Structural Classification of Proteins

Class: All beta proteins

Lineage:

Root: scop
Class: All beta proteins [48724]

Folds:

Immunoglobulin-like beta-sandwich [48725] (28)
sandwich; 7 strands in 2 sheets; greek-key
some members of the fold have additional strands
1. Immunoglobulin [48726] (4)
  uperfamily
  1. V set domains (antibody variable domain-like) [48727] (90)
    1. Immunoglobulin light chain kappa variable domain, VL-kappa [88519]
      VL-kappa domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VL-kappa domains with artificial or grafted exogenous CDRs are listed as engineered species
      1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88520] (18)
      2. Human (Homo sapiens), cluster 2 [TaxId: 9606] [88521] (10)
      3. Human (Homo sapiens), cluster 3.1 [TaxId: 9606] [88522] (10)
      4. Human (Homo sapiens), cluster 3.2 [TaxId: 9606] [88523] (68)
      5. Mouse (Mus musculus), cluster 1.1 [TaxId: 10090] [88524] (128)
        SQ P01631 #KV2G_MOUSE Ig kappa chain V-II region 26-10; 79% sequence identity ! SQ P06310 # KV2F_HUMAN IG KAPPA CHAIN V-II REGION RPMI 6410 PRECURSOR ! SQ P03976 # KV2E_MOUSE (P03976) Ig kappa chain V-II region 17S29.1 ! SQ P01642 21-115 # ! KV2G_MOUSE IG KAPPA CHAIN V-II REGION 26-10
      6. Mouse (Mus musculus), cluster 1.2 [TaxId: 10090] [88525] (36)
      7. Mouse (Mus musculus), cluster 2 [TaxId: 10090] [88526] (34)
      8. Mouse (Mus musculus), cluster 3.1 [TaxId: 10090] [88527] (14)
      9. Mouse (Mus musculus), cluster 3.2 [TaxId: 10090] [88528] (65)
        SQ P04940 # KV6F_MOUSE IG KAPPA CHAIN V-VI REGION NQ2-17.4.1
      10. Mouse (Mus musculus), cluster 3.3 [TaxId: 10090] [88529] (2)
      11. Mouse (Mus musculus), cluster 3.4 [TaxId: 10090] [88530] (6)
      12. Mouse (Mus musculus), cluster 4 [TaxId: 10090] [88531] (189)
        SQ P01645 1-106 # 95% sequense identity; KV5L_MOUSE Ig kappa chain V-V region HP 93G7 ! SQ NA # natural chimera; best hits are: SQ P01637 (Ig kappa chain V-V region T1) and SQ P01837 (Ig kappa chain C region) ! SQ NA # humanized antibody ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01642 21-115 # ! KV5I_MOUSE Ig kappa chain V-V region L7 precursor
      13. Rat (Rattus norvegicus) [TaxId: 10116] [88532] (11)
      14. Engineered (including hybrid species) [88533] (53)
        SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # Humanized antibody ! SQ NA # humanized antibody ! SQ NA # engineered antibody
      15. synthetic construct [158859] (1)
      16. Escherichia coli [TaxId: 562] [158860] (8)
    2. Immunoglobulin light chain lambda variable domain, VL-lambda [88534]
      VL-lambda domains of human antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the human genome; mouse VL-lambda domains belong to a single germline family
      1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88535] (4)
        SQ NA # Bence-Jones protein JTO ! SQ P06317 # Ig lambda chain V-VI region SUT
      2. Human (Homo sapiens), cluster 2 [TaxId: 9606] [88536] (11)
      3. Human (Homo sapiens), cluster 3.1 [TaxId: 9606] [88537] (3)
      4. Human (Homo sapiens), cluster 3.2 [TaxId: 9606] [88538] (1)
      5. Human (Homo sapiens), cluster 4 [TaxId: 9606] [88539] (23)
      6. Human (Homo sapiens), cluster 5 [TaxId: 9606] [88540] (9)
        SQ Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
      7. Mouse (Mus musculus) [TaxId: 10090] [88541] (35)
      8. Rat (Rattus norvegicus) [TaxId: 10116] [101504] (8)
      9. Hamster (Cricetulus griseus) [TaxId: 10029] [88542] (1)
    3. Immunoglobulin heavy chain variable domain, VH [88543]
      VH domains of human and mouse antibodies are clustered by the sequence similarity within the germline encoded segment and then by the size of the complementarity determining regions CDR1 and CDR2, so the clusters may correspond to putative germline families in the species genomes; VH domains with artificial or grafted exogenous CDRs are listed as engineered species
      1. Human (Homo sapiens), cluster 1 [TaxId: 9606] [88544] (47)
      2. Human (Homo sapiens), cluster 2.1 [TaxId: 9606] [88545] (3)
      3. Human (Homo sapiens), cluster 2.2 [TaxId: 9606] [88546] (3)
      4. Human (Homo sapiens), cluster 3 [TaxId: 9606] [88547] (66)
        SQ Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3)
      5. Human (Homo sapiens), cluster 4 [TaxId: 9606] [101505] (4)
      6. Mouse (Mus musculus), cluster 1 [TaxId: 10090] [88548] (51)
        SQ P01796 # ! HV27_MOUSE Ig heavy chain V-III region A4
      7. Mouse (Mus musculus), cluster 2.1 [TaxId: 10090] [88549] (14)
        SQ P18527 # HV56_MOUSE Ig heavy chain V region 914; 90% sequence identity
      8. Mouse (Mus musculus), cluster 2.2 [TaxId: 10090] [88550] (55)
        SQ P01811 # HV41_MOUSE (P01811) Ig heavy chain V region UPC10
      9. Mouse (Mus musculus), cluster 3.1 [TaxId: 10090] [88551] (34)
        SQ NA # natural chimera; best hits are: SQ P01751 (Ig heavy chain V region B1-8/186-2) and SQ P01864 (Ig gamma-2A chain C region secreted form)
      10. Mouse (Mus musculus), cluster 3.2 [TaxId: 10090] [88552] (156)
        SQ P01756 1-117 # 78% sequense identity; HV12_MOUSE Ig heavy chain V region MOPC 104E ! SQ NA # humanized antibody ! SQ P01750 # HV06_MOUSE Ig heavy chain V region 102 precursor ! SQ P01750 20-116 # ! HV06_MOUSE Ig heavy chain V region 102 precursor
      11. Mouse (Mus musculus), cluster 3.3 [TaxId: 10090] [88553] (1)
      12. Mouse (Mus musculus), cluster 4 [TaxId: 10090] [88554] (35)
        SQ P06327 20-117 # HV52_MOUSE (P06327) Ig heavy chain V region VH558 A1/A4 precursor; 57% sequence identity ! SQ P01631 # KV2G_MOUSE (P01631) Ig kappa chain V-II region 26-10
      13. Mouse (Mus musculus), cluster 5 [TaxId: 10090] [88555] (36)
      14. Mouse (Mus musculus), cluster 6 [TaxId: 10090] [88556] (12)
        SQ NA # part of Fab 28 against HIV-1 RT
      15. Mouse (Mus musculus), cluster 7.1 [TaxId: 10090] [88557] (41)
        SQ P18532 # HV61_MOUSE Ig heavy chain V region 1B43 precursor
      16. Mouse (Mus musculus), cluster 7.2 [TaxId: 10090] [88558] (29)
      17. Mouse (Mus musculus), cluster 7.3 [TaxId: 10090] [88559] (2)
      18. Rat (Rattus norvegicus) [TaxId: 10116] [88560] (17)
      19. Hamster (Cricetulus griseus) [TaxId: 10029] [88561] (1)
      20. Engineered (including hybrid species) [88562] (82)
        SQ NA # humanized antidoby; bactericidal Fab-h6831 ! SQ NA # humanized antibody ! SQ NA # Humanized antibody ! SQ NA # engineered antibody
      21. Escherichia coli [TaxId: 562] [158861] (3)
      22. synthetic construct [158862] (2)
    4. Camelid IG heavy chain variable domain, VHh [88563]
      1. Camel (Camelus dromedarius) [TaxId: 9838] [88564] (23)
        SQ NA # camelid antibody
      2. Llama (Lama glama) [TaxId: 9844] [88565] (9)
      3. Homo sapiens [TaxId: 9606] [158863] (2)
    5. T-cell antigen receptor [48933]
      sequences may differ within each classified species
      1. Mouse (Mus musculus), alpha-chain [TaxId: 10090] [48934] (25)
      2. Human (Homo sapiens), alpha-chain [TaxId: 9606] [48935] (21)
      3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [48936] (36)
      4. Human (Homo sapiens), beta-chain [TaxId: 9606] [48937] (52)
      5. Human (Homo sapiens), gamma-chain [TaxId: 9606] [63651] (11)
      6. Human (Homo sapiens), delta-chain [TaxId: 9606] [48938] (4)
    6. Immunoreceptor CTLA-4 (CD152), N-terminal fragment [48939]
      1. Human (Homo sapiens) [TaxId: 9606] [48940] (3)
      2. Mouse (Mus musculus) [TaxId: 10090] [48941] (1)
    7. Myelin membrane adhesion molecule P0 [48728]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [48729] (1)
    8. Myelin oligodendrocyte glycoprotein (MOG) [89174]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89175] (3)
    9. Coxsackie virus and adenovirus receptor (Car), domain 1 [48730]
      1. Human (Homo sapiens) [TaxId: 9606] [48731] (19)
    10. N-terminal domain of sialoadhesin [48732]
      1. Mouse (Mus musculus) [TaxId: 10090] [48733] (8)
        SQ Q62230 20-130
    11. N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) [89176]
      1. Human (Homo sapiens) [TaxId: 9606] [89177] (6)
    12. NK cell activating receptor NKP44 [89178]
      a triggering partner in natural cytotoxicity
      1. Human (Homo sapiens) [TaxId: 9606] [89179] (1)
    13. TREM-1 (triggering receptor expressed on myeloid cells 1) [101506]
      1. Human (Homo sapiens) [TaxId: 9606] [101507] (2)
        SQ Q9NP99 21-133
      2. Mouse (Mus musculus) [TaxId: 10090] [117037] (1)
        SQ Q9JKE2 25-134
    14. CD8 [48734]
      1. Human (Homo sapiens) [TaxId: 9606] [48735] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [48736] (6)
      3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [158864] (2)
        SQ P10300 22-136
    15. CD4 V-set domains [48737]
      1. Human (Homo sapiens) [TaxId: 9606] [48738] (27)
      2. Rat (Rattus rattus) [TaxId: 10117] [48739] (1)
    16. CD2, first domain [48740]
      1. Human (Homo sapiens) [TaxId: 9606] [48741] (4)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [48742] (5)
    17. CD2-binding domain of CD58, N-terminal domain [48743]
      1. Human (Homo sapiens) [TaxId: 9606] [48744] (3)
    18. CD80, N-terminal domain [48745]
      a soluble form of b7-1
      1. Human (Homo sapiens) [TaxId: 9606] [48746] (2)
    19. CD86 (b7-2), N-terminal domain [63635]
      1. Human (Homo sapiens) [TaxId: 9606] [63636] (2)
    20. Junction adhesion molecule, JAM, N-terminal domain [48747]
      1. Mouse (Mus musculus) [TaxId: 10090] [48748] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [89180] (1)
    21. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain [81942]
      1. Mouse (Mus musculus) [TaxId: 10090] [81943] (1)
    22. Tyrosine-protein kinase receptor tyro3, N-terminal domain [101508]
      1. Human (Homo sapiens) [TaxId: 9606] [101509] (1)
    23. Programmed cell death protein 1, PD1, extracellular domain [101510]
      1. Mouse (Mus musculus) [TaxId: 10090] [101511] (4)
    24. HSV glycoprotein D [63637]
      1. Herpes simplex virus type 1 [TaxId: 10298] [63638] (2)
        elaborated with insertions and N- and C-terminal extensions
    25. Novel antigen receptor (against lysozyme) [110042]
