
  uperfamily
  1. DNase I-like [56220] (8)
    1. DNA-repair enzyme exonuclease III [56221]
      1. Escherichia coli [TaxId: 562] [56222] (1)
    2. DNA repair endonuclease Hap1 [56223]
      Major apurinic/apyrimidinic endonuclease APE1
      1. Human (Homo sapiens) [TaxId: 9606] [56224] (9)
    3. Deoxyribonuclease I [56225]
      1. Cow (Bos taurus) [TaxId: 9913] [56226] (11)
    4. Endonuclease domain of LINE-1 reverse transcriptase homolog [111211]
      1. Human (Homo sapiens) [TaxId: 9606] [111212] (1)
        SQ P08547 2-237
    5. Cytolethal distending toxin subunit B [111213]
      1. Haemophilus ducreyi [TaxId: 730] [111214] (1)
        SQ O06523 23-283
      2. Actinobacillus actinomycetemcomitans [TaxId: 714] [143900] (2)
        SQ Q7DK12 23-283
      3. Escherichia coli [TaxId: 562] [143901] (1)
        SQ Q46669 19-269
    6. Endonuclease domain of TRAS1 retrotransposon (ORF2) [111215]
      1. Silkworm (Bombyx mori) [TaxId: 7091] [111216] (1)
        SQ Q93139 1-184
  2. Inositol polyphosphate 5-phosphatase (IPP5) [64422] (2)
    1. Synaptojanin, IPP5C domain [64423]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64424] (2)
    2. Salivary nitrophorin [103310]
      heme-binding homologue of IPP5
      1. Bedbug (Cimex lectularius) [TaxId: 79782] [103311] (5)
        SQ O7674 23-302
  3. Sphingomyelin phosphodiesterase-like [143902] (2)
    part of Pfam 03372
    1. Sphingomyelin phosphodiesterase C [143903]
      1. Bacillus cereus [TaxId: 1396] [143904] (10)
        SQ P11889 34-332
      2. Listeria ivanovii [TaxId: 1638] [143905] (1)
        SQ Q9RLV9 41-333
Aldehyde ferredoxin oxidoreductase, N-terminal domain [56227] (1)
contains sandwich; duplication of alpha+beta motif with single mixed sheet
motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56228] (1)
  uperfamily
  1. Aldehyde ferredoxin oxidoreductase, N-terminal domain [56229] (2)
    1. Aldehyde ferredoxin oxidoreductase [56230]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56231] (1)
    2. Formaldehyde ferredoxin oxidoreductase [56232]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [56233] (2)
Ntn hydrolase-like [56234] (2)
4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
1. N-terminal nucleophile aminohydrolases (Ntn hydrolases) [56235] (7)
  N-terminal residue provides two catalytic groups, nucleophile and proton donor
  uperfamily
  1. Class II glutamine amidotransferases [56236] (9)
    has slightly different topology than other families do
    1. Glucosamine 6-phosphate synthase, N-terminal domain [56237]
      1. Escherichia coli [TaxId: 562] [56238] (8)
        SQ P17169 1-238
    2. Glutamine PRPP amidotransferase, N-terminal domain [56239]
      1. Bacillus subtilis [TaxId: 1423] [56240] (2)
      2. Escherichia coli [TaxId: 562] [56241] (5)
    3. Asparagine synthetase B, N-terminal domain [56242]
      1. Escherichia coli [TaxId: 562] [56243] (1)
    4. beta-Lactam synthetase [69831]
      Asparagine synthetase B homologue
      1. Streptomyces clavuligerus [TaxId: 1901] [69832] (5)
      2. Pectobacterium carotovorum [TaxId: 554] [103312] (2)
        carbapenam synthetase CarA
    5. Alpha subunit of glutamate synthase, N-terminal domain [69833]
      1. Azospirillum brasilense [TaxId: 192] [69834] (7)
      2. Synechocystis sp. [TaxId: 1143] [75566] (5)
    6. Hypothetical protein YafJ (PA1307) [111217]
      1. Pseudomonas aeruginosa [TaxId: 287] [111218] (1)
        SQ Q9I437
  2. Penicillin acylase, catalytic domain [56244] (4)
    1. Penicillin acylase [56245]
      also contains 2 all-alpha and a beta-barrel domains
      will be divided into domains in future release
      1. Escherichia coli [TaxId: 562] [56246] (24)
      2. Providencia rettgeri [TaxId: 587] [56247] (1)
    2. Cephalosporin acylase [64425]
      1. Brevundimonas diminuta [TaxId: 293] [64426] (4)
      2. Pseudomonas sp., glutarylamidase [TaxId: 306] [69835] (5)
  3. Penicillin V acylase [56248] (1)
    1. Penicillin V acylase [56249]
      1. Bacillus sphaericus [TaxId: 1421] [56250] (2)
  4. Proteasome subunits [56251] (14)
    1. Proteasome beta subunit (catalytic) [56252]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56253] (50)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90043] (1)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56254] (112)
        The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
      4. Cow (Bos taurus) [TaxId: 9913] [75567] (1)
      5. Rhodococcus erythropolis [TaxId: 1833] [103313] (9)
    2. Proteasome alpha subunit (non-catalytic) [56255]
      contains an extension to the common fold at the N-terminus
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56256] (50)
      2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90044] (2)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56257] (108)
        The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
      4. Cow (Bos taurus) [TaxId: 9913] [75568] (1)
      5. Rhodococcus erythropolis [TaxId: 1833] [103314] (9)
    3. HslV (ClpQ) protease [56258]
      dodecameric prokaryotic homologue of proteasome
      1. Escherichia coli [TaxId: 562] [56259] (7)
      2. Haemophilus influenzae [TaxId: 727] [56260] (6)
      3. Thermotoga maritima [TaxId: 2336] [90045] (1)
      4. Bacillus subtilis [TaxId: 1423] [160845] (26)
        SQ P39070 2-181
  5. (Glycosyl)asparaginase [56261] (3)
    1. Glycosylasparaginase (aspartylglucosaminidase, AGA) [56262]
      the precursor chain is cleaved onto 2 fragments by autoproteolysis
      1. Human (Homo sapiens) [TaxId: 9606] [56263] (2)
      2. Flavobacterium meningosepticum [TaxId: 238] [56264] (8)
      3. Escherichia coli [TaxId: 562] [103315] (3)
        SQ P37595
        isoaspartyl peptidase with L-asparaginase activity
        putative L-asparaginase YbiK
  6. Gamma-glutamyltranspeptidase-like [143906] (4)
    Pfam 01019
    1. Hypothetical protein Ta0994 [143907]
      1. Thermoplasma acidophilum [TaxId: 2303] [143908] (4)
        SQ Q9HJH4 1-516
    2. Cephalosporin acylase [143909]
      1. Bacillus halodurans [TaxId: 86665] [143910] (4)
        SQ Q9KEI5 3-539
    3. Gamma-glutamyltranspeptidase, GGT [143911]
      1. Helicobacter pylori [TaxId: 210] [143912] (1)
        SQ O25743 29-375,380-565
      2. Escherichia coli [TaxId: 562] [143913] (14)
        SQ P18956 29-387,391-580! SQ P18956 29-580
  7. SPO2555-like [160846] (1)
    Pfam 06267; DUF1028
    1. Hypothetical protein SPO2555 [160847]
      1. Silicibacter pomeroyi [TaxId: 89184] [160848] (1)
        SQ Q5LQD5 1-229
2. Archaeal IMP cyclohydrolase PurO [75569] (1)
  has a putative active site in the same topological location as the Ntn hydrolase but lacks the N-terminal nucleophile
  uperfamily
  1. Archaeal IMP cyclohydrolase PurO [75570] (1)
    Pfam 07826
    1. Hypothetical protein MTH1020 [75571]
      1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75572] (13)
DmpA/ArgJ-like [56265] (1)
duplication of beta(3)-alpha-beta-alpha motif; 4 layers: alpha/beta/beta/alpha
1. DmpA/ArgJ-like [56266] (2)
  convergent similarity to the Ntn amidohydrolases
  uperfamily
  1. DmpA-like [56267] (1)
    Pfam 03576
    1. L-aminopeptidase D-Ala-esterase/amidase DmpA [56268]
      1. Ochrobactrum anthropi [TaxId: 529] [56269] (1)
  2. ArgJ-like [111219] (1)
    Pfam 01960; contains extra C-terminal alpha+beta domain [beta-alpha(2)-beta(2)-alpha-beta(2); 2 layers, a/b; mixed beta-sheet, order: 51423, strands 1 and 4 are parallel to each other]
    1. Glutamate N-acetyltransferase 2 (ornithine acetyltransferase) [111220]
      1. Streptomyces clavuligerus [TaxId: 1901] [111221] (3)
        SQ Q53940
        d1: 8-260; d2: 261-390
Pyruvoyl-dependent histidine and arginine decarboxylases [56270] (1)
duplication of beta-alpha-beta(2) motif; 4 layers: alpha/beta/beta/alpha; contains "silk" beta-sandwich
1. Pyruvoyl-dependent histidine and arginine decarboxylases [56271] (2)
  two chains result from self-processing single-chain precursor; form heterohexamer
  uperfamily
  1. Arginine decarboxylase [90046] (1)
    1. Arginine decarboxylase [90047]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [90048] (3)
  2. Histidine decarboxylase [56272] (1)
    1. Histidine decarboxylase [56273]