      1. Nurse shark (Ginglymostoma cirratum) [TaxId: 7801] [110043] (7)
        SQ Q8AXI4 # fragment
    26. Novel antigen receptor 12Y-1 [110044]
      1. Spotted wobbegong (Orectolobus maculatus) [TaxId: 168098] [110045] (1)
        SQ Q6X1E7 # fragment
    27. Novel antigen receptor 12Y-2 [110046]
      1. Spotted wobbegong (Orectolobus maculatus) [TaxId: 168098] [110047] (1)
        SQ Q6X1E6 # fragment
    28. Polymeric-immunoglobulin receptor, PIGR [117038]
      1. Human (Homo sapiens) [TaxId: 9606] [117039] (1)
        SQ P01833 20-127 # N-terminal, ligand-binding domain
    29. Alphaherpesvirus glycoprotein E [141008]
      elaborated with insertions and C-terminal extensions
      1. Human herpesvirus 1 [TaxId: 10298] [141009] (4)
        SQ P04488 218-394! SQ P04488 220-390
    30. CD28 [158865]
      T-cell-specific surface glycoprotein
      1. Human (Homo sapiens) [TaxId: 9606] [158866] (1)
        SQ P10747 19-136
    31. Kin of IRRE-like protein 3, KIRREL3 [158867]
      1. Human (Homo sapiens) [TaxId: 9606] [158868] (1)
        SQ Q8IZU9 413-521
    32. B- and T-lymphocyte attenuator CD272 [158869]
      1. Human (Homo sapiens) [TaxId: 9606] [158870] (2)
        SQ Q7Z6A9 34-137
  2. C1 set domains (antibody constant domain-like) [48942] (70)
    1. Immunoglobulin light chain kappa constant domain, CL-kappa [88566]
      1. Mouse (Mus musculus) [TaxId: 10090] [88567] (347)
        SQ P01837# KAC_MOUSE Ig kappa chain C region; 99% sequence identity ! SQ NA # natural chimera; best hits are: SQ P01637 (Ig kappa chain V-V region T1) and SQ P01837 (Ig kappa chain C region) ! SQ P01837 # KAC_MOUSE Ig kappa chain C region ! SQ P01837 # KAC_MOUSE (P01837) Ig kappa chain C region ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01837 # ! KAC_MOUSE Ig kappa chain C region
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88568] (8)
      3. Human (Homo sapiens) [TaxId: 9606] [88569] (168)
        SQ NA # humanized antibody ! SQ P01834 # KAC_HUMAN Ig kappa chain C region ! SQ P01834 # KAC_HUMAN Ig kappa chain C region. ! SQ NA # engineered antibody
        including humanized antibodies (chimeric proteins with human constant domains)
      4. synthetic construct [158871] (1)
      5. Escherichia coli [TaxId: 562] [158872] (8)
    2. Immunoglobulin light chain lambda constant domain, CL-lambda [88570]
      1. Mouse (Mus musculus) [TaxId: 10090] [88571] (21)
        SQ Q8N355 20-230 # 94% sequence identity; natural chimera: antibody light chain (Fab HYB3)
      2. Human (Homo sapiens) [TaxId: 9606] [88572] (49)
      3. Hamster (Cricetulus griseus) [TaxId: 10029] [88573] (1)
    3. Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma [88574]
      1. Human (Homo sapiens) [TaxId: 9606] [88575] (256)
        SQ Q6N089 20-243 # 95% sequence identity; natural chimera: antibody heavy chain (Fab HYB3) ! SQ NA # humanized antibody ! SQ P01857 # IGHG1_HUMAN Ig gamma-1 chain C region ! SQ NA # engineered antibody
        including humanized antibodies (chimeric proteins with human constant domains)
      2. Mouse (Mus musculus) [TaxId: 10090] [88576] (412)
        SQ P01864 # GCAB_MOUSE Ig gamma-2A chain C region secreted form (B allele) ! SQ P01863 #GCAA_MOUSE Ig gamma-2A chain C region, A allele; 86% sequence identity ! SQ NA # natural chimera; best hits are: SQ P01751 (Ig heavy chain V region B1-8/186-2) and SQ P01864 (Ig gamma-2A chain C region secreted form) ! SQ P01868 # GC1_MOUSE Ig gamma-1 chain C region secreted form ! SQ P01864 # GCAB_MOUSE (P01864) Ig gamma-2A chain C region ! SQ P01837 # KAC_MOUSE (P01837) Ig kappa chain C region ! SQ P01863 # GCAA_MOUSE Ig gamma-2A chain C region, A allele ! SQ NA # part of Fab 28 against HIV-1 RT ! SQ P01868 # ! GC1_MOUSE Ig gamma-1 chain C region secreted form
      3. Mouse (Mus musculus), gamma3 [TaxId: 10090] [88577] (8)
        SQ P22436 # GC3_MOUSE (P22436) Ig gamma-3 chain C region
      4. Rat (Rattus norvegicus) [TaxId: 10116] [88578] (6)
      5. Hamster (Cricetulus griseus) [TaxId: 10029] [88579] (1)
      6. Escherichia coli [TaxId: 562] [158873] (3)
      7. synthetic construct [158874] (2)
    4. Immunoglobulin heavy chain alpha constant domain 1, CH1-alpha [88580]
      1. Mouse (Mus musculus) [TaxId: 10090] [88581] (3)
    5. Immunoglobulin heavy chain mu constant domain 1, CH1-mu [88582]
      1. Human (Homo sapiens) [TaxId: 9606] [88583] (8)
    6. Immunoglobulin heavy chain gamma constant domain 2, CH2-gamma [88584]
      1. Human (Homo sapiens) [TaxId: 9606] [88585] (34)
        SQ P01857 #118-327 ! SQ P01857 118-327 # GC1_HUMAN Ig gamma-1 chain C region
      2. Mouse (Mus musculus) [TaxId: 10090] [88586] (1)
      3. Mouse (Mus musculus), gamma2 [TaxId: 10090] [88587] (1)
      4. Rat (Rattus norvegicus) [TaxId: 10116] [88588] (2)
    7. Immunoglobulin heavy chain gamma constant domain 3, CH3-gamma [88589]
      1. Human (Homo sapiens) [TaxId: 9606] [88590] (37)
        SQ P01857 #118-327 ! SQ P01857 118-327 # GC1_HUMAN Ig gamma-1 chain C region
      2. Mouse (Mus musculus) [TaxId: 10090] [88591] (2)
      3. Mouse (Mus musculus), gamma2 [TaxId: 10090] [88592] (1)
      4. Rat (Rattus norvegicus) [TaxId: 10116] [88593] (2)
      5. Guinea pig (Cavia porcellus) [TaxId: 10141] [49123] (1)
    8. Immunoglobulin heavy chain alpha constant domain 2, CH2-alpha [89181]
      1. Human (Homo sapiens) [TaxId: 9606] [89182] (3)
    9. Immunoglobulin heavy chain alpha constant domain 3, CH3-alpha [89183]
      1. Human (Homo sapiens) [TaxId: 9606] [89184] (3)
    10. Immunoglobulin heavy chain epsilon constant domain 2, CH2-epsilon [88594]
      1. Human (Homo sapiens) [TaxId: 9606] [88595] (2)
    11. Immunoglobulin heavy chain epsilon constant domain 3, CH3-epsilon [88596]
      1. Human (Homo sapiens) [TaxId: 9606] [88597] (3)
    12. Immunoglobulin heavy chain epsilon constant domain 4, CH4-epsilon [88598]
      1. Human (Homo sapiens) [TaxId: 9606] [88599] (3)
    13. T-cell antigen receptor [49125]
      1. Mouse (Mus musculus), alpha-chain [TaxId: 10090] [49126] (15)
      2. Human (Homo sapiens), alpha-chain [TaxId: 9606] [49127] (24)
      3. Mouse (Mus musculus), beta-chain [TaxId: 10090] [49128] (19)
      4. Human (Homo sapiens), beta-chain [TaxId: 9606] [49129] (39)
      5. Human (Homo sapiens), gamma-chain [TaxId: 9606] [63661] (3)
      6. Human (Homo sapiens), delta-chain [TaxId: 9606] [63662] (3)
    14. beta2-microglobulin [88600]
      1. Cow (Bos taurus) [TaxId: 9913] [48946] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88601] (6)
      3. Human (Homo sapiens) [TaxId: 9606] [88602] (228)
        SQ P61769 21-119 ! SQ P01884
      4. Mouse (Mus musculus) [TaxId: 10090] [88603] (106)
        SQ P01887
    15. Class I MHC, alpha-3 domain [88604]
      1. Human (Homo sapiens) [TaxId: 9606] [88605] (189)
        SQ P30685 25-300 ! SQ P30443 25-298 # 1A01_HUMAN HLA class I histocompatibility antigen, A-1 alpha chain precursor ! SQ P30481 25-300 ! SQ P01892 25-298 ! SQ P13746 25-299 # 1A11_HUMAN HLA class I histocompatibility antigen, A-11 alpha chain precursor
      2. Mouse (Mus musculus) [TaxId: 10090] [88606] (109)
        SQ P01901 22-299
      3. Rat (Rattus norvegicus), RT1-AA [TaxId: 10116] [88607] (3)
      4. Rhesus monkey (Macaca mulatta) [TaxId: 9544] [158875] (2)
    16. Hemochromatosis protein Hfe, alpha-3 domain [88608]
      1. Human (Homo sapiens) [TaxId: 9606] [88609] (2)
    17. Zinc-alpha-2-glycoprotein, ZAG, alpha-3 domain [48965]
      fat depleting factor related to class I MHC
      1. Human (Homo sapiens) [TaxId: 9606] [48966] (7)
        SQ P25311 22-294
    18. Class I MHC homolog, alpha-3 domain [88610]
      gamma, delta T-cell ligand
      1. Human (Homo sapiens), Mic-a [TaxId: 9606] [48968] (2)
      2. Human (Homo sapiens), Mic-b [TaxId: 9606] [74826] (1)
      3. Mouse (Mus musculus), t22 [TaxId: 10090] [88611] (3)
      4. Mouse (Mus musculus), t10 [TaxId: 10090] [101512] (1)
    19. Fc (IgG) receptor, alpha-3 domain [88612]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [88613] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [88614] (1)
    20. CD1, alpha-3 domain [88615]
      1. Mouse (Mus musculus) [TaxId: 10090] [88616] (10)
      2. Human (Homo sapiens), CD1b [TaxId: 9606] [88617] (3)
      3. Human (Homo sapiens), CD1a [TaxId: 9606] [101513] (4)
      4. Human (Homo sapiens), CD1d [TaxId: 9606] [158876] (4)
        SQ P15813 202-295
    21. Class II MHC alpha chain, C-terminal domain [88618]
      1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88619] (1)
        probably orthologous to the mouse H2-DM
      2. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88620] (1)
        probably orthologous to the human HLA-DM
      3. Human (Homo sapiens), HLA-DR group [TaxId: 9606] [88621] (29)
        SQ P01903 28-207
        probably orthologous to the mouse I-E group
      4. Mouse (Mus musculus), I-E group [TaxId: 10090] [88622] (9)
        probably orthologous to the human HLA-DR group
      5. Human (Homo sapiens), HLA-DQ group [TaxId: 9606] [88623] (3)
        probably orthologous to the mouse I-A group
      6. Mouse (Mus musculus), I-A group [TaxId: 10090] [88624] (39)
        probably orthologous to the human HLA-DQ group
    22. Class II MHC beta chain, C-terminal domain [88625]
      1. Human (Homo sapiens), HLA-DM [TaxId: 9606] [88626] (1)
        probably orthologous to the mouse H2-DM
      2. Mouse (Mus musculus), H2-DM [TaxId: 10090] [88627] (1)
        probably orthologous to the human HLA-DM
      3. Human (Homo sapiens), HLA-DR group [TaxId: 9606] [88628] (48)
        SQ P04229 30-219
        probably orthologous to the mouse I-E group
      4. Mouse (Mus musculus), I-E group [TaxId: 10090] [88629] (9)
        probably orthologous to the human HLA-DR group
      5. Human (Homo sapiens), HLA-DQ group [TaxId: 9606] [88630] (3)
        probably orthologous to the mouse I-A group
      6. Mouse (Mus musculus), I-A group [TaxId: 10090] [88631] (20)
        probably orthologous to the human HLA-DQ group
    23. Immunomodulatory protein m144, alpha-3 domain [110048]
      1. Murine cytomegalovirus [TaxId: 10366] [110049] (2)
        SQ Q69G19 27-263 # 95% sequence identity
  3. C2 set domains [49142] (10)