      1. Lactobacillus sp., strain 30a [TaxId: 1591] [56274] (6)
S-adenosylmethionine decarboxylase [56275] (1)
duplication of beta-alpha-beta(4)-alpha-beta-alpha-beta(2) motif; 4 layers a/b/b/a; antiparallel beta-sheets: order 23451687
1. S-adenosylmethionine decarboxylase [56276] (2)
  uperfamily
  1. S-adenosylmethionine decarboxylase [56277] (2)
    1. S-adenosylmethionine decarboxylase [56278]
      1. Human (Homo sapiens) [TaxId: 9606] [56279] (8)
      2. Potato (Solanum tuberosum) [TaxId: 4113] [82801] (1)
  2. Bacterial S-adenosylmethionine decarboxylase [111222] (1)
    Pfam 02675;homodimer; the subunit fold and assembly are similar to those of the structural repeats of the eukaryotic enzyme
    1. S-adenosylmethionine decarboxylase (SamDC, SpeH) [111223]
      1. Thermotoga maritima [TaxId: 2336] [111224] (4)
        SQ Q9WZC3
Metallo-hydrolase/oxidoreductase [56280] (1)
duplication of beta(4)-alpha-beta-alpha motif; 4 layers a/b/b/a; mixed beta-sheets
1. Metallo-hydrolase/oxidoreductase [56281] (14)
  uperfamily
  1. Zn metallo-beta-lactamase [56282] (10)
    1. Zn metallo-beta-lactamase [56283]
      1. Bacillus cereus [TaxId: 1396] [56284] (7)
        SQ P04190 31-257
      2. Bacteroides fragilis [TaxId: 817] [56285] (9)
      3. Xanthomonas maltophilia [TaxId: 40324] [56286] (20)
      4. Pseudomonas aeruginosa, IMP-1 [TaxId: 287] [56287] (8)
      5. Pseudomonas aeruginosa, VIM-2 [TaxId: 287] [103316] (2)
      6. Fluoribacter gormanii, (Legionella gormanii) FEZ-1 [TaxId: 464] [82802] (3)
      7. Chryseobacterium meningosepticum, carbapenemase BLAB-1 [TaxId: 238] [90049] (1)
      8. Aeromonas hydrophila, CphA [TaxId: 644] [118144] (5)
        SQ P26918 28-252
      9. Bradyrhizobium japonicum [TaxId: 375] [160849] (2)
        SQ Q89GW5 29-292
      10. Pseudomonas putida [TaxId: 303] [160850] (2)
  2. Hypothetical protein TM0207 [103317] (1)
    1. Hypothetical protein TM0207 [103318]
      1. Thermotoga maritima [TaxId: 2336] [103319] (1)
  3. Glyoxalase II (hydroxyacylglutathione hydrolase) [56288] (3)
    1. Glyoxalase II (hydroxyacylglutathione hydrolase) [56289]
      1. Human (Homo sapiens) [TaxId: 9606] [56290] (2)
      2. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [118145] (3)
        SQ Q9SID3
      3. Salmonella typhimurium [TaxId: 90371] [160851] (1)
        SQ Q8ZRM2 1-251
  4. ROO N-terminal domain-like [56291] (3)
    1. Rubredoxin oxygen:oxidoreductase (ROO), N-terminal domain [56292]
      1. Desulfovibrio gigas [TaxId: 879] [56293] (1)
    2. ROO-like flavoprotein TM0755, N-terminal domain [111225]
      1. Thermotoga maritima [TaxId: 2336] [111226] (1)
        SQ Q9WZL4 #
    3. Nitric oxide reductase N-terminal domain [143914]
      1. Moorella thermoacetica [TaxId: 1525] [143915] (12)
        SQ Q9FDN7 2-250
  5. Methyl parathion hydrolase [111227] (1)
    1. Methyl parathion hydrolase [111228]
      1. Pseudomonas sp. WBC-3 [TaxId: 165468] [111229] (1)
        SQ Q841S6 Q693X1 Q93SP1
  6. Coenzyme PQQ synthesis protein B, PqqB [118146] (1)
    1. Coenzyme PQQ synthesis protein B, PqqB [118147]
      1. Pseudomonas putida [TaxId: 303] [118148] (1)
        SQ Q88QV5
  7. RNase Z-like [143916] (3)
    part of Pfam 00753; tRNA 3'-endonuclease; elaborated with additional structures and insert alpha(2)-beta(2) subdomain
    1. Ribonuclease Z (RNase Z) [143917]
      1. Bacillus subtilis [TaxId: 1423] [143918] (3)
        SQ P54548 1-307
      2. Escherichia coli [TaxId: 562] [143919] (1)
        SQ P0A8V0 1-305
      3. Thermotoga maritima [TaxId: 2336] [143920] (4)
        SQ Q9WZW8 1-280
  8. Pce catalytic domain-like [143921] (1)
    part of Pfam 00753
    1. Teichoic acid phosphorylcholine esterase Pce (LytD), N-terminal domain [143922]
      1. Streptococcus pneumoniae [TaxId: 1313] [143923] (3)
        SQ Q8DQ62 26-334! SQ Q8DQ62 30-334
  9. YhfI-like [143924] (1)
    part of Pfam 00753
    1. Hypothetical protein BA1088 (BAS1016) [143925]
      B. subtilis YhfI ortholog
      1. Bacillus anthracis [TaxId: 1392] [143926] (4)
        SQ Q81U06 1-244
  10. beta-CASP RNA-metabolising hydrolases [143927] (4)
    contains insertion of a single helicase-like alpha/beta domain (from scop_sf 52540) but without the P-loop motif
    1. Hypothetical protein EF2904 [143928]
      1. Enterococcus faecalis [TaxId: 1351] [143929] (2)
        SQ Q82ZZ3 5-429
    2. Cleavage factor two protein 2, CFT2 [160852]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [160853] (1)
        SQ Q12102 1-422,627-717
    3. Putative RNA-degradation protein TTHA0252 [160854]
      1. Thermus thermophilus [TaxId: 274] [160855] (1)
        SQ Q5SLP1 1-431
    4. Cleavage and polyadenylation specificity factor subunit 3 [160856]
      1. Human (Homo sapiens) [TaxId: 9606] [160857] (1)
        SQ Q9UKF6 9-459
  11. TM0894-like [143930] (1)
    part of Pfam 00753
    1. Hypothetical protein TM0894 [143931]
      1. Thermotoga maritima [TaxId: 2336] [143932] (4)
        SQ Q9WZZ6 1-207
  12. Ava3068-like [160858] (1)
    1. Hypothetical protein Ava3068 [160859]
      1. Anabaena variabilis [TaxId: 1172] [160860] (2)
        SQ Q3M8K9 1-200
  13. Alkylsulfatase-like [160861] (1)
    subfamily of Pfam 00753; includes all-alpha linker subdomain
    1. Alkylsulfatase SdsA1 [160862]
      1. Pseudomonas aeruginosa [TaxId: 287] [160863] (4)
        SQ Q9I5I9 20-524
  14. PqsE-like [160864] (1)
    part of Pfam 00753; extended C-terminal region with extra helices
    1. Quinolone signal response protein PqsE [160865]
      1. Pseudomonas aeruginosa [TaxId: 287] [160866] (3)
        SQ Q02IG5 1-301
PP2C-like [81607] (1)
4 layers: alpha/beta/beta/alpha; antiparallel beta sheets
1. PP2C-like [81606] (1)
  contain binuclear metal (Mn) centre
  uperfamily
  1. PP2C-like [81605] (2)
    Pfam 00481
    1. Protein serine/threonine phosphatase 2C, catalytic domain [81604]
      1. Human (Homo sapiens) [TaxId: 9606] [81603] (1)
    2. putative serine/threonine phosphatase pstp/ppp [118149]
      1. Mycobacterium tuberculosis [TaxId: 1773] [118150] (1)
        SQ P71588
Metallo-dependent phosphatases [56299] (1)
4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
1. Metallo-dependent phosphatases [56300] (12)
  different families of this superfamily are groupped in a single Pfam family, Pfam 00149
  uperfamily
  1. Purple acid phosphatase-like [56301] (4)
    1. Plant purple acid phosphatase, catalytic domain [56302]
      also contain an Ig-like domain
      1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [56303] (9)
      2. Sweet potato (Ipomoea batatas) [TaxId: 4120] [118151] (1)
        SQ Q9SE00 39-462
    2. Mammalian purple acid phosphatase [56304]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [56305] (2)
      2. Pig (Sus scrofa) [TaxId: 9823] [56306] (1)
  2. DNA double-strand break repair nuclease [64427] (1)
    contains C-terminal alpha/beta subdomain
    1. Mre11 [64428]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64429] (3)
        SQ Q8U1N9
  3. 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [56307] (3)
    1. 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain [56308]
      1. Escherichia coli [TaxId: 562] [56309] (8)
        SQ P07024 26-550
      2. Thermus thermophilus [TaxId: 274] [160867] (1)
        SQ Q5SIP1 28-534
      3. Candida albicans [TaxId: 5476] [160868] (2)
        SQ Q5A5Q7 16-337
  4. Protein serine/threonine phosphatase [56310] (9)
    1. Protein phosphatase-1 (PP-1) [56311]
      1. Rabbit (Oryctolagus cuniculus), alpha isoform [TaxId: 9986] [56312] (1)
      2. Human (Homo sapiens), beta isoform [TaxId: 9606] [64430] (5)
        SQ P36873
      3. Human (Homo sapiens), gamma isoform [TaxId: 9606] [111230] (1)
        SQ P37140 1-308
      4. Rattus norvegicus [TaxId: 10116] [160869] (4)
    2. Protein phosphatase-2B (PP-2B, calcineurin A subunit) [56313]
      1. Cow (Bos taurus) [TaxId: 9913] [56314] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [56315] (5)
    3. lambda ser/thr protein phosphatase [64431]
      1. Bacteriophage lambda [TaxId: 10710] [64432] (1)
    4. Serine/threonine protein phosphatase 5, PP5 [111231]
      1. Human (Homo sapiens) [TaxId: 9606] [111232] (5)
        SQ P53041 176-499