    1. Vascular cell adhesion molecule-1 (VCAM-1) [49143]
      1. Human (Homo sapiens) [TaxId: 9606] [49144] (3)
    2. Intercellular cell adhesion molecule-1 (ICAM-1) [49145]
      1. Human (Homo sapiens) [TaxId: 9606] [49146] (8)
    3. Intercellular cell adhesion molecule-2 (ICAM-2) [49147]
      1. Human (Homo sapiens) [TaxId: 9606] [49148] (1)
    4. CD4 C2-set domains [49149]
      1. Human (Homo sapiens) [TaxId: 9606] [49150] (27)
      2. Rat (Rattus rattus) [TaxId: 10117] [49151] (1)
    5. CD2, second domain [49152]
      1. Human (Homo sapiens) [TaxId: 9606] [49153] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [49154] (1)
    6. CD2-binding domain of CD58, second domain [49155]
      1. Human (Homo sapiens) [TaxId: 9606] [49156] (1)
    7. CD80, second domain [49157]
      a soluble form of b7-1
      1. Human (Homo sapiens) [TaxId: 9606] [49158] (2)
    8. Granulocyte colony-stimulating factor (GC-SF) receptor, N-terminal domain [141010]
      1. Human (Homo sapiens) [TaxId: 9606] [141011] (1)
        SQ Q99062 26-119
  4. I set domains [49159] (53)
    1. Vascular cell adhesion molecule-1 (VCAM-1) [49160]
      1. Human (Homo sapiens) [TaxId: 9606] [49161] (3)
    2. Intercellular adhesion molecule-1, ICAM-1 [49162]
      1. Human (Homo sapiens) [TaxId: 9606] [49163] (10)
    3. Intercellular adhesion molecule-2, ICAM-2 [49164]
      1. Human (Homo sapiens) [TaxId: 9606] [49165] (1)
    4. Neural cell adhesion molecule (NCAM) [49166]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49167] (4)
        Rat and mouse sequences are identical for the two N-terminal modules
      2. Chicken (Gallus gallus) [TaxId: 9031] [63664] (1)
    5. Mucosal addressin cell adhesion molecule-1 (MADCAM-1) [49168]
      1. Human (Homo sapiens) [TaxId: 9606] [49169] (2)
    6. Telokin [49170]
      1. Turkey (Meleagris gallopavo) [TaxId: 9103] [49171] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [141012] (1)
        SQ Q9UIT9 1238-1338
    7. Cardiac myosin binding protein C, different domains [89185]
      1. Human (Homo sapiens) [TaxId: 9606] [89186] (3)
        SQ Q14896 358-451, 641-770
    8. Titin [49172]
      1. Human (Homo sapiens), different modules [TaxId: 9606] [49173] (5)
    9. Twitchin [49174]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [49175] (3)
        different modules
      2. Human (Homo sapiens), Ig repeat 27 [TaxId: 9606] [49176] (2)
    10. Type-1 interleukin-1 receptor [49177]
      duplication: tandem repeat of 3 domains
      1. Human (Homo sapiens) [TaxId: 9606] [49178] (3)
    11. Fibroblast growth factor receptor, FGFR [49179]
      1. Human (Homo sapiens), FGFR1 [TaxId: 9606] [49180] (7)
      2. Human (Homo sapiens), FGFR2a [TaxId: 9606] [49181] (8)
      3. Human (Homo sapiens), FGFR2b [TaxId: 9606] [81955] (1)
      4. Human (Homo sapiens), FGFR3c [TaxId: 9606] [101514] (1)
    12. Hemolin [49182]
      Duplication: tandem repeat of 4 domains, known as L1 domains
      1. Moth (Hyalophora cecropia) [TaxId: 7123] [49183] (1)
    13. Semaphorin 4d Ig-like domain [101515]
      1. Human (Homo sapiens) [TaxId: 9606] [101516] (1)
    14. Axonin-1 [49184]
      tandem repeat of 4 L1 domains
      1. Chicken (Gallus gallus) [TaxId: 9031] [49185] (1)
    15. Perlecan Ig3 domain [69158]
      1. Mouse (Mus musculus) [TaxId: 10090] [69159] (1)
    16. Junction adhesion molecule, JAM, C-terminal domain [49186]
      1. Mouse (Mus musculus) [TaxId: 10090] [49187] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [89187] (1)
    17. Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), C-terminal domain [81956]
      1. Mouse (Mus musculus) [TaxId: 10090] [81957] (1)
    18. Second domain of the Flt-1 receptor [49188]
      1. Human (Homo sapiens) [TaxId: 9606] [49189] (5)
    19. Tyrosine-protein kinase receptor tyro3, second domain [101517]
      1. Human (Homo sapiens) [TaxId: 9606] [101518] (1)
    20. High affinity nerve growth factor receptor TrkA, different domains [49190]
      1. Human (Homo sapiens) [TaxId: 9606] [49191] (7)
    21. Ligand binding domain of trkB receptor [49192]
      1. Human (Homo sapiens) [TaxId: 9606] [49193] (2)
    22. NT3 binding domain of trkC receptor [49194]
      1. Human (Homo sapiens) [TaxId: 9606] [49195] (1)
    23. Fc gamma receptor ectodomain (CD32) [49196]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens), IIa [TaxId: 9606] [49197] (2)
      2. Human (Homo sapiens), IIb [TaxId: 9606] [49198] (1)
      3. Human (Homo sapiens), III [TaxId: 9606] [49199] (5)
        SQ O75015 23-189
    24. IgE high affinity receptor alpha subunit [49200]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens) [TaxId: 9606] [49201] (7)
        SQ P12319 29-196
    25. Ig alpha Fc receptor, FCARI (CD89) [89188]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens) [TaxId: 9606] [89189] (3)
    26. Killer cell inhibitory receptor [49202]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens), kir2dl3 [TaxId: 9606] [49203] (2)
      2. Human (Homo sapiens), kir2ds3, CD158j [TaxId: 9606] [89190] (1)
      3. Human (Homo sapiens), p58-cl42 kir [TaxId: 9606] [49204] (2)
      4. Human (Homo sapiens), 2dl2 [TaxId: 9606] [49205] (2)
    27. Ligand binding domain of lir-1 (ilt2) [49206]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens) [TaxId: 9606] [49207] (8)
        SQ Q8NHL6 25-218
    28. Ligand binding domain of NK receptor NKp46 [101519]
      possibly an intermediate structure between the I set and FnIII domains
      1. Human (Homo sapiens) [TaxId: 9606] [101520] (2)
    29. The p40 domain of interleukin-12 (IL-12 beta chain), N-terminal domain [63665]
      1. Human (Homo sapiens) [TaxId: 9606] [63666] (7)
    30. Interleukin-6 receptor alpha chain, N-terminal domain [81958]
      1. Human (Homo sapiens) [TaxId: 9606] [81959] (1)
    31. CD3 gamma chain ectodomain fragment [69160]
      possibly an intermediate structure between the I set and FnIII domains
      1. Mouse (Mus musculus) [TaxId: 10090] [69161] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [110050] (1)
        SQ P09693 # CD3G_HUMAN T-cell surface glycoprotein CD3 gamma chain precursor
    32. CD3 epsilon chain ectodomain fragment [69162]
      possibly an intermediate structure between the I set and FnIII domains
      1. Mouse (Mus musculus) [TaxId: 10090] [69163] (2)
        SQ P22646 22-100
      2. Human (Homo sapiens) [TaxId: 9606] [110051] (2)
        SQ P07766 33-123 ! SQ P07766 # CD3E_HUMAN T-cell surface glycoprotein CD3 epsilon chain precursor
      3. Sheep (Ovis aries) [TaxId: 9940] [117040] (1)
        SQ P18438 22-88
    33. B and T lymphocyte attenuator, Btla [117041]
      1. Mouse (Mus musculus) [TaxId: 10090] [117042] (1)
        SQ Q7TSA3 40-143
    34. CD3 delta chain ectodomain fragment [117043]
      1. Human (Homo sapiens) [TaxId: 9606] [117044] (1)
        SQ P04234 23-95
    35. Myosin-binding protein C, slow-type [141013]
      1. Human (Homo sapiens) [TaxId: 9606] [141014] (2)
        SQ Q00872 342-431! SQ Q00872 58-170
    36. Receptor-type tyrosine-protein phosphatase mu [141015]
      1. Human (Homo sapiens) [TaxId: 9606] [141016] (1)
        SQ P28827 184-279
    37. Cervical EMMPRIN [158877]
      contains two Ig-domains in the N-terminal part
      1. Human (Homo sapiens) [TaxId: 9606] [158878] (8)
        SQ Q54A51 103-203! SQ Q54A51 23-102
    38. Ligand binding domain of lir-2 (ilt4) [158879]
      1. Human (Homo sapiens) [TaxId: 9606] [158880] (2)
        SQ Q8N423 120-218! SQ Q8N423 26-109
2. E set domains [81296] (23)
  "Early" Ig-like fold families possibly related to the immunoglobulin and/or fibronectin type III superfamilies
  uperfamily
  1. NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain [81279] (10)
    subgroup of the larger IPT/TIG domain family
    1. T-cell transcription factor NFAT1 (NFATC2) [49246]
      1. Human (Homo sapiens) [TaxId: 9606] [49247] (10)
    2. T-cell transcription factor NFAT5 (TONEBP) [69170]
      1. Human (Homo sapiens) [TaxId: 9606] [69171] (1)
    3. p50 subunit of NF-kappa B transcription factor [49248]
      1. Human (Homo sapiens) [TaxId: 9606] [49249] (9)
        SQ P25799 245-350
      2. Mouse (Mus musculus) [TaxId: 10090] [49250] (10)
    4. p52 subunit of NF-kappa B (NFKB) [49251]
      1. Human (Homo sapiens) [TaxId: 9606] [49252] (1)
    5. p65 subunit of NF-kappa B (NFKB), dimerization domain [49253]
      1. Mouse (Mus musculus) [TaxId: 10090] [49254] (10)
      2. Human (Homo sapiens) [TaxId: 9606] [49255] (4)
      3. Chicken (Gallus gallus), C-rel [TaxId: 9031] [74848] (1)
    6. DNA-binding protein LAG-1 (CSL) [110052]
      1. Caenorhabditis elegans [TaxId: 6239] [110053] (4)
        SQ Q9TYY1 195-660
    7. Calmodulin binding transcription activator 1 [141017]
      this domain is in the middle of long protein chain
      1. Human (Homo sapiens) [TaxId: 9606] [141018] (5)
        SQ Q9Y6Y1 872-953
  2. E-set domains of sugar-utilizing enzymes [81282] (30)
    domains of unknown function associated with different type of catalytic domains in a different sequential location
    subgroup of the larger IPT/TIG domain family
    1. Galactose oxidase, C-terminal domain [49209]
      follows the catalytic seven-bladed beta-propeller domain
      1. Dactylium dendroides [TaxId: 5132] [49210] (8)
        SQ Q01745 42-680
      2. Fungi (Fusarium sp.) [TaxId: 29916] [69164] (1)
        sequence identical to that of Dactylium dendroides
      3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [158881] (3)
    2. Sialidase, "linker" domain [49237]
      follows the catalytic six-bladed beta-propeller domain
      1. Micromonospora viridifaciens [TaxId: 1881] [49238] (8)
        SQ Q02834 47-647
    3. CelD cellulase, N-terminal domain [49231]
      precedes the catalytic alpha6/alpha6 domain
      1. Clostridium thermocellum [TaxId: 1515] [49232] (1)
    4. Cellulose 1,4-beta-cellobiosidase CbhA, precatalytic domain [101521]
      1. Clostridium thermocellum [TaxId: 1515] [101522] (2)
    5. Hyaluronate lyase precatalytic domain [69167]
      precedes the catalytic incomplete alpha5/alpha5 barrel
      a rudiment form of Ig-like domain
      1. Streptococcus agalactiae [TaxId: 1311] [69168] (3)