    5. Protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha [143933]
      1. Human (Homo sapiens) [TaxId: 9606] [143934] (11)
        SQ P67775 2-294
  5. Phosphoesterase-related [82803] (1)
    1. Hypothetical protein PF1291 [82804]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82805] (1)
  6. TT1561-like [103320] (2)
    similar to purple acid and protein phosphatases
    1. Hypothetical protein TT1561 [103321]
      1. Thermus thermophilus [TaxId: 274] [103322] (1)
    2. Uncharacterized protein Aq_1956 [160870]
      1. Aquifex aeolicus [TaxId: 63363] [160871] (1)
        SQ O67769 4-260
  7. YfcE-like [111233] (6)
    1. Putative phosphodiesterase MJ0936 [111234]
      1. Methanococcus jannaschii [TaxId: 2190] [111235] (7)
        SQ Q58346
    2. Phosphodiesterase yfcE [111236]
      1. Escherichia coli [TaxId: 562] [111237] (1)
        SQ P76495
    3. Vacuolar protein sorting 29, VPS29 [143935]
      1. Mouse (Mus musculus) [TaxId: 10090] [143936] (5)
        SQ Q9QZ88 1-182
      2. Cryptosporidium parvum [TaxId: 5807] [143937] (2)
        SQ Q5CYJ7 5-197
      3. Homo sapiens [TaxId: 9606] [160872] (2)
    4. Uncharacterized protein SP1879 [160873]
      1. Streptococcus pneumoniae [TaxId: 1313] [160874] (1)
        SQ Q97NX4 1-173
  8. Hypothetical protein aq_1666 [118152] (1)
    1. Hypothetical protein aq_1666 [118153]
      1. Aquifex aeolicus [TaxId: 63363] [118154] (1)
        SQ O67582
  9. DR1281-like [118155] (2)
    1. Putative phosphatase DR1281 [118156]
      1. Deinococcus radiodurans [TaxId: 1299] [118157] (1)
        SQ Q9RUV0
    2. Hypothetical protein MPN349 [118158]
      1. Mycoplasma pneumoniae [TaxId: 2104] [118159] (1)
        SQ P75429
  10. TTHA0625-like [143938] (1)
    part of Pfam 00149
    1. Hypothetical protein TTHA0625 [143939]
      1. Thermus thermophilus [TaxId: 274] [143940] (8)
        SQ Q5SKL8 1-252
  11. GpdQ-like [160875] (2)
    part of Pfam 00149
    1. Rv0805 cyclic nucleotide phosphodiesterase [160876]
      1. Mycobacterium tuberculosis [TaxId: 1773] [160877] (3)
        SQ O06629 10-265
    2. Glycerophosphodiesterase GpdQ [160878]
      1. Enterobacter aerogenes [TaxId: 548] [160879] (14)
        SQ Q6XBH1 1-271
  12. ADPRibase-Mn-like [160880] (1)
    contains Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase (ADPRibase-Mn); part of Pfam 00149
    1. Uncharacterized C17orf48 homolog zgc:64213 [160881]
      1. Zebrafish (Danio rerio) [TaxId: 7955] [160882] (1)
        SQ Q7T291 3-322
Carbon-nitrogen hydrolase [56316] (1)
4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
1. Carbon-nitrogen hydrolase [56317] (2)
  Pfam 00795; some topological similarities to the metallo-dependent phosphatases and DNase I-like nucleases
  uperfamily
  1. Nitrilase [56318] (2)
    1. NIT-FHIT fusion protein, N-terminal domain [56319]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [56320] (1)
    2. hypothetical protein yl85 [69836]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69837] (1)
  2. Carbamilase [64433] (3)
    1. N-carbamoyl-D-aminoacid amidohydrolase [64434]
      1. Agrobacterium sp. [TaxId: 361] [64435] (5)
        SQ P60327
      2. Agrobacterium radiobacter [TaxId: 358] [64436] (9)
    2. Hypothetical protein PH0642 [103323]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103324] (1)
CNF1/YfiH-like putative cysteine hydrolases [64437] (1)
4 layers: alpha/beta/beta/alpha; mixed beta sheets
1. CNF1/YfiH-like putative cysteine hydrolases [64438] (3)
  uperfamily
  1. Type 1 cytotoxic necrotizing factor, catalytic domain [64439] (1)
    1. Type 1 cytotoxic necrotizing factor, catalytic domain [64440]
      1. Escherichia coli [TaxId: 562] [64441] (2)
  2. YfiH-like [111238] (5)
    Pfam 02578; COG1496
    1. Hypothetical protein YlmD [111239]
      1. Bacillus stearothermophilus [TaxId: 1422] [111240] (1)
        SQ P84138
    2. Hypothetical protein NMB0706 [111241]
      1. Neisseria meningitidis, serogroup B [TaxId: 487] [111242] (1)
        SQ Q9K0A8
    3. Hypothetical protein yfiH [111243]
      1. Salmonella typhi [TaxId: 90370] [111244] (1)
        SQ Q8Z4J1
      2. Shigella flexneri [TaxId: 623] [111245] (2)
        SQ Q83K13
    4. Hypothetical protein CC0490 [111246]
      1. Caulobacter crescentus [TaxId: 155892] [111247] (1)
        SQ Q9AAV3
  3. CheD-like [160883] (1)
    Pfam 03975
    1. Chemoreceptor glutamine deamidase CheD [160884]
      1. Thermotoga maritima [TaxId: 2336] [160885] (2)
        SQ Q9X005 1-157
ADC synthase [56321] (1)
duplication: contains four repeats of alpha-beta(2)-beta motif arranged in a 4 layer core structure: alpha/beta/beta/alpha; orthogonally packed beta-sheets
1. ADC synthase [56322] (1)
  the active site is formed by additional structures inserted into the core structure
  uperfamily
  1. ADC synthase [56323] (7)
    1. Anthranilate synthase aminodeoxyisochorismate synthase/lyase subunit, TrpE [56324]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [56325] (1)
      2. Salmonella typhimurium [TaxId: 90371] [64442] (1)
      3. Serratia marcescens [TaxId: 615] [64443] (2)
    2. P-aminobenzoate synthase component I [69838]
      Aminodeoxychorismate synthase
      1. Escherichia coli [TaxId: 562] [69839] (2)
    3. Menaquinone-specific isochorismate synthase MenF [143941]
      1. Escherichia coli [TaxId: 562] [143942] (4)
        SQ P38051 2-429
    4. Salicylate synthetase Irp9 [143943]
      1. Yersinia enterocolitica [TaxId: 630] [143944] (4)
        SQ Q9X9I8 2-434
    5. Salicylate synthase MbtI [143945]
      Mycobactin synthetase protein I
      1. Mycobacterium tuberculosis [TaxId: 1773] [143946] (5)
        SQ Q7D785 15-449
Sulfolobus fructose-1,6-bisphosphatase-like [111248] (1)
4 layers: a/b/b/a; antiparallel beta sheets; similarities to ferredoxin-like fold (scop_cf 54861) in the N-terminal part (1-120) and to the Bacterial S-adenosylmethionine decarboxylase subunit (scop_fa 997656) in the C-terminal part (121-340)
1. Sulfolobus fructose-1,6-bisphosphatase-like [111249] (1)
  uperfamily
  1. Sulfolobus fructose-1,6-bisphosphatase-like [111250] (1)
    Pfam 01950
    1. ST0318 [111251]
      1. Archaeon Sulfolobus tokodaii [TaxId: 111955] [111252] (1)
        SQ Q975V5
LDH C-terminal domain-like [56326] (1)
unusual fold, defines family
1. LDH C-terminal domain-like [56327] (2)
  uperfamily
  1. Lactate & malate dehydrogenases, C-terminal domain [56328] (28)
    N-terminal domain is NAD-binding module (alpha/beta Rossmann-fold domain)
    1. Malate dehydrogenase [56329]
      1. Pig (Sus scrofa) [TaxId: 9823] [56330] (3)
      2. Sorghum (Sorghum vulgare), chloroplast [TaxId: 4558] [56331] (1)
      3. Flaveria bidentis, chloroplast [TaxId: 4224] [56332] (1)
      4. Escherichia coli [TaxId: 562] [56333] (8)
      5. Thermus flavus [TaxId: 274] [56334] (2)
      6. Thermus thermophilus [TaxId: 274] [82806] (9)
        identical sequence to that from the Thermus flavus enzyme
      7. Archaeon Haloarcula marismortui [TaxId: 2238] [56335] (17)
      8. Aquaspirillum arcticum [TaxId: 87645] [56336] (3)
      9. Chloroflexus aurantiacus [TaxId: 1108] [69840] (7)
        SQ P80040
      10. Chlorobium tepidum [TaxId: 1097] [69841] (1)
      11. Chlorobium vibrioforme [TaxId: 1098] [69842] (2)
    2. L-2-hydroxyisocapronate dehydrogenase, L-HICDH [56337]
      1. Lactobacillus confusus [TaxId: 1583] [56338] (1)
    3. Lactate dehydrogenase [56339]
      1. Pig (Sus scrofa) [TaxId: 9823] [56340] (3)
      2. Human (Homo sapiens), heart isoform (H chain) [TaxId: 9606] [64444] (2)
      3. Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606] [64445] (1)
      4. Mouse (Mus musculus) [TaxId: 10090] [56341] (4)
      5. Dogfish (Squalus acanthias) [TaxId: 7797] [56342] (3)
      6. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [56343] (9)
      7. Plasmodium berghei [TaxId: 5821] [103325] (7)
      8. Toxoplasma gondii [TaxId: 5811] [103326] (4)
      9. Bacillus stearothermophilus [TaxId: 1422] [56344] (9)
      10. Lactobacillus casei [TaxId: 1582] [56345] (1)
      11. Lactobacillus pentosus [TaxId: 1589] [69843] (1)
      12. Bifidobacterium longum, strain am101-2 [TaxId: 216816] [56346] (2)
      13. Thermotoga maritima [TaxId: 2336] [56347] (1)
      14. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [111253] (2)
        SQ O08349
      15. Clostridium thermocellum [TaxId: 1515] [118160] (1)
        SQ Q4CDK5
    4. MJ0490, lactate/malate dehydrogenase [64446]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [64447] (2)
  2. AglA-like glucosidase [90050] (5)
    family 4 glycosyl hydrolase
    1. Alpha-glucosidase AglA [90051]
      1. Thermotoga maritima [TaxId: 2336] [90052] (1)
        TM1834
    2. Putative alpha-glucosidase TM0752 [103327]
      1. Thermotoga maritima [TaxId: 2336] [103328] (1)
    3. Maltose-6'-phosphate glucosidase GlvA [103329]
      1. Bacillus subtilis [TaxId: 1423] [103330] (1)
        SQ P54716
    4. 6-phospho-beta-glucosidase [111254]
      1. Bacillus stearothermophilus [TaxId: 1422] [111255] (1)
        SQ P84135
      2. Thermotoga maritima [TaxId: 2336] [111256] (3)
        SQ Q9X108
DNA breaking-rejoining enzymes [56348] (1)
core: alpha3-beta3-alpha4; one side of beta-sheet is exposed
1. DNA breaking-rejoining enzymes [56349] (2)
  uperfamily
  1. Lambda integrase-like, catalytic core [56350] (5)
    1. Integrase [56351]
      1. Bacteriophage HP1 [TaxId: 10690] [56352] (1)
    2. Integrase (Int) [56353]
      1. Bacteriophage lambda [TaxId: 10710] [56354] (8)
    3. Cre recombinase [56355]
      1. Bacteriophage P1 [TaxId: 10678] [56356] (24)
        SQ P06956 20-341
    4. Recombinase XerD [56357]
      1. Escherichia coli [TaxId: 562] [56358] (1)
    5. Flp recombinase [56359]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56360] (3)
  2. Eukaryotic DNA topoisomerase I, catalytic core [56361] (2)
    1. Eukaryotic DNA topoisomerase I, catalytic core [56362]
      1. Human (Homo sapiens) [TaxId: 9606] [56363] (15)
        SQ P11387 203-765 ! SQ P11387 203-767
      2. Vaccinia virus [TaxId: 10245] [56364] (1)
Replication modulator SeqA, C-terminal DNA-binding domain [82807] (1)
consists of seven alpha-helices and three-stranded beta-sheet
1. Replication modulator SeqA, C-terminal DNA-binding domain [82808] (1)
  uperfamily
  1. Replication modulator SeqA, C-terminal DNA-binding domain [82809] (1)
    1. Replication modulator SeqA, C-terminal DNA-binding domain [82810]
      binds to fully methylated and hemimethylated GATC sequences at oriC
      1. Escherichia coli [TaxId: 562] [82811] (3)
        SQ P36658 71-181
SMAD MH1 domain [56365] (1)
consists of four alpha-helices and three beta-ribbons
1. SMAD MH1 domain [56366] (1)
  uperfamily
  1. SMAD MH1 domain [56367] (1)
    1. SMAD MH1 domain [56368]
      1. Human (Homo sapiens) [TaxId: 9606] [56369] (2)
YopH tyrosine phosphatase N-terminal domain [64448] (1)
consists of four alpha-helices and two beta-hairpins
1. YopH tyrosine phosphatase N-terminal domain [64449] (1)
  uperfamily
  1. YopH tyrosine phosphatase N-terminal domain [64450] (2)
    1. YopH tyrosine phosphatase N-terminal domain [64451]
      1. Yersinia pestis [TaxId: 632] [64452] (1)
      2. Yersinia pseudotuberculosis [TaxId: 633] [69844] (2)
Rotavirus NSP2 fragment, N-terminal domain [75573] (1)
consists of six alpha-helices and two beta-hairpins
1. Rotavirus NSP2 fragment, N-terminal domain [75574] (1)
  uperfamily
  1. Rotavirus NSP2 fragment, N-terminal domain [75575] (1)
    1. Rotavirus NSP2 fragment, N-terminal domain [75576]
      1. Simian 11 rotavirus [TaxId: 10923] [75577] (5)
Rv2827c C-terminal domain-like [160886] (1)
multihelical array flanked by two three-stranded mixed beta-sheets
1. Rv2827c C-terminal domain-like [160887] (1)
  1. Rv2827c C-terminal domain-like [160888] (1)
    the C-terminal part (~210 residues) of Pfam 09407; DUF2005
    1. Hypothetical protein Rv2827c [160889]
      1. Mycobacterium tuberculosis [TaxId: 1773] [160890] (2)
        SQ P71625 83-294
Phosphoprotein oligomerization domain-like [160891] (1)
intertwinned homodimer of beta(2)-alpha-beta(2) motifs; 3 layers: b/a/b; each antiparallel beta-sheet is formed by the N-terminal beta-hairpin of one subunit and the C-terminal beta-hairpin of the other subunit; order 1243
1. Phosphoprotein oligomerization domain-like [160892] (1)
  1. Phosphoprotein oligomerization domain-like [160893] (1)
    middle part of Pfam 00922
    1. Phosphoprotein P (M1) [160894]
      1. Vesicular stomatitis indiana virus [TaxId: 11277] [160895] (6)
        SQ P04880 107-171
Taf5 N-terminal domain-like [160896] (1)
multihelical cluster with a C-terminal beta-alpha(2)-beta motif; one central buried helix; parallel beta-ribbon
1. Taf5 N-terminal domain-like [160897] (1)
  1. Taf5 N-terminal domain-like [160898] (3)
    Pfam 04494
    1. TAF5 subunit of TFIID [160899]
      1. Human (Homo sapiens) [TaxId: 9606] [160900] (8)
        SQ Q15542 195-343
      2. Saccharomyces cerevisiae [TaxId: 4932] [160901] (1)
        SQ P38129 149-282
      3. Encephalitozoon cuniculi [TaxId: 6035] [160902] (5)
        SQ Q8SQS4 18-148
Jann2411-like [160903] (1)
unusual fold; consists of seven alpha-helices and three beta-hairpins
1. Jann2411-like [160904] (1)
  1. Jann2411-like [160905] (1)
    Pfam 07336; DUF1470
    1. Uncharacterized protein Jann2411 [160906]
      1. Jannaschia sp. ccs1 [TaxId: 290400] [160907] (1)
        SQ Q28PN4 1-184
ATP12-like [160908] (1)
contains an N-terminal beta-sheet that forms a beta-triangle structure; the remainder is a multihelical array of long and short helices
1. ATP12-like [160909] (1)
  1. ATP12-like [160910] (2)
    Pfam 07542; F1-ATPase chaperone
    1. Uncharacterized protein Atu1473 [160911]
      1. Agrobacterium tumefaciens [TaxId: 358] [160912] (2)
        SQ A9CJ14 1-261
    2. ATP12 ATPase [160913]
      1. Paracoccus denitrificans [TaxId: 266] [160914] (5)
        SQ A1B060 2-235! SQ A1B060 3-235
Ribosome inactivating proteins (RIP) [56370] (1)
contains mixed beta-sheet
1. Ribosome inactivating proteins (RIP) [56371] (2)
  uperfamily
  1. Plant cytotoxins [56372] (17)
    1. alpha-Trichosanthin [56373]
      1. Mongolian snake gourd (Trichosanthes kirilowii Maxim.) [TaxId: 3677] [56374] (10)
    2. Bryodin [56375]
      1. Red briony (Bryonia dioica) [TaxId: 3652] [56376] (1)
    3. Beta-luffin [103331]
      1. Smooth loofah (Luffa cylindrica) [TaxId: 3670] [103332] (1)
    4. alpha-Momorcharin (momordin) [56377]
      1. Bitter gourd (Momordica charantia) [TaxId: 3673] [56378] (8)
    5. Beta-momorcharin [56379]
      (almost) identical with the anti-tumor and anti-HIV-1 protein MAP30
      1. Bitter gourd (Momordica charantia) [TaxId: 3673] [56380] (2)
    6. Mistletoe lectin I A-chain [56381]
      1. European mistletoe (Viscum album) [TaxId: 3972] [56382] (12)
        different sequence variants
        SQ P81446 1-249
        SQ Q6ITZ3 1-240
    7. Abrin A-chain [56383]
      1. Abrus precatorius [TaxId: 3816] [56384] (1)
    8. Lectin 1 A-chain [90053]
      1. Mongolian snake-gourd (Trichosanthes kirilowii) [TaxId: 3677] [90054] (1)
    9. Pokeweed antiviral protein alpha [56385]
      1. Pokeweed (Phytolacca americana) [TaxId: 3527] [56386] (7)
    10. Antiviral protein 3 [90055]
      1. Pokeweed (Phytolacca americana) [TaxId: 3527] [90056] (1)
    11. Antiviral protein S [103333]
      seed isoform
      1. Pokeweed (Phytolacca americana) [TaxId: 3527] [103334] (4)
    12. Dianthin 30 [103335]
      1. Clove pink (Dianthus caryophyllus) [TaxId: 3570] [103336] (4)
        SQ P24476 24-278
    13. Saporin So6 [56387]
      1. Common soapwort (Saponaria officinalis) [TaxId: 3572] [56388] (1)
    14. Ricin A-chain [56389]
      1. Castor bean (Ricinus communis) [TaxId: 3988] [56390] (24)
        SQ P06750 28-286
    15. Ebulin A-chain [56391]
      1. Sambucus ebulus [TaxId: 28503] [56392] (4)
    16. Bouganin [160915]
      1. Bougainvillea (Bougainvillea spectabilis) [TaxId: 146096] [160916] (1)
        SQ Q8W4U4 27-272
    17. Agglutinin-1 chain A [160917]
      1. Abrus precatorius [TaxId: 3816] [160918] (1)
        SQ Q9M6E9 22-268
  2. Shiga toxin, A-chain [56395] (2)
    1. Shiga toxin, A-chain [56396]
      1. Shigella dysenteriae, toxin I [TaxId: 622] [56397] (2)
      2. Shigella dysenteriae, toxin II [TaxId: 622] [103337] (2)
ADP-ribosylation [56398] (1)
unusual fold
1. ADP-ribosylation [56399] (7)
  uperfamily
  1. ADP-ribosylating toxins [56400] (12)