    6. Bacterial chitobiase (N-acetyl-beta-glucoseaminidase), C-terminal domain [49211]
      rudiment form of Ig-like domain; follows the catalytic (beta/alpha)8-barrel domain; family 20 glycosyl hydrolases
      1. Serratia marcescens [TaxId: 615] [49212] (4)
    7. Cyclomaltodextrin glycanotransferase, domain D [49215]
      follows the starch-binding domain C; the catalytic domain A has (beta/alpha)8-barrel fold; family 13 glycosyl hydrolases
      1. Bacillus circulans, different strains [TaxId: 1397] [49216] (36)
      2. Bacillus stearothermophilus [TaxId: 1422] [49217] (1)
      3. Bacillus sp., strain 1011 [TaxId: 1409] [49219] (8)
        SQ P05618
      4. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [49220] (2)
      5. Thermoanaerobacterium [TaxId: 28895] [158882] (2)
    8. Five domain "maltogenic" alpha-amylase (glucan 1,4-alpha-maltohydrolase), domain D [81280]
      domain architecture similar to cyclomaltodextrin glycosylhydrolases
      1. Bacillus stearothermophilus [TaxId: 1422] [81281] (2)
    9. Maltogenic amylase, N-terminal domain N [49221]
      precedes the catalytic (beta/alpha)8-barrel domain
      1. Thermus sp. [TaxId: 275] [49222] (2)
      2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [74842] (1)
      3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [74843] (9)
      4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [49223] (25)
    10. Neopullulanase, N-terminal domain [81960]
      homologous to maltogenic amylase
      1. Bacillus stearothermophilus [TaxId: 1422] [81961] (4)
    11. Cyclomaltodextrinase, N-terminal domain [101523]
      protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
      1. Flavobacterium sp. 92 [TaxId: 197856] [101524] (1)
    12. Isoamylase, N-terminal domain N [49226]
      elaborated with a few large insertions in the common fold
      precedes the catalytic (beta/alpha)8-barrel domain, the domain architecture similar to maltogenic amylases
      1. Pseudomonas amyloderamosa [TaxId: 32043] [49227] (1)
    13. Glycosyltrehalose trehalohydrolase, N-terminal domain N [49224]
      domain architecture similar to isoamylase
      1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [49225] (2)
      2. Deinococcus radiodurans [TaxId: 1299] [141019] (9)
        SQ Q9RX51 14-110
    14. 1,4-alpha-glucan branching enzyme, N-terminal domain N [81962]
      domain architecture similar to isoamylase
      1. Escherichia coli [TaxId: 562] [81963] (1)
    15. Chitinase A, N-terminal domain N [49233]
      precedes the catalytic (beta/alpha)8-barrel domain
      1. Serratia marcescens [TaxId: 615] [49234] (11)
        SQ P07254 24-563
    16. Glucodextranase, domain B [101525]
      1. Arthrobacter globiformis [TaxId: 1665] [101526] (2)
    17. Glucans biosynthesis protein G (MdoG, OpgG), C-terminal domain [110054]
      1. Escherichia coli [TaxId: 562] [110055] (1)
        SQ P33136 23-511
    18. Chitin-binding protein CBP21 [117045]
      member of Pfam 03067; elaborated fold with a large insertion between strands A and A'
      1. Serratia marcescens [TaxId: 615] [117046] (2)
        SQ O83009 28-197
    19. Beta-1,4-mannanase domain 2 (postcatalytic) [141020]
      1. Cellulomonas fimi [TaxId: 1708] [141021] (3)
        SQ Q9XCV5 421-514
    20. Pullulanase PulA [158883]
      contains two E-set domains in tandem
      1. Klebsiella pneumoniae [TaxId: 573] [158884] (6)
        SQ P07206 170-294! SQ P07206 295-409
  3. Other IPT/TIG domains [89191] (1)
    apart from the domains of transcription factors and sugar-utilizing enzymes
    1. Exocyst complex component Sec5, Ral-binding domain [89192]
      1. Mouse (Mus musculus) [TaxId: 10090] [89193] (2)
  4. Arthropod hemocyanin, C-terminal domain [81283] (2)
    1. Arthropod hemocyanin, C-terminal domain [49228]
      elaborated with many loop insertions in the common fold
      1. Horseshoe crab (Limulus polyphemus) [TaxId: 6850] [49229] (4)
      2. Spiny lobster (Panulirus interruptus) [TaxId: 6735] [49230] (7)
  5. Class II viral fusion proteins C-terminal domain [81284] (6)
    1. Envelope glycoprotein [49213]
      1. Tick-borne encephalitis virus [TaxId: 11084] [49214] (2)
      2. Dengue virus type 2 [TaxId: 11060] [89194] (12)
        SQ P12823 281-675 # 99% sequence identity
      3. Japanese encephalitis virus [TaxId: 11072] [101527] (1)
      4. West Nile virus [TaxId: 11082] [110056] (5)
        SQ Q8JU42 586-696
      5. Langat virus [TaxId: 11085] [141022] (2)
        SQ P29838 583-765
    2. Fusion glycoprotein E1 [74840]
      1. Semliki forest virus [TaxId: 11033] [74841] (5)
  6. Cytomegalovirus protein US2 [81285] (1)
    1. Cytomegalovirus protein US2 [63668]
      similar to both C1 and C2 set
      1. Human cytomegalovirus [TaxId: 10359] [63669] (1)
  7. Molybdenum-containing oxidoreductases-like dimerisation domain [81286] (2)
    1. Sulfite oxidase, C-terminal domain [49259]
      1. Chicken (Gallus gallus) [TaxId: 9031] [49260] (5)
      2. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [101528] (1)
  8. ML domain [81287] (3)
    implicated in lipid recognition, particularly in the recognition of pathogen related products
    1. Epididymal secretory protein E1 (Niemann-Pick C2 protein) [81964]
      a cholesterol binding protein
      1. Cow (Bos taurus) [TaxId: 9913] [81965] (4)
    2. Major mite allergen [49256]
      contains additional N-terminal strand
      1. House-dust mite (Dermatophagoides farinae), Der f 2 [TaxId: 6954] [49257] (8)
        SQ Q00855 18-146
      2. House-dust mite (Dermatophagoides pteronyssinus), Der p 2 [TaxId: 6956] [49258] (2)
  9. RhoGDI-like [81288] (3)
    1. Rho GDP-dissociation inhibitor 1, RhoGDI [49241]
      1. Human (Homo sapiens) [TaxId: 9606] [49242] (17)
      2. Cow (Bos taurus) [TaxId: 9913] [49243] (4)
    2. GMP-PDE delta [74846]
      1. Human (Homo sapiens) [TaxId: 9606] [74847] (3)
  10. Cytoplasmic domain of inward rectifier potassium channel [81966] (3)
    1. G protein-gated inward rectifier Girk1 [81967]
      forms tetrameric cytoplasmic pore; contains a C-terminal extension
      1. Mouse (Mus musculus) [TaxId: 10090] [81968] (1)
    2. Inward rectifier potassium channel Kirbac1.1 [89195]
      1. Burkholderia pseudomallei [TaxId: 28450] [89196] (1)
    3. Inward rectifier potassium channel kirbac3.1 [117047]
      1. Magnetospirillum magnetotacticum [TaxId: 188] [117048] (2)
        SQ Q8YY97 # 46% sequence identity; Anabaena sp. PCC 7120 TaxID: 103690
  11. Transglutaminase N-terminal domain [81289] (4)
    1. Transglutaminase N-terminal domain [49235]
      elaborated with many loop insertions in the common fold
      1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [49236] (8)
        Coagulation factor XIII
      2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [74844] (2)
        GDP-binding protein
      3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [74845] (8)
      4. Red sea bream (Chrysophrys major) [TaxId: 143350] [63667] (1)
  12. Filamin repeat (rod domain) [81290] (4)
    Pfam 00630
    1. F-actin cross-linking gelation factor (ABP-120) repeats [49239]
      1. Dictyostelium discoideum [TaxId: 44689] [49240] (3)
        SQ P13466 547-857
    2. Filamin C [117049]
      1. Human (Homo sapiens) [TaxId: 9606] [117050] (7)
        SQ Q14315 2633-2725
    3. Filamin a [141023]
      1. Human (Homo sapiens) [TaxId: 9606] [141024] (8)
        SQ P21333 1863-1953! SQ P21333 1863-1955! SQ P21333 2236-2328
    4. Filamin b [141025]
      1. Human (Homo sapiens) [TaxId: 9606] [141026] (14)
        SQ O75369 1017-1134! SQ O75369 1130-1229! SQ O75369 1215-1329! SQ O75369 1325-1442! SQ O75369 1418-1518! SQ O75369 1611-1721! SQ O75369 1899-2001! SQ O75369 1999-2096! SQ O75369 2104-2192
  13. Arrestin/Vps26-like [81291] (2)
    1. Arrestin [49244]
      duplication: contains tandem repeat of two elaborated Ig-like domains contacting each other head-to-head
      1. Cow (Bos taurus), visual arrestin [TaxId: 9913] [49245] (2)
      2. Cow (Bos taurus), beta-arrestin 1 [TaxId: 9913] [69169] (5)
  14. Gingipain R (RgpB), C-terminal domain [81292] (1)
    1. Gingipain R (RgpB), C-terminal domain [49261]
      Arginine-specific cysteine proteinase
      follows the catalytic alpha/beta domains
      1. Porphyromonas gingivalis [TaxId: 837] [49262] (1)
  15. Copper resistance protein C (CopC, PcoC) [81969] (2)
    1. Copper resistance protein C (CopC, PcoC) [81970]
      1. Pseudomonas syringae [TaxId: 317] [81971] (7)
      2. Escherichia coli [TaxId: 562] [81972] (2)
  16. Cellulosomal scaffoldin protein CipC, module x2.1 [81293] (1)
    1. Cellulosomal scaffoldin protein CipC, module x2.1 [49263]
      1. Clostridium cellulolyticum [TaxId: 1521] [49264] (1)
  17. Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 [81294] (2)
    1. Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 [69176]
      duplication: tandem repeat of two Ig-like domains
      1. Paracoccus denitrificans [TaxId: 266] [69177] (2)
      2. Pseudomonas putida [TaxId: 303] [69178] (2)
  18. Internalin Ig-like domain [81295] (3)
    truncated fold fused to an LRR domain
    1. Internalin A [81973]
      1. Listeria monocytogenes [TaxId: 1639] [81974] (7)
    2. Internalin B [69172]
      1. Listeria monocytogenes [TaxId: 1639] [69173] (5)
    3. Internalin H [69174]
      1. Listeria monocytogenes [TaxId: 1639] [69175] (1)
  19. SoxZ-like [141027] (1)
    1. Sulfur oxidation protein SoxZ [141028]
      1. Thermus thermophilus [TaxId: 274] [141029] (2)
        SQ Q5SME6 2-107
        TTHA1420
  20. Enterochelin esterase N-terminal domain-like [141030] (2)
    PfamB 013071
    1. Enterochelin esterase [141031]
      1. Shigella flexneri [TaxId: 623] [141032] (1)
        SQ Q83SB9 3-150
      2. Shigella flexneri 2a str. 2457T [TaxId: 198215] [158885] (10)
  21. AMPK-beta glycogen binding domain-like [158886] (3)
    lacks the N-terminal strand (A) and contains a beta-hairpin insertion in the C-terminal strand (G)
    1. 5'-AMP-activated protein kinase subunit beta-2 [158887]
      1. Human (Homo sapiens) [TaxId: 9606] [158888] (1)
        SQ O43741 75-163
    2. SIP2 [158889]
      1. Saccharomyces cerevisiae [TaxId: 4932] [158890] (2)
        SQ P34164 161-247
    3. 5'-AMP-activated protein kinase subunit beta-1 [158891]
      1. Rattus norvegicus [TaxId: 10116] [158892] (6)
        SQ P80386 76-162
  22. Sec63 C-terminal domain-like [158893] (1)
    C-terminal part of Pfam 02889
    1. Protein pro2281 [158894]
      1. Human (Homo sapiens) [TaxId: 9606] [158895] (1)
        SQ Q9P172 209-322
  23. SVA-like [158896] (1)
    Pfam 05326
    1. Prolactin-inducible protein, PIP [158897]
      1. Human (Homo sapiens) [TaxId: 9606] [158898] (1)
        SQ P12273 29-146
3. Fibronectin type III [49265] (1)
  uperfamily
  1. Fibronectin type III [49266] (53)
    Pfam 00041
    1. Extracellular region of human tissue factor [49267]
      tandem of fibronectin type III domains
      1. Human (Homo sapiens) [TaxId: 9606] [49268] (13)
        SQ P13726 33-242
      2. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [49269] (35)
    2. Fibronectin, different Fn3 modules [49270]
      1. Human (Homo sapiens) [TaxId: 9606] [49271] (9)
      2. Mouse (Mus musculus) [TaxId: 10090] [49272] (2)
      3. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [158899] (1)
    3. Tenascin [49273]
      1. Chicken (Gallus gallus) [TaxId: 9031] [49274] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [49275] (1)
      3. Rat (Rattus norvegicus) [TaxId: 10116] [110057] (1)
        SQ Q05546 502-770
    4. Neuroglian, two amino proximal Fn3 repeats [49276]
      tandem of fibronectin type III domains
      1. Drosophila melanogaster [TaxId: 7227] [49277] (1)
    5. Neural cell adhesion molecule 1, NCAM [89197]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89198] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [141033] (17)
        SQ P13592 498-598
    6. Fibronectin type III domain from chitinase A1. [81975]
      1. Bacillus circulans [TaxId: 1397] [81976] (1)
    7. Integrin beta-4 subunit [49278]
      1. Human (Homo sapiens) [TaxId: 9606] [49279] (1)
    8. Growth hormone receptor [49280]
      1. Human (Homo sapiens) [TaxId: 9606] [49281] (10)
        tandem of fibronectin type III domains
    9. Erythropoietin (EPO) receptor [49282]
      1. Human (Homo sapiens) [TaxId: 9606] [49283] (5)
      2. Escherichia coli [TaxId: 562] [158900] (6)
    10. Prolactin receptor [49284]
      1. Human (Homo sapiens) [TaxId: 9606] [49285] (3)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [49286] (1)
    11. Interleukin-4 receptor alpha chain [49287]
      1. Human (Homo sapiens) [TaxId: 9606] [49288] (1)
    12. Common beta-chain in the GM-CSF, IL-3 and IL-5 receptors [49289]
      duplication: consists of four similar domains; dimerizes by swapping the C-terminal strands of domains 1 and 3
      1. Human (Homo sapiens) [TaxId: 9606] [49290] (11)
    13. Granulocyte colony-stimulating factor (GC-SF) receptor [49291]
      1. Mouse (Mus musculus) [TaxId: 10090] [49292] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [141034] (2)
        SQ Q99062 120-226! SQ Q99062 227-331
    14. Interferon-gamma receptor alpha chain [49293]
      1. Human (Homo sapiens) [TaxId: 9606] [49294] (3)
    15. Cytokine receptor gp130 cytokine-binding domains [49295]
      1. Human (Homo sapiens) [TaxId: 9606] [49296] (5)
    16. Interleukin-10 receptor 1, IL-10R1 [63670]
      1. Human (Homo sapiens) [TaxId: 9606] [63671] (8)
    17. Type I titin module [49297]
      1. Human (Homo sapiens) [TaxId: 9606] [49298] (1)
    18. The p40 domain of interleukin-12 (IL-12 beta chain), domains 2 and 3 [63672]
      1. Human (Homo sapiens) [TaxId: 9606] [63673] (12)
    19. Interleukin-6 receptor alpha chain, domains 2 and 3 [81977]
      1. Human (Homo sapiens) [TaxId: 9606] [81978] (3)
    20. Interferon-alpha/beta receptor beta chain [89199]
      1. Human (Homo sapiens) [TaxId: 9606] [89200] (4)
    21. KIAA1568 protein [101529]
      1. Human (Homo sapiens) [TaxId: 9606] [101530] (2)
    22. KIAA0343 protein [101531]
      1. Human (Homo sapiens) [TaxId: 9606] [101532] (2)
    23. KIAA1355 [110058]
      1. Human (Homo sapiens) [TaxId: 9606] [110059] (1)
        SQ Q9P2J2 [Fragment] 634-728
    24. Ciliary neurotrophic factor receptor alpha [110060]
      1. Human (Homo sapiens) [TaxId: 9606] [110061] (1)
        SQ P26992 202-305
    25. Host cell factor 2, HCF-2 [117051]
      1. Mouse (Mus musculus) [TaxId: 10090] [117052] (1)
        SQ Q9D968 127-236
    26. Fibronectin type 3 and ankyrin repeat domains 1 protein, FANK1 [117053]
      1. Mouse (Mus musculus) [TaxId: 10090] [117054] (1)
        SQ Q9DAM9 1-107
    27. Contactin 3 (KIAA1496) [117055]
      1. Human (Homo sapiens) [TaxId: 9606] [117056] (1)
        SQ Q9P232 893-996
    28. Fibronectin type-III domain containing protein 3a, FNDC3A (KIAA0970) [117057]
      1. Human (Homo sapiens) [TaxId: 9606] [117058] (6)
        SQ Q9Y2H6 192-315
    29. Ephrin type-B receptor 1 [141035]
      1. Human (Homo sapiens) [TaxId: 9606] [141036] (1)
        SQ P54762 434-528
    30. Brother of CDO precursor (BOC) [141037]
      1. Mouse (Mus musculus) [TaxId: 10090] [141038] (2)
        SQ Q6AZB0 591-689! SQ Q6AZB0 707-807
    31. Ephrin type-A receptor 8 [141039]
      1. Human (Homo sapiens) [TaxId: 9606] [141040] (1)
        SQ P29322 473-534
        structure of the C-terminal SAM domain is known (scop_sp 101243)
    32. Cytokine receptor common gamma chain [141041]
      1. Human (Homo sapiens) [TaxId: 9606] [141042] (8)
        SQ P31785 142-246! SQ P31785 142-248! SQ P31785 54-141! SQ P31785 56-141
    33. Rim binding protein 2 [141043]
      1. Human (Homo sapiens) [TaxId: 9606] [141044] (1)
        SQ O15034 477-593
    34. Tenascin-X [141045]
      1. Human (Homo sapiens) [TaxId: 9606] [141046] (3)
        SQ P22105 3699-3798! SQ P22105 3890-3991! SQ P22105 3977-4069
    35. Interleukin-2 receptor beta chain [141047]
      1. Human (Homo sapiens) [TaxId: 9606] [141048] (6)
        SQ P14784 130-232! SQ P14784 130-233! SQ P14784 32-129
    36. Receptor-type tyrosine-protein phosphatase delta, PTPRD [141049]
      1. Human (Homo sapiens) [TaxId: 9606] [141050] (1)
        SQ P23468 504-607
    37. Sidekick 2 [141051]
      1. Human (Homo sapiens) [TaxId: 9606] [141052] (4)
        SQ Q58EX2 1279-1395! SQ Q58EX2 578-685! SQ Q58EX2 881-988! SQ Q58EX2 981-1081
    38. Neogenin [141053]
      1. Human (Homo sapiens) [TaxId: 9606] [141054] (6)
        SQ Q92859 429-535! SQ Q92859 529-631! SQ Q92859 623-741! SQ Q92859 718-830! SQ Q92859 853-952! SQ Q92859 942-1054
    39. Down syndrome cell adhesion molecule-like protein 1, DSCAML1 [141055]
      1. Human (Homo sapiens) [TaxId: 9606] [141056] (1)
        SQ Q8TD84 979-1087
    40. Myosin binding protein C, fast-type [141057]
      1. Mouse (Mus musculus) [TaxId: 10090] [141058] (1)
        SQ Q5XKE0 731-828
    41. Receptor-type tyrosine-protein phosphatase F, PTPRF [141059]
      1. Human (Homo sapiens) [TaxId: 9606] [141060] (1)
        SQ P10586 811-904
    42. Hedgehog receptor iHog [141061]
      Cg9211-PA
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141062] (12)
        SQ Q9VM64 466-572! SQ Q9VM64 573-667
    43. Ephrin type-A receptor 1 [141063]
      1. Mouse (Mus musculus) [TaxId: 10090] [141064] (1)
        SQ Q60750 446-539
    44. Insulin receptor [158901]
      1. Human (Homo sapiens) [TaxId: 9606] [158902] (3)
        SQ P06213 495-618
4. PKD domain [49299] (1)
  uperfamily
  1. PKD domain [49300] (3)
    Pfam 00801
    1. Polycystein-1, PKD-1 [49301]
      1. Human (Homo sapiens) [TaxId: 9606] [49302] (1)
    2. Surface layer protein [81979]
      1. Archaeon Methanosarcina mazei [TaxId: 2209] [81980] (1)
    3. VPS10 domain-containing receptor SorCS2 [117059]
      1. Human (Homo sapiens) [TaxId: 9606] [117060] (1)
        SQ Q96PQ0 760-869
5. beta-Galactosidase/glucuronidase domain [49303] (1)
  uperfamily
  1. beta-Galactosidase/glucuronidase domain [49304] (5)
    1. beta-Galactosidase, domains 2 and 4 [49305]
      1. Escherichia coli [TaxId: 562] [49306] (25)
        SQ P00722
      2. Arthrobacter sp. c2-2 [TaxId: 192168] [141065] (12)
        SQ Q8KRF6 220-312! SQ Q8KRF6 610-721
    2. beta-Glucuronidase [49307]
      1. Human (Homo sapiens) [TaxId: 9606] [49308] (1)
    3. Exochitosanase CsxA, domains 2, 4 and 5 [158903]
      1. Amycolatopsis orientalis [TaxId: 31958] [158904] (6)
        SQ Q56F26 226-335! SQ Q56F26 675-777! SQ Q56F26 778-899
    4. Beta-mannosidase, domains 2, 4 and 5 [158905]
      truncated domain 5 lacks the last strand
      1. Bacteroides thetaiotaomicron [TaxId: 818] [158906] (54)
        SQ Q8AAK6 220-330! SQ Q8AAK6 679-783! SQ Q8AAK6 784-864
6. Transglutaminase, two C-terminal domains [49309] (1)
  uperfamily
  1. Transglutaminase, two C-terminal domains [49310] (4)
    1. Transglutaminase, two C-terminal domains [49311]
      duplication
      1. Human (Homo sapiens), blood isozyme [TaxId: 9606] [49312] (8)
        Coagulation factor XIII,
      2. Human (Homo sapiens), tissue isozyme [TaxId: 9606] [74849] (3)
        GDP-binding protein
      3. Human (Homo sapiens), TGase E3 [TaxId: 9606] [74850] (8)
      4. Red sea bream (Chrysophrys major) [TaxId: 143350] [63674] (1)
7. Cadherin-like [49313] (2)
  uperfamily
  1. Cadherin [49314] (4)
    1. N-cadherin (neural) [49315]
      1. Mouse (Mus musculus) [TaxId: 10090] [49316] (7)
    2. E-cadherin (epithelial) [49317]
      synonym: uvomorulin
      1. Mouse (Mus musculus) [TaxId: 10090] [49318] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [81981] (7)
    3. C-cadherin ectodomain [74851]
      five-domain fragment
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [74852] (1)
  2. Dystroglycan, N-terminal domain [110062] (1)
    1. Dystroglycan, N-terminal domain [110063]
      1. Mouse (Mus musculus) [TaxId: 10090] [110064] (1)
        SQ Q62165 58-303
8. Actinoxanthin-like [49319] (1)
  uperfamily
  1. Actinoxanthin-like [49320] (5)
    1. Macromycin [49321]
      1. Streptomyces macromomyceticus [TaxId: 1917] [49322] (1)
    2. Neocarzinostatin [49323]
      1. Streptomyces carzinostaticus [TaxId: 1897] [49324] (7)
    3. Actinoxanthin [49325]
      1. Actinomyces globisporus, number 1131 [TaxId: 1908] [49326] (1)
    4. Antitumor antibiotic C-1027 [63675]
      1. Streptomyces globisporus [TaxId: 1908] [63676] (3)