    1. Heat-labile toxin, A-chain [56401]
      1. Escherichia coli, type IB [TaxId: 562] [56402] (9)
      2. Escherichia coli, type IIB [TaxId: 562] [56403] (1)
    2. Diphtheria toxin, N-terminal domain [56404]
      1. Corynebacterium diphtheriae [TaxId: 1717] [56405] (7)
    3. Exotoxin A, C-terminal domain [56406]
      1. Pseudomonas aeruginosa [TaxId: 287] [56407] (21)
    4. Pertussis toxin, S1 subunit [56408]
      1. Bordetella pertussis [TaxId: 520] [56409] (3)
    5. Cholera toxin [56410]
      1. Vibrio cholerae [TaxId: 666] [56411] (9)
    6. Vegetative insecticidal protein 2 (VIP2) [56412]
      duplication: consists of two domains of this fold, the second of which is catalytic
      1. Bacillus cereus [TaxId: 1396] [56413] (2)
    7. Enzymatic component (Ia) of iota-toxin [82812]
      mammalian-targeted relative of VIP2; C-terminal domain is catalytic, N-terminal domain interacts with Ib (binding component)
      1. Clostridium perfringens [TaxId: 1502] [82813] (4)
    8. Exoenzyme c3 [56414]
      1. Clostridium botulinum [TaxId: 1491] [56415] (14)
        SQ P15879 41-251
      2. Staphylococcus aureus [TaxId: 1280] [103338] (2)
      3. Clostridium botulinum C bacteriophage [TaxId: 12336] [118161] (2)
        SQ Q00901 44-244
    9. Anthrax toxin lethal factor, middle domain [69845]
      includes an all-alpha insert subdomain
      1. Bacillus anthracis [TaxId: 1392] [69846] (10)
  2. Ecto-ART [82814] (1)
    the two disulfide bridges and N-terminal alpha helices are characteristic for all ecto-ARTs
    1. Eukaryotic mono-ADP-ribosyltransferase ART2.2 [82815]
      NAD glycohydrolase and auto-ADP-ribosylation activity
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82816] (6)
  3. Poly(ADP-ribose) polymerase, C-terminal domain [56416] (3)
    1. Poly(ADP-ribose) polymerase, C-terminal domain [56417]
      1. Chicken (Gallus gallus) [TaxId: 9031] [56418] (7)
      2. Mouse (Mus musculus) [TaxId: 10090] [82817] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [103339] (8)
        SQ P09874 661-1010
  4. AvrPphF ORF2, a type III effector [111257] (1)
    shares the common structural core with other families; unknown function
    1. AvrPphF ORF2, a type III effector [111258]
      1. Pseudomonas syringae pv. phaseolicola [TaxId: 319] [111259] (1)
        SQ Q9K2L5 29-204
  5. Tpt1/KptA [118162] (1)
    Pfam 01885; contains extra N-terminal domain similar to the "winged helix" DNA-binding domain (scop_sf 46785)
    1. Probable RNA 2'-phosphotransferase KptA [118163]
      1. Aeropyrum pernix [TaxId: 56636] [118164] (1)
        SQ Q9YFP5 37-216; d1: (1-76); d2: (88-182)
  6. BC2332-like [143947] (1)
    minimized common structural core with two large, mainly helical insertions on one side forming dimerization "domain"
    1. Hypothetical protein BC2332 [143948]
      1. Bacillus cereus [TaxId: 1396] [143949] (2)
        SQ Q81DM5 2-195
  7. CC0527-like [143950] (1)
    Pfam 06108; DUF952
    1. Hypothetical protein CC0527 [143951]
      1. Caulobacter crescentus [TaxId: 155892] [143952] (3)
        SQ Q9AAR9 2-114
Peptide deformylase [56419] (1)
alpha-beta(5)-alpha; 3 layers: a/b/a; meander beta-sheet wraps around the C-terminal alpha-helix
1. Peptide deformylase [56420] (1)
  nickel-dependent enzyme
  uperfamily
  1. Peptide deformylase [56421] (9)
    1. Peptide deformylase [56422]
      1. Escherichia coli [TaxId: 562] [56423] (21)
      2. Pseudomonas aeruginosa [TaxId: 287] [75578] (4)
      3. Leptospira interrogans [TaxId: 173] [103340] (1)
        SQ Q72S74
      4. Staphylococcus aureus [TaxId: 1280] [75579] (6)
        SQ Q9F4L4
      5. Streptococcus pneumoniae [TaxId: 1313] [90057] (1)
      6. Thermotoga maritima [TaxId: 2336] [90058] (1)
      7. Bacillus stearothermophilus [TaxId: 1422] [75580] (1)
      8. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [75581] (3)
      9. Thermus thermophilus [TaxId: 274] [118165] (1)
        SQ P43522
LCCL domain [69847] (1)
unusual fold
1. LCCL domain [69848] (1)
  uperfamily
  1. LCCL domain [69849] (1)
    1. Cochlin [69850]
      1. Human (Homo sapiens) [TaxId: 9606] [69851] (1)
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56424] (1)
unusual fold
1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56425] (1)
  uperfamily
  1. Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain [56426] (7)
    1. L-aspartate oxidase [56427]
      1. Escherichia coli [TaxId: 562] [56428] (3)
    2. Succinate dehydogenase [82818]
      1. Escherichia coli [TaxId: 562] [82819] (2)
    3. Fumarate reductase [56429]
      1. Escherichia coli [TaxId: 562] [56430] (7)
      2. Wolinella succinogenes [TaxId: 844] [56431] (8)
    4. Flavocytochrome c3 (respiratory fumarate reductase) [56432]
      contains additional N-terminal multiheme domain
      1. Shewanella frigidimarina [TaxId: 56812] [56433] (16)
      2. Shewanella putrefaciens [TaxId: 24] [56434] (3)
    5. Adenylylsulfate reductase A subunit [69852]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [69853] (2)
C-type lectin-like [56435] (1)
unusual fold
1. C-type lectin-like [56436] (8)
  uperfamily
  1. C-type lectin domain [56437] (51)
    Pfam 00059
    1. Lithostathine, inhibitor of stone formation [56438]
      1. Human (Homo sapiens) [TaxId: 9606] [56439] (2)
    2. Pancreatitis-associated protein 1 [103341]
      1. Human (Homo sapiens) [TaxId: 9606] [103342] (2)
    3. CD94 [56440]
      1. Human (Homo sapiens) [TaxId: 9606] [56441] (7)
    4. CD69 [56442]
      1. Human (Homo sapiens) [TaxId: 9606] [56443] (3)
    5. NK cell-activating receptor nkg2d [64453]
      1. Mouse (Mus musculus) [TaxId: 10090] [64454] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [64455] (3)
    6. Macrophage mannose receptor, CRD4 [56444]
      1. Human (Homo sapiens) [TaxId: 9606] [56445] (2)
    7. Ovocleidin-17 [90059]
      major protein of the eggshell calcified layer
      1. Chicken (Gallus gallus) [TaxId: 9031] [90060] (1)
    8. Galactose-specific C-type lectin [90061]
      1. Western diamondback rattlesnake (Crotalus atrox) [TaxId: 8730] [90062] (2)
    9. Snake coagglutinin alpha chain [88861]
      heterodimeric coagulation factors IX/X-binding protein (IX/X-BP)
      1. Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] [88862] (7)
      2. Habu snake (Trimeresurus flavoviridis), flavocetin-A [TaxId: 88087] [88863] (1)
      3. Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] [88864] (4)
      4. Hundred-pace snake (Deinagkistrodon acutus), different isoforms [TaxId: 36307] [88865] (3)
      5. Puff adder (Bitis arietans), bitiscetin [TaxId: 8692] [88866] (2)
      6. Snake (Echis multisquamatus), Ems16 [TaxId: 93050] [103343] (2)
        SQ Q7T2Q1 24-157
      7. South american rattlesnake (Crotalus durissus terrificus), convulxin [TaxId: 8732] [103344] (1)
      8. Taiwan habu (Trimeresurus mucrosquamatus), mucrocetin [TaxId: 103944] [103345] (1)
      9. Saw-scaled viper (Echis carinatus), echicetin [TaxId: 40353] [103346] (1)
      10. Malayan pit viper (Calloselasma rhodostoma), rhodocetin [TaxId: 8717] [143953] (1)
        SQ P81397 1-132
    10. Snake coagglutinin beta chain [88867]
      heterodimeric coagulation factors IX/X-binding protein (IX/X-BP)
      1. Habu snake (Trimeresurus flavoviridis) [TaxId: 88087] [88868] (7)
      2. Habu snake (Trimeresurus flavoviridis), flavocetin-A [TaxId: 88087] [88869] (1)
      3. Jararaca (Bothrops jararaca), botrocetin [TaxId: 8724] [88870] (4)
      4. Sharp-nosed viper (Deinagkistrodon acutus) [TaxId: 36307] [88871] (3)
      5. Puff adder (Bitis arietans), bitiscetin [TaxId: 8692] [88872] (2)
      6. Snake (Echis multisquamatus), Ems16 [TaxId: 93050] [103347] (2)
        SQ Q7T2Q0 27-153
      7. South american rattlesnake (Crotalus durissus terrificus), convulxin [TaxId: 8732] [103348] (1)
      8. Taiwan habu (Trimeresurus mucrosquamatus), mucrocetin [TaxId: 103944] [103349] (1)
      9. Saw-scaled viper (Echis carinatus), echicetin [TaxId: 40353] [103350] (1)
      10. Malayan pit viper (Calloselasma rhodostoma), rhodocetin [TaxId: 8717] [143954] (1)
        SQ P81398 2-128
    11. Type II antifreeze protein [56450]
      1. Sea raven (Hemitripterus americanus) [TaxId: 8094] [56451] (1)