    5. Kedarcidin [49327]
      1. Actinomycete ATCC 53650, strain L585-6 [TaxId: 38989] [49328] (1)
9. Cu,Zn superoxide dismutase-like [49329] (1)
  has additional strand at N-terminus
  uperfamily
  1. Cu,Zn superoxide dismutase-like [49330] (13)
    1. Cu,Zn superoxide dismutase, SOD [49331]
      1. Cow (Bos taurus) [TaxId: 9913] [49332] (27)
      2. Human (Homo sapiens) [TaxId: 9606] [49333] (32)
      3. African clawed frog (Xenopus laevis) [TaxId: 8355] [49334] (1)
      4. Spinach (Spinacia oleracea) [TaxId: 3562] [49335] (1)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49336] (12)
      6. Photobacterium leiognathi [TaxId: 553611] [49337] (9)
      7. Escherichia coli [TaxId: 562] [49338] (1)
        Monomeric enzyme
      8. Salmonella typhimurium [TaxId: 90371] [49339] (1)
      9. Actinobacillus pleuropneumoniae [TaxId: 715] [49340] (1)
      10. Mycobacterium tuberculosis [TaxId: 1773] [110065] (1)
        SQ P96278
      11. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [110066] (2)
        SQ Q01137
    2. Copper chaperone for superoxide dismutase, C-terminal domain [49341]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49342] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [49343] (1)
10. CBD9-like [49344] (3)
  has additional strand at N-terminus; the active site in a similar topological location as the Cu,Zn SOD site
  uperfamily
  1. Cytochrome domain of cellobiose dehydrogenase [49345] (1)
    1. Cytochrome domain of cellobiose dehydrogenase [49346]
      1. Fungus (Phanerochaete chrysosporium) [TaxId: 5306] [49347] (4)
  2. Family 9 carbohydrate-binding module, CBD9 [63677] (1)
    1. Xylanase 10A [63678]
      1. Thermotoga maritima [TaxId: 2336] [63679] (3)
  3. Glucodextranase, domain C [101533] (1)
    1. Glucodextranase, domain C [101534]
      1. Arthrobacter globiformis [TaxId: 1665] [101535] (2)
11. Lamin A/C globular tail domain [74853] (1)
  uperfamily
  1. Lamin A/C globular tail domain [74854] (2)
    1. Lamin A/C globular tail domain [74855]
      1. Human (Homo sapiens) [TaxId: 9606] [74856] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [110067] (1)
        SQ P48678 408-546
12. Clathrin adaptor appendage domain [49348] (3)
  contains an additional N-terminal strand
  uperfamily
  1. Alpha-adaptin ear subdomain-like [49349] (2)
    ear domain consists of two different subdomains
    1. Alpha-adaptin AP2 ear domain, N-terminal subdomain [49350]
      1. Mouse (Mus musculus) [TaxId: 10090] [49351] (10)
        SQ P17427 694-938 # 98% sequence identity
    2. Beta2-adaptin AP2 ear domain, N-terminal subdomain [49352]
      1. Human (Homo sapiens) [TaxId: 9606] [49353] (5)
  2. gamma-adaptin C-terminal appendage domain-like [74857] (3)
    consist of a single subdomain
    1. Gamma1-adaptin domain [74858]
      1. Human (Homo sapiens) [TaxId: 9606] [74859] (5)
    2. ADP-ribosylation factor binding protein Gga1 domain [89201]
      1. Human (Homo sapiens) [TaxId: 9606] [89202] (10)
    3. ADP-ribosylation factor binding protein Gga3 domain [89203]
      1. Human (Homo sapiens) [TaxId: 9606] [89204] (1)
  3. Coatomer appendage domain [101536] (2)
    1. Coatomer gamma subunit C-terminal domain, first subdomain [101537]
      1. Human (Homo sapiens) [TaxId: 9606] [101538] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [101539] (1)
13. Integrin domains [69179] (1)
  uperfamily
  1. Integrin domains [69180] (2)
    1. Thigh, calf-1 and calf-2 domains of integrin alpha [69181]
      1. Human (Homo sapiens) [TaxId: 9606] [69182] (4)
        SQ P06756 31-986
    2. Hybrid domain of integrin beta [69183]
      1. Human (Homo sapiens) [TaxId: 9606] [69184] (5)
        SQ P05106 27-466
14. PapD-like [49354] (2)
  contains PP switch between strands D and C'
  uperfamily
  1. Pilus chaperone [49355] (5)
    1. Pilus chaperone PapD, N-domain [49356]
      consists of two domains of this fold; domain 2 has an additional strand at the C-terminus
      1. Escherichia coli [TaxId: 562] [49357] (12)
    2. Periplasmic chaperone FimC [49358]
      1. Escherichia coli [TaxId: 562] [49359] (6)
    3. Periplasmic chaperone SfaE [74860]
      1. Escherichia coli [TaxId: 562] [74861] (1)
    4. Chaperone protein Caf1m [89205]
      1. Yersinia pestis [TaxId: 632] [89206] (9)
    5. Periplasmic chaperone SafB [158907]
      1. Salmonella typhimurium [TaxId: 90371] [158908] (2)
        SQ Q8ZRK3 21-151
  2. MSP-like [49360] (5)
    Pfam 00635
    1. Major sperm protein, MSP [49361]
      1. Pig roundworm (Ascaris suum), alpha isoform [TaxId: 6253] [49362] (3)
      2. Nematode (Caenorhabditis elegans) [TaxId: 6239] [74862] (1)
    2. WR4 [89207]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89208] (1)
        4L504 (ZC168.6) gene product
    3. SSP-19 [101540]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [101541] (1)
        C55C2.2 gene product
    4. MSP domain containing protein 2, Mospd2 [117061]
      1. Mouse (Mus musculus) [TaxId: 10090] [117062] (1)
        SQ Q9CWP6 317-455
15. Purple acid phosphatase, N-terminal domain [49363] (1)
  uperfamily
  1. Purple acid phosphatase, N-terminal domain [49364] (2)
    1. Purple acid phosphatase, N-terminal domain [49365]
      1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49366] (9)
      2. Sweet potato (Ipomoea batatas) [TaxId: 4120] [117063] (1)
        SQ Q9SE00 39-462
16. Fungal immunomodulatory protein, FIP [101542] (1)
  uperfamily
  1. Fungal immunomodulatory protein, FIP [101543] (1)
    1. Fungal immunomodulatory protein, FIP [101544]
      contains extra N-terminal sudbomain involved in dimerisation
      1. Golden needle mushroom (Flammulina velutipes) [TaxId: 38945] [101545] (1)
17. Superoxide reductase-like [49367] (1)
  uperfamily
  1. Superoxide reductase-like [49368] (3)
    binds iron in the site that is topologically equivalent to the copper-binding site of cupredoxins
    1. Superoxide reductase (SOR) [49369]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [49370] (3)
    2. Desulfoferrodoxin C-terminal domain [49371]
      1. Desulfovibrio desulfuricans [TaxId: 876] [49372] (13)
      2. Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887] [110068] (3)
        SQ Q46495
18. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74863] (1)
  uperfamily
  1. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74864] (1)
    1. Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha) [74865]
      1. Escherichia coli [TaxId: 562] [74866] (6)
19. Invasin/intimin cell-adhesion fragments [49373] (1)
  uperfamily
  1. Invasin/intimin cell-adhesion fragments [49374] (2)
    1. Intimin [49375]
      1. Escherichia coli [TaxId: 562] [49376] (3)
        an enteropathogenic serotype
    2. Invasin [49377]
      1. Yersinia pseudotuberculosis [TaxId: 633] [49378] (1)
20. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81982] (1)
  uperfamily
  1. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81983] (1)
    1. Antigen MPT63/MPB63 (immunoprotective extracellular protein) [81984]
      1. Mycobacterium tuberculosis [TaxId: 1773] [81985] (1)
21. Tp47 lipoprotein, middle and C-terminal domains [81986] (1)
  uperfamily
  1. Tp47 lipoprotein, middle and C-terminal domains [81987] (1)
    contains two different domains of immunoglobulin-like fold
    1. Tp47 lipoprotein, middle and C-terminal domains [81988]
      a penicillin-binding protein with carboxypeptidase activity
      1. Treponema pallidum [TaxId: 160] [81989] (1)
22. ASF1-like [101546] (1)
  contains extra C-terminal strand
  uperfamily
  1. ASF1-like [101547] (3)
    1. Anti-silencing protein 1, ASF1 [101548]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101549] (3)
      2. Schizosaccharomyces pombe [TaxId: 4896] [158909] (13)
        SQ O74515 1-161
      3. Human (Homo sapiens) [TaxId: 9606] [158910] (5)
        SQ Q6IA08 1-154! SQ Q9Y294 1-154! SQ Q9Y294 1-156
23. ApaG-like [110069] (1)
  uperfamily
  1. ApaG-like [110070] (3)
    Pfam 04379; dimeric in crystals; this dimer is a probable biological unit
    1. ApaG [110071]
      1. Shewanella oneidensis [TaxId: 70863] [110072] (1)
        SQ Q8EB92
      2. Bordetella pertussis [TaxId: 520] [117064] (1)
        SQ Q7VU61
      3. Vibrio cholerae [TaxId: 666] [117065] (1)
        SQ Q9KUS3
24. Accessory protein X4 (ORF8, ORF7a) [117066] (1)
  uperfamily
  1. Accessory protein X4 (ORF8, ORF7a) [117067] (1)
    1. Accessory protein X4 (ORF8, ORF7a) [117068]
      1. SARS coronavirus [TaxId: 227859] [117069] (1)
        SQ P59635 15-82
25. LEA14-like [117070] (1)
  uperfamily
  1. LEA14-like [117071] (1)
    Pfam 03168
    1. Putative dessication related protein LEA14 [117072]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117073] (1)
        SQ O03983
26. ICP-like [141066] (1)
  topological variant with similarity to the Cupredoxin-like fold (scop_cf 49502) in the N-terminal region
  uperfamily
  1. ICP-like [141067] (2)
    PfamB 014070
    1. Chagasin [141068]
      1. Trypanosoma cruzi [TaxId: 5693] [141069] (9)
        SQ Q966X9 3-110
    2. Inhibitor of cysteine peptidases, ICP [141070]
      1. Leishmania mexicana [TaxId: 5665] [141071] (1)
        SQ Q868H1 1-113
27. CalX-like [141072] (1)
  uperfamily
  1. CalX-beta domain [141073] (1)
    Pfam 03160
    1. Sodium/calcium exchanger 1 [141074]
      1. Dog (Canis familiaris) [TaxId: 9615] [141075] (3)
        SQ P23685 402-534! SQ P23685 403-541! SQ P23685 533-724
28. NEAT domain-like [158911] (1)
  1. NEAT domain [158912] (3)
    Pfam 05031; iron transport-associated domain
    1. Iron-regulated surface determinant protein C, IsdC [158913]
      1. Staphylococcus aureus [TaxId: 1280] [158914] (2)
        SQ Q7A654 29-150
    2. Iron-regulated surface determinant protein A, IsdA [158915]
      1. Staphylococcus aureus [TaxId: 1280] [158916] (7)
        SQ Q7A152 64-184! SQ Q99UX4 63-184
    3. Iron-regulated surface determinant protein H, IsdH [158917]
      1. Staphylococcus aureus [TaxId: 1280] [158918] (1)
        SQ Q6G8J7 86-229
Common fold of diphtheria toxin/transcription factors/cytochrome f [49379] (10)
sandwich; 9 strands in 2 sheet; greek-key; subclass of immunoglobin-like fold
1. Diphtheria toxin, C-terminal domain [49380] (1)
  uperfamily
  1. Diphtheria toxin, C-terminal domain [49381] (1)
    1. Diphtheria toxin, C-terminal domain [49382]
      1. Corynebacterium diphtheriae [TaxId: 1717] [49383] (6)
2. Carbohydrate-binding domain [49384] (3)
  uperfamily
  1. Cellulose-binding domain family II [49385] (2)
    1. Exo-1,4-beta-D-glycanase (cellulase, xylanase), cellulose-binding domain, CBD [49386]
      belongs to subfamily IIa
      1. Cellulomonas fimi [TaxId: 1708] [49387] (2)
    2. Endo-1,4-beta xylanase D, xylan binding domain, XBD [49388]
      belongs to subfamily IIb
      1. Cellulomonas fimi [TaxId: 1708] [49389] (6)
  2. Cellulose-binding domain family III [49390] (11)
    Pfam 00963
    1. Cellusomal scaffolding protein A, scaffoldin [49391]
      1. Clostridium thermocellum [TaxId: 1515] [49392] (1)
      2. Clostridium cellulolyticum [TaxId: 1521] [49393] (1)
    2. Endo/exocellulase:cellobiose E-4, C-terminal domain [49394]
      1. Thermomonospora fusca [TaxId: 2021] [49395] (4)
      2. Clostridium cellulolyticum, atcc 35319 [TaxId: 1521] [89209] (4)
        endoglucanase 9G
    3. Cohesin domain [49396]
      1. Clostridium thermocellum, cellulosome, various modules [TaxId: 1515] [49397] (6)
      2. Clostridium cellulolyticum [TaxId: 1521] [158919] (3)
    4. Cellulosomal scaffoldin adaptor protein B, ScaB [110073]
      1. Acetivibrio cellulolyticus [TaxId: 35830] [110074] (2)
        SQ Q7WYN3 29-199
    5. Cellulosomal scaffoldin ScaA [141076]
      1. Bacteroides cellulosolvens [TaxId: 35825] [141077] (1)
        SQ Q9FDJ9 2073-2242
    6. Scaffolding dockerin binding protein A, SdbA [141078]
      1. Clostridium thermocellum [TaxId: 1515] [141079] (2)
        SQ P71143 30-191! SQ P71143 30-195
    7. Exo-alpha-sialidase [158920]
      pre C-terminal domain
      1. Clostridium perfringens [TaxId: 1502] [158921] (1)
        SQ Q0TTQ4 945-1080
    8. O-GlcNAcase NagJ [158922]
      pre C-terminal domain
      1. Clostridium perfringens [TaxId: 1502] [158923] (5)
        SQ Q0TR53 768-909! SQ Q0TR53 774-906
  3. Bacterial chitobiase, n-terminal domain [49398] (1)
    1. Bacterial chitobiase, n-terminal domain [49399]
      1. Serratia marcescens [TaxId: 615] [49400] (4)
3. Bacterial adhesins [49401] (6)
  uperfamily
  1. Collagen-binding domain of adhesin [49402] (1)
    1. Collagen-binding domain of adhesin [49403]
      1. Staphylococcus aureus [TaxId: 1280] [49404] (1)
  2. Fibrinogen-binding domain [89210] (2)
    duplication: contains two differently decorated domains of this fold
    1. Clumping factor A [89211]
      1. Staphylococcus aureus [TaxId: 1280] [89212] (1)
    2. Fibrinogen-binding adhesin SdrG [101550]
      1. Staphylococcus epidermidis [TaxId: 1282] [101551] (6)
  3. Pilus subunits [49405] (8)
    1. Mannose-specific adhesin FimH [49406]
      duplication: consists of two domains of this fold; C-terminal domain lacks the last strand
      1. Escherichia coli [TaxId: 562] [49407] (9)
    2. PapK pilus subunit [49408]
      similar to C-terminal domain of FimH
      1. Escherichia coli [TaxId: 562] [49409] (1)
    3. PapE pilus subunit [81990]
      1. Escherichia coli [TaxId: 562] [81991] (2)
    4. F1 capsule antigen Caf1 [89213]
      1. Yersinia pestis [TaxId: 632] [89214] (3)
    5. SafA pilus subunit [141080]
      1. Salmonella typhimurium [TaxId: 90371] [141081] (13)
        SQ Q8ZRK4 36-168! SQ Q8ZRK4 46-170
    6. PAP fimbrial minor pilin protein PapH [158924]
      1. Escherichia coli [TaxId: 562] [158925] (1)
        SQ P07111 46-195
    7. Pap fimbrial major pilin protein PapA [158926]
      1. Escherichia coli [TaxId: 562] [158927] (5)
        SQ P04127 30-185! SQ P04127 32-185
    8. Invasin AfaD [158928]
      1. Escherichia coli [TaxId: 562] [158929] (4)
        SQ Q47038 27-147
  4. PapG adhesin receptor-binding domain [63680] (1)
    1. PapG adhesin receptor-binding domain [63681]
      1. Escherichia coli [TaxId: 562] [63682] (2)
  5. F17c-type adhesin [89215] (2)
    1. Fimbrial adhesin F17-AG lectin domain [89216]
      1. Escherichia coli [TaxId: 562] [89217] (6)
    2. Fimbrial lectin GafD [101552]
      1. Escherichia coli [TaxId: 562] [101553] (1)
  6. Dr-family adhesin [110075] (1)
    Pfam 04619
    1. DraA/Afimbrial adhesin Afa-III [110076]
      1. Escherichia coli [TaxId: 562] [110077] (7)
        SQ Q57254 P24093 23-159
4. Alpha-macroglobulin receptor domain [49410] (1)
  uperfamily
  1. Alpha-macroglobulin receptor domain [49411] (3)
    1. alpha-1-macroglobulin [49412]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49413] (1)
    2. alpha-2-macroglobulin [49414]
      1. Human (Homo sapiens) [TaxId: 9606] [49415] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [49416] (1)
5. p53-like transcription factors [49417] (7)
  uperfamily
  1. p53 DNA-binding domain-like [81314] (3)
    1. p53 tumor suppressor, DNA-binding domain [49419]
      1. Human (Homo sapiens) [TaxId: 9606] [49420] (37)
      2. Mouse (Mus musculus) [TaxId: 10090] [63683] (1)
    2. Transcription factor CEP-1 [110078]
      1. Caenorhabditis elegans [TaxId: 6239] [110079] (1)
        SQ Q20646 223-418
  2. Rel/Dorsal transcription factors, DNA-binding domain [81315] (9)
    1. T-cell transcription factor NFAT1 (NFATC), DNA-binding domain [49421]
      1. Human (Homo sapiens) [TaxId: 9606] [49422] (12)
    2. T-cell transcription factor NFAT5 (TONEBP), DNA-binding domain [69185]
      1. Human (Homo sapiens) [TaxId: 9606] [69186] (1)
    3. p50 subunit of NF-kappa B (NFKB), N-terminal domain [49423]
      1. Human (Homo sapiens) [TaxId: 9606] [49424] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [49425] (8)
    4. p52 subunit of NF-kappa B (NFKB), N-terminal domain [49426]
      1. Human (Homo sapiens) [TaxId: 9606] [49427] (1)
    5. p65 subunit of NF-kappa B (NFKB), N-terminal domain [49428]
      1. Mouse (Mus musculus) [TaxId: 10090] [49429] (8)
      2. Human (Homo sapiens) [TaxId: 9606] [49430] (1)
      3. Chicken (Gallus gallus), C-rel [TaxId: 9031] [74867] (1)
    6. Dorsal homologue Gambif1 [49431]
      1. African malaria mosquito (Anopheles gambiae) [TaxId: 7165] [49432] (1)
  3. T-box [81316] (2)
    1. T domain from Brachyury transcription factor [49433]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [49434] (1)
    2. T-box protein 3, tbx3 [74868]
      1. Human (Homo sapiens) [TaxId: 9606] [74869] (1)
  4. STAT DNA-binding domain [81317] (3)
    1. STAT-1, DNA-binding domain [49435]
      1. Human (Homo sapiens) [TaxId: 9606] [49436] (1)
    2. STAT3b [49437]
      1. Mouse (Mus musculus) [TaxId: 10090] [49438] (1)
    3. STAT homologue [101554]
      1. Dictyostelium discoideum [TaxId: 44689] [101555] (2)
  5. RUNT domain [81318] (2)
    1. Acute myeloid leukemia 1 protein (AML1), RUNT domain [49439]
      synonym: core binding factor alpha, cbfa
      1. Human (Homo sapiens) [TaxId: 9606] [49440] (5)
      2. Mouse (Mus musculus) [TaxId: 10090] [63684] (6)
        almost identical sequence to the human protein
  6. DNA-binding domain from NDT80 [81992] (1)
    1. DNA-binding domain from NDT80 [81993]
      common fold is decorated with many additional structures
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81994] (14)
  7. DNA-binding protein LAG-1 (CSL) [110080] (1)
    1. DNA-binding protein LAG-1 (CSL) [110081]
      1. Caenorhabditis elegans [TaxId: 6239] [110082] (4)
        SQ Q9TYY1 195-660
6. Cytochrome f, large domain [49441] (1)
  uperfamily
  1. Cytochrome f, large domain [49442] (5)
    1. Cytochrome f, large domain [49443]
      this domain is interrupted by a small domain which is barrel-sandwich hybrid fold
      1. Turnip (Brassica rapa) [TaxId: 3711] [49444] (2)
      2. Chlamydomonas reinhardtii [TaxId: 3055] [49445] (6)
      3. Phormidium laminosum [TaxId: 32059] [49446] (1)
      4. Mastigocladus laminosus [TaxId: 83541] [101556] (1)
      5. Anabaena sp., PCC 7120 [TaxId: 1167] [158930] (1)
        SQ Q93SW9 45-213,280-298
7. beta-sandwich domain of Sec23/24 [81995] (1)
  uperfamily
  1. beta-sandwich domain of Sec23/24 [81996] (2)
    1. Sec23 [81997]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [81998] (3)
    2. Sec24 [81999]
      includes the N-terminal tail
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82000] (4)
8. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49447] (1)
  duplication: one domain of this fold is inserted into another domain of the same fold
  uperfamily
  1. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49448] (2)
    1. Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor [49449]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49450] (6)
      2. Human (Homo sapiens) [TaxId: 9606] [69187] (1)
9. Peptidylarginine deiminase Pad4, middle domain [110083] (1)
  uperfamily
  1. Peptidylarginine deiminase Pad4, middle domain [110084] (1)
    1. Peptidylarginine deiminase Pad4, middle domain [110085]
      1. Human (Homo sapiens) [TaxId: 9606] [110086] (7)
        SQ Q9UM07
10. DR1885-like metal-binding protein [110087] (1)
  uperfamily
  1. DR1885-like metal-binding protein [110088] (1)
    Pfam 04314
    1. Hypothetical protein DR1885 [110089]
      1. Deinococcus radiodurans [TaxId: 1299] [110090] (2)
        SQ Q9RT80 35-178
Prealbumin-like [49451] (7)
sandwich; 7 strands in 2 sheets, greek-key
variations: some members have additional 1-2 strands to common fold
1. Starch-binding domain-like [49452] (3)
  uperfamily
  1. Rhamnogalacturonase B, RhgB, middle domain [110091] (1)
    1. Rhamnogalacturonase B, RhgB, middle domain [110092]
      1. Aspergillus aculeatus [TaxId: 5053] [110093] (1)
        SQ Q00019
  2. Starch-binding domain [49453] (8)
    1. Cyclodextrin glycosyltransferase, C-terminal domain [49454]
      this domain is the last one in the protein chain
      1. Bacillus circulans, different strains [TaxId: 1397] [49455] (36)
      2. Bacillus stearothermophilus [TaxId: 1422] [49456] (1)
      3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [49457] (2)
      4. Bacillus sp., strain 1011 [TaxId: 1409] [49458] (8)
        SQ P05618
      5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [49459] (2)
      6. Thermoanaerobacterium [TaxId: 28895] [158931] (2)
    2. Glucoamylase, granular starch-binding domain [49460]