    12. Eosinophil major basic protein [64457]
      1. Human (Homo sapiens) [TaxId: 9606] [64458] (3)
    13. NK cell receptor [56452]
      1. Mouse (Mus musculus), ly49-a [TaxId: 10090] [56453] (1)
      2. Mouse (Mus musculus), ly49-c [TaxId: 10090] [103351] (7)
      3. Mouse (Mus musculus), ly49-i [TaxId: 10090] [75582] (1)
    14. H1 subunit of the asialoglycoprotein receptor [56454]
      1. Human (Homo sapiens) [TaxId: 9606] [56455] (1)
    15. DC-SIGN (dendritic cell-specific ICAM-3 grabbing nonintegrin) [69855]
      1. Human (Homo sapiens) [TaxId: 9606] [69856] (6)
        SQ Q9NNX6 253-384
    16. DC-SIGNR (DC-SIGN related receptor) [69857]
      1. Human (Homo sapiens) [TaxId: 9606] [69858] (4)
        SQ Q9NNX6 219-397
    17. EBV gp42 [75583]
      1. Epstein-Barr virus [TaxId: 10376] [75584] (1)
    18. E-selectin, C-lectin domain [56456]
      folowed by EGF-like module
      1. Human (Homo sapiens) [TaxId: 9606] [56457] (2)
    19. P-selectin, C-lectin domain [116731]
      followed by EGF-like module
      1. Human (Homo sapiens) [TaxId: 9606] [116732] (3)
    20. Mannose-binding protein A, C-lectin domain [56458]
      1. Human (Homo sapiens) [TaxId: 9606] [56459] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [56460] (38)
    21. Surfactant protein, lectin domain [56461]
      1. Human (Homo sapiens), SP-D [TaxId: 9606] [56462] (36)
      2. Rat (Rattus norvegicus), SP-A [TaxId: 10116] [103352] (2)
    22. Lectin TC14 [56463]
      1. Tunicate (Polyandrocarpa misakiensis) [TaxId: 7723] [56464] (2)
    23. Tetranectin [56465]
      trimeric plasminogen binding protein with an alpha-helical coiled coil
      1. Human (Homo sapiens) [TaxId: 9606] [56466] (3)
        SQ P05452 85-202
    24. Aggrecan core protein [111260]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [111261] (1)
        SQ P07897 1912-2037
    25. Lectin CEL-I [111262]
      1. Cucumaria echinata [TaxId: 40245] [111263] (2)
        SQ Q7M462
    26. Hypothetical protein F28B4.3 [118166]
      1. Caenorhabditis elegans [TaxId: 6239] [118167] (1)
        SQ Q19853 1193-1329
    27. Oxidised low density lipoprotein [143955]
      1. Human (Homo sapiens) [TaxId: 9606] [143956] (16)
        SQ P78380 140-270
    28. Low affinity immunoglobulin epsilon Fc receptor [143957]
      1. Human (Homo sapiens) [TaxId: 9606] [143958] (2)
        SQ P06734 156-298
  2. Aerolysin/Pertussis toxin (APT) domain [56467] (2)
    1. Pertussis toxin, S2/S3 subunits, N-terminal domain [56468]
      1. Bordetella pertussis [TaxId: 520] [56469] (3)
    2. Proaerolysin, N-terminal domain [56470]
      1. Aeromonas hydrophila [TaxId: 644] [56471] (9)
  3. Invasin/intimin cell-adhesion fragment, C-terminal domain [56472] (2)
    1. Intimin [56473]
      1. Escherichia coli [TaxId: 562] [56474] (3)
        an enteropathogenic serotype
    2. Invasin [56475]
      1. Yersinia pseudotuberculosis [TaxId: 633] [56476] (1)
  4. Link domain [56477] (2)
    1. TSG-6, Link module [56478]
      1. Human (Homo sapiens) [TaxId: 9606] [56479] (7)
    2. CD44, hyaluronan binding domain [103353]
      contains extra N-terminal beta-strand and C-terminal beta-hairpin
      1. Human (Homo sapiens) [TaxId: 9606] [103354] (3)
  5. Endostatin [56480] (3)
    decorated with many insertions in the common fold
    1. Endostatin [56481]
      1. Human (Homo sapiens) [TaxId: 9606] [56482] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [56483] (3)
    2. Endostatin domain of collagen alpha1(xv) [56484]
      1. Mouse (Mus musculus) [TaxId: 10090] [56485] (1)
  6. Noncollagenous (NC1) domain of collagen IV [75585] (2)
    duplication: consists of two subdomains of this fold; segment swapping within and between individual domains
    1. Noncollagenous (NC1) domain of collagen IV [75586]
      1. Human (Homo sapiens) [TaxId: 9606] [75587] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [82820] (3)
        SQ P02462 1445-1667
  7. Sulfatase-modifying factor-like [143959] (2)
    Pfam 03781 (DUF323); fold decorated with many additional structures; C-alpha-formyglycine-generating enzyme
    1. Sulfatase modifying factor 1 [143960]
      1. Human (Homo sapiens) [TaxId: 9606] [143961] (14)
        SQ Q8NBK3 86-371
    2. Sulfatase modifying factor 2 [143962]
      1. Human (Homo sapiens) [TaxId: 9606] [143963] (2)
        SQ Q8NBJ7 28-294
  8. Mtd variable domain [143964] (1)
    fold decorated with many additional structures; overall similarity to the Sulfatase modifying factor family; lacks the characteristic disulfide
    1. Major tropism determinant (Mtd), C-terminal domain [143965]
      1. Bordetella phage bpp-1 [TaxId: 194699] [143966] (13)
        SQ Q775D6 171-380
        includes related Bordetella phage proteins
Hemolytic lectin CEL-III, C-terminal domain [111264] (1)
unusual fold
1. Hemolytic lectin CEL-III, C-terminal domain [111265] (1)
  uperfamily
  1. Hemolytic lectin CEL-III, C-terminal domain [111266] (1)
    1. Hemolytic lectin CEL-III, C-terminal domain [111267]
      1. Cucumaria echinata [TaxId: 40245] [111268] (5)
        SQ Q868M7 11-442
SRCR-like [56486] (2)
unusual fold; disulfide-rich; core: beta-x-alpha-beta-loop-beta
1. SRCR-like [56487] (2)
  uperfamily
  1. Scavenger receptor cysteine-rich (SRCR) domain [56488] (1)
    has some structural similarity to the long-chain scorpion toxins
    1. M2BP [56489]
      1. Human (Homo sapiens) [TaxId: 9606] [56490] (1)
  2. Hepsin, N-terminal domain [103355] (1)
    1. Hepsin, N-terminal domain [103356]
      1. Human (Homo sapiens) [TaxId: 9606] [103357] (4)
        SQ P05981 50-159
2. A heparin-binding domain [56491] (1)
  uperfamily
  1. A heparin-binding domain [56492] (1)
    1. N-terminal domain of the amyloid precursor protein [56493]
      1. Human (Homo sapiens) [TaxId: 9606] [56494] (1)
Fibrinogen C-terminal domain-like [56495] (1)
unusual fold
1. Fibrinogen C-terminal domain-like [56496] (1)
  uperfamily
  1. Fibrinogen C-terminal domain-like [56497] (8)
    1. Fibrinogen C-terminal domains [56498]
      1. Human (Homo sapiens), gamma [TaxId: 9606] [68904] (21)
        SQ P02679
      2. Human (Homo sapiens), beta [TaxId: 9606] [68903] (14)
        SQ P02675
      3. Human (Homo sapiens), fibrinogen-420, alpha-E [TaxId: 9606] [56500] (1)
      4. Chicken (Gallus gallus), gamma [TaxId: 9031] [69859] (1)
      5. Chicken (Gallus gallus), beta [TaxId: 9031] [69860] (1)
      6. Sea lamprey (Petromyzon marinus), beta [TaxId: 7757] [75588] (2)
      7. Sea lamprey (Petromyzon marinus), gamma [TaxId: 7757] [75589] (2)
    2. Tachylectin 5a [69861]
      1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [69862] (1)
gp120 core [56501] (1)
unusual fold
1. gp120 core [56502] (1)
  uperfamily
  1. gp120 core [56503] (1)
    1. gp120 core [56504]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [56505] (24)
Methionine synthase activation domain-like [56506] (1)
unusual fold; core: beta-alpha(2)-beta(2)-alpha(2)-beta-alpha-beta; antiparallel beta-sheet: order 12354
1. Methionine synthase activation domain-like [56507] (2)
  uperfamily
  1. Methionine synthase SAM-binding domain [56508] (1)
    1. Methionine synthase SAM-binding domain [56509]
      1. Escherichia coli [TaxId: 562] [56510] (4)
  2. Hypothetical protein TM0269 [75590] (1)
    1. Hypothetical protein TM0269 [75591]
      1. Thermotoga maritima [TaxId: 2336] [75592] (1)
UbiD C-terminal domain-like [143967] (1)
alpha-beta(2)-alpha-beta-alpha-beta(2); 3 layers, a/b/a; mixed beta-sheet, order: 12354, strands 2,3 and 5 are parallel to each other
1. UbiD C-terminal domain-like [143968] (1)
  uperfamily
  1. UbiD C-terminal domain-like [143969] (1)
    C-terminal part of Pfam 01977; hexamerisation domain
    1. 3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD [143970]
      1. Escherichia coli [TaxId: 562] [143971] (3)
        SQ P0AAB4 326-491
Hypothetical protein TM0875 [90063] (1)
unusual fold; core: beta(2)-loop-beta(2)-alpha-beta; mixed beta-sheet: order 51243; parallel strands 2 and 4
1. Hypothetical protein TM0875 [90064] (1)
  uperfamily
  1. Hypothetical protein TM0875 [90065] (1)
    1. Hypothetical protein TM0875 [90066]
      1. Thermotoga maritima [TaxId: 2336] [90067] (1)
Metal cation-transporting ATPase, ATP-binding domain N [81661] (1)
unusual fold; core: beta-alpha(2)-beta(3)-alpha(2)-beta(2); 6-stranded antiparallel beta-sheet, order: 165432
1. Metal cation-transporting ATPase, ATP-binding domain N [81660] (1)
  uperfamily
  1. Metal cation-transporting ATPase, ATP-binding domain N [81659] (5)
    1. Calcium ATPase [81658]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81657] (17)
        SQ P04191
    2. Sodium/potassium-transporting ATPase alpha chain [90068]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [90069] (2)
      2. Pig (Sus scrofa) [TaxId: 9823] [111269] (1)
        SQ Q6PIE5 384-590
    3. Potassium-transporting ATPase B chain, KdpB [111270]
      minimal fold of this domain:
      1. Escherichia coli [TaxId: 562] [111271] (4)
        SQ P03960 316-451
    4. Cation-transporting ATPase [143972]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [143973] (3)
        SQ O29777 435-547
Suppressor of Fused, N-terminal domain [103358] (1)
unusual fold; bifurcated beta-sheet; left-handed beta-alpha-beta unit
1. Suppressor of Fused, N-terminal domain [103359] (1)
  uperfamily
  1. Suppressor of Fused, N-terminal domain [103360] (1)
    1. Suppressor of Fused, N-terminal domain [103361]
      1. Human (Homo sapiens) [TaxId: 9606] [103362] (1)
Nitric oxide (NO) synthase oxygenase domain [56511] (1)
unusual fold
1. Nitric oxide (NO) synthase oxygenase domain [56512] (1)
  uperfamily
  1. Nitric oxide (NO) synthase oxygenase domain [56513] (6)
    1. Nitric oxide (NO) synthase oxygenase domain [56514]
      1. Mouse (Mus musculus) [TaxId: 10090] [56515] (51)
        SQ P29477 77-496 ! SQ P29477 77-495
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82821] (45)
        SQ P29476 298-716
      3. Human (Homo sapiens) [TaxId: 9606] [56516] (15)
      4. Cow (Bos taurus) [TaxId: 9913] [56517] (43)
        SQ P29473 67-482
      5. Bacillus subtilis [TaxId: 1423] [82822] (4)
      6. Staphylococcus aureus [TaxId: 1280] [82823] (1)
Penicillin binding protein dimerisation domain [56518] (1)
unusual fold
1. Penicillin binding protein dimerisation domain [56519] (1)
  uperfamily
  1. Penicillin binding protein dimerisation domain [56520] (2)
    contains an insert subdomain of ClpS-like fold
    1. Penicillin-binding protein 2x (pbp-2x), N-terminal domain [56521]
      the insert subdomain (residues 93-183) is usually disordered in the structures
      1. Streptococcus pneumoniae [TaxId: 1313] [56522] (6)
    2. Penicillin binding protein 2a (PBP2A), middle domain [82824]
      the insert subdomain (residues 168-239) is fully ordered
      1. Staphylococcus aureus [TaxId: 1280] [82825] (5)
        SQ O54286 27-668
Oxidoreductase molybdopterin-binding domain [56523] (1)
unusual fold; contains 3 layers of beta-sheet structure and a beta-grasp like motif
1. Oxidoreductase molybdopterin-binding domain [56524] (1)
  uperfamily
  1. Oxidoreductase molybdopterin-binding domain [56525] (3)
    Pfam 00174
    1. Sulfite oxidase, middle catalytic domain [56526]
      1. Chicken (Gallus gallus) [TaxId: 9031] [56527] (5)
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [103363] (1)
    2. Bacterial sulfite oxidase YedY [118168]
      1. Escherichia coli [TaxId: 562] [118169] (2)
        SQ P76342 63-329
FAH [56528] (1)
unusual fold; contains 3 layers of beta-sheet structure
1. FAH [56529] (1)
  uperfamily
  1. FAH [56530] (6)
    1. Fumarylacetoacetate hydrolase, FAH, C-terminal domain [63432]
      1. Mouse (Mus musculus) [TaxId: 10090] [56532] (6)
    2. Putative isomerase YcgM [90070]
      1. Escherichia coli [TaxId: 562] [90071] (1)
    3. 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase HpcE [64459]
      duplication: tandem repeat of two FAH domains
      1. Escherichia coli [TaxId: 562] [64460] (2)
    4. Hypothetical protein Ynl168c [111272]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111273] (1)
        SQ P53889
    5. 2-keto-4-pentenoate hydratase MhpD [111274]
      1. Escherichia coli [TaxId: 562] [111275] (1)
        SQ P77608
    6. FAHD1 (Flj36880, YISKL) [118170]
      1. Human (Homo sapiens) [TaxId: 9606] [118171] (1)
        SQ Q6P587
Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56533] (1)
unusual fold
1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56534] (1)
  uperfamily
  1. Aromatic aminoacid monoxygenases, catalytic and oligomerization domains [56535] (5)
    1. Tyrosine hydroxylase [56536]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [56537] (2)
    2. Phenylalanine hydroxylase, PAH [56538]
      1. Human (Homo sapiens) [TaxId: 9606] [56539] (15)
        SQ P00439 117-424
      2. Rat (Rattus norvegicus) [TaxId: 10116] [56540] (2)
      3. Chromobacterium violaceum [TaxId: 536] [75593] (3)
    3. Tryptophan hydroxylase [82826]
      1. Human (Homo sapiens) [TaxId: 9606] [82827] (1)
Substrate-binding domain of HMG-CoA reductase [56541] (1)
unusual fold
1. Substrate-binding domain of HMG-CoA reductase [56542] (1)
  uperfamily
  1. Substrate-binding domain of HMG-CoA reductase [56543] (2)
    1. Substrate-binding domain of HMG-CoA reductase [56544]
      1. Human (Homo sapiens) [TaxId: 9606] [56545] (9)
      2. Pseudomonas mevalonii [TaxId: 32044] [56546] (5)
        SQ P13702 4-377
Argininosuccinate synthetase, C-terminal domain [69863] (1)
unusual fold
1. Argininosuccinate synthetase, C-terminal domain [69864] (1)
  uperfamily
  1. Argininosuccinate synthetase, C-terminal domain [69865] (3)
    1. Argininosuccinate synthetase, C-terminal domain [69866]
      1. Escherichia coli [TaxId: 562] [69867] (4)
      2. Thermus thermophilus [TaxId: 274] [75594] (7)
      3. Thermotoga maritima [TaxId: 2336] [111276] (1)
        SQ Q9X2A1
Hypothetical protein PH1602 [103364] (1)
complex alpha+beta fold; contains a region of similarity to the ferredoxin-like fold
1. Hypothetical protein PH1602 [103365] (1)
  uperfamily
  1. Hypothetical protein PH1602 [103366] (1)
    1. Hypothetical protein PH1602 [103367]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [103368] (1)
IlvD/EDD N-terminal domain-like [143974] (1)
contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
1. IlvD/EDD N-terminal domain-like [143975] (1)
  uperfamily
  1. lvD/EDD N-terminal domain-like [143976] (1)
    N-terminal part of Pfam 00920
    1. 6-phosphogluconate dehydratase EDD [143977]
      1. Shewanella oneidensis [TaxId: 70863] [143978] (2)
        SQ Q8EEA0 1-418
DNA methylase specificity domain [116733] (1)
comprises the N-terminal, double beta-helix like structure and C-terminal alpha-hairpin
1. DNA methylase specificity domain [116734] (2)
  uperfamily
  1. TaqI C-terminal domain-like [116735] (1)
    1. DNA methylase TaqI, C-terminal domain [116736]
      1. Thermus aquaticus [TaxId: 271] [116737] (18)
  2. Type I restriction modification DNA specificity domain [143979] (2)
    Pfam 01420
    1. Bipartite methylase S protein MG438 [143980]
      duplication; contains two structural repeats made of this domain and extra C-terminal coiled coil each; overall structure is similar to MJ0130
      1. Mycoplasma genitalium [TaxId: 2097] [143981] (2)
        SQ Q49434 1-193! SQ Q49434 194-374
    2. Bipartite methylase S protein MJ0130 [143982]
      duplication: comprises two repeats of this domain, separated by a coiled coil made by additional long helices at the C-end of each repeat
      1. Methanocaldococcus jannaschii [TaxId: 2190] [143983] (4)
        SQ Q57594 1-220! SQ Q57594 221-425
GCM domain [90072] (1)
consists of two different alpha+beta subdomains; 2 zinc-binding sites
1. GCM domain [90073] (1)
  DNA-binding domain
  uperfamily
  1. GCM domain [90074] (1)
    1. Mgcm1 [90075]
      1. Mouse (Mus musculus) [TaxId: 10090] [90076] (1)
Conserved core of transcriptional regulatory protein vp16 [56547] (1)
unusual fold
1. Conserved core of transcriptional regulatory protein vp16 [56548] (1)
  uperfamily
  1. Conserved core of transcriptional regulatory protein vp16 [56549] (1)
    1. Conserved core of transcriptional regulatory protein vp16 [56550]
      1. Herpes simplex virus type 1 [TaxId: 10298] [56551] (1)
Insert subdomain of RNA polymerase alpha subunit [56552] (1)
unusual fold; contains a left-handed beta-alpha-beta unit
1. Insert subdomain of RNA polymerase alpha subunit [56553] (1)
  uperfamily
  1. Insert subdomain of RNA polymerase alpha subunit [56554] (4)
    1. RNA polymerase alpha subunit [56555]
      1. Escherichia coli [TaxId: 562] [56556] (1)
      2. Thermus aquaticus [TaxId: 271] [64461] (7)
      3. Thermus thermophilus [TaxId: 274] [75595] (30)
        SQ Q9Z9H6; part of multichain biological unit
    2. RPB3 [64462]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [64463] (25)
        SQ P16370; part of multichain biological unit
Baseplate structural protein gp11 [56557] (1)
unusual fold; trimer
1. Baseplate structural protein gp11 [56558] (1)
  uperfamily
  1. Baseplate structural protein gp11 [56559] (1)
    1. Baseplate structural protein gp11 [56560]
      1. Bacteriophage T4 [TaxId: 10665] [56561] (1)
Receptor-binding domain of short tail fibre protein gp12 [88873] (1)
unusual fold; trimer
1. Receptor-binding domain of short tail fibre protein gp12 [88874] (1)
  uperfamily
  1. Receptor-binding domain of short tail fibre protein gp12 [88875] (1)
    1. Receptor-binding domain of short tail fibre protein gp12 [88876]
      intertwinned homotrimer; subdivided into the neck, collar, head and bonnet regions
      1. Bacteriophage T4 [TaxId: 10665] [88877] (2)
Outer capsid protein sigma 3 [64464] (1)
unusual fold
1. Outer capsid protein sigma 3 [64465] (1)
  uperfamily
  1. Outer capsid protein sigma 3 [64466] (1)
    1. Outer capsid protein sigma 3 [64467]
      1. Reovirus [TaxId: 10891] [64468] (12)
Phosphoprotein M1, C-terminal domain [118172] (1)
consists of 6 helices and one beta-hairpin
1. Phosphoprotein M1, C-terminal domain [118173] (1)
  uperfamily
  1. Phosphoprotein M1, C-terminal domain [118174] (1)
    C-terminal part of Pfam 03012
    1. Phosphoprotein M1, C-terminal domain [118175]
      1. Rabies virus, strain CVS-11 [TaxId: 11292] [118176] (1)
        SQ P22363 186-296
L,D-transpeptidase pre-catalytic domain-like [143984] (1)
unusual fold, made of four helices and four 2-3 stranded beta-sheets
1. L,D-transpeptidase pre-catalytic domain-like [143985] (1)
  uperfamily
  1. L,D-transpeptidase pre-catalytic domain-like [143986] (1)
    1. L,D-transpeptidase, pre-catalytic domain [143987]
      1. Enterococcus faecium [TaxId: 1352] [143988] (1)
        SQ Q3Y185 217-338
YbiA-like [143989] (1)
consists of six alpha-helices and two two-stranded beta-sheets
1. YbiA-like [143990] (1)
  uperfamily
  1. YbiA-like [143991] (1)
    1. Hypothetical protein YbiA [143992]
      1. Escherichia coli [TaxId: 562] [143993] (1)
        SQ P30176 1-160
NinB [103369] (1)
unusual fold; intertwined dimer; consists of two different structural domains
1. NinB [103370] (1)
  uperfamily
  1. NinB [103371] (1)
    1. NinB [103372]
      1. Bacteriophage lambda [TaxId: 10710] [103373] (1)
AF2331-like [143994] (1)
interlocked dimer of beta-alpha-beta(2)-alpha-beta-(alpha) subunits; 3 layers: b/b/a
1. AF2331-like [143995] (1)
  uperfamily
  1. AF2331-like [143996] (1)
    1. Hypothetical protein AF2331 [143997]
      1. Archaeoglobus fulgidus [TaxId: 2234] [143998] (2)
        SQ O27953 1-92
SSo0622-like [111277] (1)
alpha(2)-beta(2)-alpha-beta-alpha-beta(2)-alpha; 2 layers: a/b; antiparallel beta-sheet: order 21354; strands 1,3 and 5 and the C-terminal helix are longer than other secondary structures
1. SSo0622-like [111278] (1)
  the dimer, formed in the crystals, is a probable biological unit
  uperfamily
  1. SSo0622-like [111279] (1)
    Pfam 02676
    1. Hypothetical protein SSo0622 [111280]
      1. Sulfolobus solfataricus [TaxId: 2287] [111281] (1)
        SQ Q9UX16
Putative modulator of DNA gyrase, PmbA/TldD [111282] (1)
consists of two different alpha+beta domains; d1: [duplication of alpha-beta(3)-alpha motif; 2 layers: a/b; antiparallel beta-sheet, order: 321456; strands 1, 2, 4 and 5 are twice longer than other secondary structures]; d2 [ complex fold; contains beta-barrel (n=5, S=10)]
1. Putative modulator of DNA gyrase, PmbA/TldD [111283] (1)
  uperfamily
  1. Putative modulator of DNA gyrase, PmbA/TldD [111284] (2)
    Pfam 01523
    1. PmbA-related protein TM0727 [111285]
      1. Thermotoga maritima [TaxId: 2336] [111286] (1)
        SQ Q9WZI6; d1: 1-214; d2: 215-433
    2. Putative modulator of DNA gyrase BT3649 [118177]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [118178] (1)
        SQ Q8A1L2
PSTPO5379-like [160919] (1)
complex fold; consists of two alpha+beta subdomains, one is inserted in the other
1. PSTPO5379-like [160920] (1)
  1. PSTPO5379-like [160921] (1)
    Pfam 07286; DUF1445
    1. Uncharacterized protein PSTPO5379 [160922]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [160923] (2)
        SQ Q87UC6 7-262
PG1388-like [160924] (1)
consists of 2 alpha+beta subdomains, each having a meander beta-sheet; d1: alpha(2)-beta(7); d2: alpha(2)-beta(2)-alpha(2)-beta(2)
1. PG1388-like [160925] (1)
  1. PG1388-like [160926] (1)
    PfamB 104512
    1. Hypothetical protein PG1388 [160927]
      1. Porphyromonas gingivalis [TaxId: 837] [160928] (2)
        SQ Q7MUU3 66-262
Oxysterol-binding protein-like [143999] (1)
core: large meander beta-sheet of 12 strands wrapped around the N-terminal (distorted) alpha-hairpin; some similarity to transmembrane beta-barrel proteins
1. Oxysterol-binding protein-like [144000] (1)
  uperfamily
  1. Oxysterol-binding protein [144001] (1)
    Pfam 01237
    1. Oxysterol-binding protein homolog 4, KES1 [144002]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144003] (8)
        SQ P35844 2-434! SQ P35844 30-434
ORC1-binding domain [144004] (1)
complex fold, composed of an alpha hairpin, meander beta-sheet and a five-stranded barrel of unusual topology
1. ORC1-binding domain [144005] (1)
  uperfamily
  1. ORC1-binding domain [144006] (1)
    1. Regulatory protein SIR1 [144007]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [144008] (4)
        SQ P21691 484-611! SQ P21691 485-613! SQ P21691 487-611
CofE-like [144009] (1)
consists of two different domains; d1: beta-alpha-beta-alpha-beta(2)-alpha-beta, mixed sheet of 5 strands, order:15234, strands 2 and 3 are parralel; d2 is inserted in d1 after strand 2 and comprises a helix-turn-helix motif and two 3-stranded sheets
1. CofE-like [144010] (1)
  uperfamily
  1. CofE-like [144011] (1)
    Pfam 01996; DUF129; contains known activity
    1. F420-0:gamma-glutamyl ligase CofE [144012]
      1. Archaeoglobus fulgidus [TaxId: 2234] [144013] (4)
        SQ O28028 1-249
Peptidoglycan deacetylase N-terminal noncatalytic region [144014] (1)
consists of two different domains, d1: [alpha-beta(2)-alpha-beta(3); 3 layers: a/b/a; mixed beta-sheet, order 12345, strands 2 and 3 are parallel to each other with a left-handed crossover connection], d2: alpha-beta(3)-alpha; 2 layers; antiparallel beta-sheet, order 123]
1. Peptidoglycan deacetylase N-terminal noncatalytic region [144015] (1)
  uperfamily
  1. Peptidoglycan deacetylase N-terminal noncatalytic region [144016] (1)
    1. Peptidoglycan GlcNAc deacetylase [144017]
      1. Streptococcus pneumoniae [TaxId: 1313] [144018] (2)
        SQ Q8DP63 46-267
Non-globular alpha+beta subunits of globular proteins [56567] (1)
not a true fold
1. Non-globular alpha+beta subunits of globular proteins [56568] (3)
  not a true superfamily
  uperfamily
  1. Phycoerythrin 545 alpha-subunits [56569] (1)
    consists of a long beta-hairpin and a single alpha-helix
    1. Phycoerythrin 545 alpha-subunits [56570]
      1. Cryptophyte (Rhodomonas sp. CS24) [TaxId: 79257] [56571] (5)
        SQ P30943 38-104 ! SQ Q00433 53-128
  2. Virulence effector SptP domain [69868] (1)
    1. Virulence effector SptP domain [69869]
      1. Salmonella typhimurium [TaxId: 90371] [69870] (1)
  3. Ubiquinol-cytochrome c reductase 8 kDa protein [90077] (1)
    beta-hairpin and a short alpha-helix bound to the core subunits
    1. Ubiquinol-cytochrome c reductase 8 kDa protein [90078]
      1. Cow (Bos taurus) [TaxId: 9913] [90079] (14)
        SQ P13272 1-57 ! SQ P13272
        there are other PDB entries with lower resolution structures of the Ubiquinol-cytochrome c reductase complex, in which this subunit has incomplete and probably mistraced structure that is not classified in scop