      1. Aspergillus niger [TaxId: 5061] [49461] (4)
    3. beta-amylase [49462]
      1. Bacillus cereus [TaxId: 1396] [49463] (15)
  3. PUD-like [158932] (4)
    Pfam 03714; bacterial pullanase-associated domain
    1. Pullulanase PulA [158933]
      1. Klebsiella pneumoniae [TaxId: 573] [158934] (3)
        SQ P07206 39-169
      2. Streptococcus pneumoniae [TaxId: 1313] [158935] (2)
        SQ Q97SQ7 135-237! SQ Q97SQ7 238-353
      3. Streptococcus pyogenes [TaxId: 1314] [158936] (4)
        SQ Q1JEU6 105-211! SQ Q1JEU6 212-323
      4. Thermotoga maritima [TaxId: 2336] [158937] (5)
        SQ O33840 19-102
2. Carboxypeptidase regulatory domain-like [49464] (2)
  uperfamily
  1. Carboxypeptidase regulatory domain [49465] (2)
    1. Carboxypeptidase D C-terminal domain [49466]
      1. Crested duck (Lophonetta specularioides) [TaxId: 8836] [49467] (2)
    2. Carboxypeptidase M C-terminal domain [101557]
      1. Human (Homo sapiens) [TaxId: 9606] [101558] (1)
  2. Pre-dockerin domain [141082] (1)
    PfamB 085396
    1. Cellulosomal scaffolding protein A [141083]
      1. Clostridium thermocellum [TaxId: 1515] [141084] (1)
        SQ Q06851 1697-1792
3. VHL [49468] (1)
  uperfamily
  1. VHL [49469] (1)
    1. VHL [49470]
      1. Human (Homo sapiens) [TaxId: 9606] [49471] (3)
4. Transthyretin (synonym: prealbumin) [49472] (1)
  uperfamily
  1. Transthyretin (synonym: prealbumin) [49473] (4)
    1. Transthyretin (synonym: prealbumin) [49474]
      sandwich; 8 strands in 2 sheets
      1. Human (Homo sapiens) [TaxId: 9606] [49475] (117)
        SQ P02766 31-143
      2. Rat (Rattus norvegicus) [TaxId: 10116] [49476] (4)
      3. Chicken (Gallus gallus) [TaxId: 9031] [49477] (1)
      4. Gilthead seabream (Sparus aurata) [TaxId: 8175] [101559] (4)
        SQ Q9PTT3
5. Cna protein B-type domain [49478] (1)
  uperfamily
  1. Cna protein B-type domain [49479] (2)
    Pfam 05738
    1. B repeat unit of collagen binding surface protein (cna) [49480]
      duplication: consists of two similar prealbumin-like domains
      1. Staphylococcus aureus [TaxId: 1280] [49481] (2)
    2. Transhydroxylase beta subunit, BthL, C-terminal domain [110094]
      the penultimate strand is in the other beta-sheet than in the Cna repeats
      1. Pelobacter acidigallici [TaxId: 35816] [110095] (6)
        SQ P80564
6. Aromatic compound dioxygenase [49482] (1)
  uperfamily
  1. Aromatic compound dioxygenase [49483] (6)
    sandwich; 9 strands in 2 sheets
    1. Catechol 1,2-dioxygenase [49484]
      contains alpha-helical dimerization subdomain at the N-terminus
      1. Acinetobacter calcoaceticus [TaxId: 471] [49485] (4)
    2. Protocatechuate-3,4-dioxygenase, alpha chain [49486]
      alpha and beta chains are derived from a single-chain protomer and share this fold
      1. Pseudomonas putida [TaxId: 303] [49487] (51)
      2. Acinetobacter calcoaceticus, adp1 [TaxId: 471] [49488] (16)
    3. Protocatechuate-3,4-dioxygenase, beta chain [49489]
      1. Pseudomonas putida [TaxId: 303] [49490] (51)
      2. Acinetobacter calcoaceticus, adp1 [TaxId: 471] [49491] (16)
    4. Chlorocatechol 1,2-dioxygenase [110096]
      similar overall structure to Catechol 1,2-dioxygenase
      1. Rhodococcus opacus [TaxId: 37919] [110097] (1)
        SQ O67987
7. Hypothetical protein PA1324 [117074] (1)
  uperfamily
  1. Hypothetical protein PA1324 [117075] (1)
    1. Hypothetical protein PA1324 [117076]
      1. Pseudomonas aeruginosa [TaxId: 287] [117077] (1)
        SQ Q9I420 21-170
HSP40/DnaJ peptide-binding domain [49492] (1)
sandwich; 6 strands in 2 sheets
1. HSP40/DnaJ peptide-binding domain [49493] (1)
  uperfamily
  1. HSP40/DnaJ peptide-binding domain [49494] (2)
    1. Heat shock protein 40 Sis1 [49495]
      duplication: contains two domains of this fold
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49496] (5)
    2. Mitochondrial protein import protein mas5 (Hsp40, Ydj1), C-terminal domain [101560]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101561] (1)
Penicillin-binding protein associated domain [69188] (1)
sandwich; 6 strands in 2 sheets
1. Penicillin-binding protein associated domain [69189] (2)
  uperfamily
  1. PBP5 C-terminal domain-like [69190] (2)
    1. Penicillin-binding protein 5, C-terminal domain [69191]
      1. Escherichia coli [TaxId: 562] [69192] (8)
    2. D,D-carboxypeptidase DacA, C-terminal domain [117078]
      1. Streptococcus pneumoniae [TaxId: 1313] [117079] (1)
        SQ P72518 25-393
  2. Pencillin binding protein 4 (PbpD), C-terminal domain [110098] (1)
    rudiment form of the PBP-5-like domain
    1. Pencillin binding protein 4 (PbpD), C-terminal domain [110099]
      1. Staphylococcus aureus [TaxId: 1280] [110100] (1)
        SQ Q53613 21-383
alpha-Amylase inhibitor tendamistat [49497] (1)
sandwich; 6 strands in 2 sheets
1. alpha-Amylase inhibitor tendamistat [49498] (1)
  uperfamily
  1. alpha-Amylase inhibitor tendamistat [49499] (1)
    1. alpha-Amylase inhibitor tendamistat [49500]
      1. Streptomyces tendae [TaxId: 1932] [49501] (6)
C-terminal domain of mollusc hemocyanin [81278] (1)
six-stranded beta-sandwich, jelly-roll/greek-key topology
1. C-terminal domain of mollusc hemocyanin [81277] (1)
  analogous to the Ig-like domain of arthropod hemocyanin; similar sequential but different spatial position relative the shared domain
  uperfamily
  1. C-terminal domain of mollusc hemocyanin [81276] (2)
    1. C-terminal domain of mollusc hemocyanin [69165]
      1. Giant octopus (Octopus dofleini) [TaxId: 267067] [69166] (1)
      2. Mollusca (Rapana thomasiana) [TaxId: 29165] [89218] (1)
HPA-like [141085] (1)
sandwich, 6 strands in 2 sheets; jelly-roll (truncated); also includes the pending PCSK9 V domain-like superfamily (the C-terminal domains of 2p4e and 2pmw)
1. Agglutinin HPA-like [141086] (1)
  forms similar trimers to the PCSK9 V domain; strand directions of the subunit beta-sheets are parallel to the three-fold symmetry axis;
  uperfamily
  1. Agglutinin HPA-like [141087] (1)
    1. Agglutinin HPA [141088]
      1. Roman snail (Helix pomatia) [TaxId: 6536] [141089] (2)
        SQ Q2F1K8 21-119! SQ Q2F1K8 21-120
L21p-like [141090] (1)
core: sandwich, 6 strands in 2 sheets
1. L21p-like [141091] (1)
  uperfamily
  1. Ribosomal protein L21p [141092] (3)
    Pfam 00829
    1. Ribosomal protein L21p [141093]
      1. Escherichia coli [TaxId: 562] [141094] (27)
        SQ P0AG48 1-103
      2. Deinococcus radiodurans [TaxId: 1299] [158938] (10)
        SQ Q9RY64 5-98
      3. Thermus thermophilus [TaxId: 274] [158939] (11)
        SQ P60492 1-101
Cupredoxin-like [49502] (2)
sandwich; 7 strands in 2 sheets, greek-key
variations: some members have additional 1-2 strands
1. Cupredoxins [49503] (7)
  contains copper-binding site
  uperfamily
  1. Plastocyanin/azurin-like [49504] (32)
    mono-domain proteins
    1. Amicyanin [49505]
      1. Paracoccus denitrificans [TaxId: 266] [49506] (31)
        SQ P22364
      2. Paracoccus versutus (Thiobacillus versutus) [TaxId: 34007] [63685] (1)
    2. Plastocyanin [49507]
      1. Poplar (Populus nigra), variant italica [TaxId: 3691] [49508] (10)
      2. French bean (Phaseolus vulgaris) [TaxId: 3885] [49509] (1)
      3. Parsley (Petroselinum crispum) [TaxId: 4043] [49510] (2)
      4. Spinach (Spinacia oleracea) [TaxId: 3562] [49511] (2)
      5. White campion (Silene pratensis) [TaxId: 52853] [49512] (2)
      6. Ulva pertusa, a sea lettuce [TaxId: 3120] [49513] (1)
      7. Green alga (Chlamydomonas reinhardtii) [TaxId: 3055] [49514] (1)
      8. Green alga (Enteromorpha prolifera) [TaxId: 3117] [49515] (1)
      9. Fern (Adiantum capillus-veneris) [TaxId: 13818] [49516] (2)
      10. Anabaena variabilis [TaxId: 1172] [49517] (7)
      11. Cyanobacterium (Phormidium laminosum) [TaxId: 32059] [49518] (4)
      12. Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId: 1143] [49519] (6)
      13. Cyanobacterium (Synechocystis sp.), pcc 7942 [TaxId: 1143] [49520] (2)
      14. Photosynthetic prokaryote (Prochlorothrix hollandica) [TaxId: 1223] [49521] (3)
    3. Pseudoazurin [49522]
      1. Alcaligenes faecalis, strain s-6 [TaxId: 511] [49523] (12)
        SQ P04377
      2. Methylobacterium extorquens, strain am1 [TaxId: 408] [49524] (1)
      3. Achromobacter cycloclastes [TaxId: 223] [49525] (4)
      4. Thiosphaera pantotropha [TaxId: 82367] [49526] (1)
    4. Plantacyanin [49527]
      basic blue protein
      1. Cucumber (Cucumis sativus) [TaxId: 3659] [49528] (1)
      2. Spinach (Spinacia oleracea) [TaxId: 3562] [49529] (1)
    5. Azurin [49530]
      1. Alcaligenes denitrificans [TaxId: 32002] [49531] (8)
      2. Alcaligenes xylosoxidans, NCIMB (11015), different isoforms [TaxId: 85698] [49532] (4)
      3. Pseudomonas aeruginosa [TaxId: 287] [49533] (36)
        SQ P00282
      4. Pseudomonas fluorescens [TaxId: 294] [49534] (1)
      5. Pseudomonas putida [TaxId: 303] [49535] (2)
      6. Methylomonas sp. j [TaxId: 32038] [49536] (2)
    6. Auracyanin [63686]
      azurin-related protein
      1. Chloroflexus aurantiacus [TaxId: 1108] [63687] (2)
    7. Rusticyanin [49537]
      1. Thiobacillus ferrooxidans [TaxId: 920] [49538] (7)
    8. Stellacyanin [49539]
      1. Cucumber (Cucumis sativus) [TaxId: 3659] [49540] (1)
    9. Mavicyanin [117080]
      Plantacyanin and stellacyanin homologue
      1. Zucchini (Cucurbita pepo) [TaxId: 3663] [117081] (2)
        SQ P80728
  2. Nitrosocyanin [63392] (3)
    1. Red copper protein nitrosocyanin [63688]
      1. Nitrosomonas europaea [TaxId: 915] [63689] (3)
    2. Nitrous oxide reductase, C-terminal domain [49548]
      1. Pseudomonas nautica [TaxId: 2743] [49549] (1)
      2. Paracoccus denitrificans [TaxId: 266] [63690] (1)
  3. Periplasmic domain of cytochrome c oxidase subunit II [49541] (5)
    1. Quinol oxidase (CyoA) [49542]
      1. Escherichia coli [TaxId: 562] [49543] (3)
    2. Cytochrome c oxidase [49544]
      1. Cow (Bos taurus) [TaxId: 9913] [49545] (21)
      2. Paracoccus denitrificans [TaxId: 266] [49546] (3)
      3. Rhodobacter sphaeroides [TaxId: 1063] [74870] (6)
      4. Thermus thermophilus, ba3 type [TaxId: 274] [49547] (7)
  4. Multidomain cupredoxins [49550] (15)
    1. Nitrite reductase, NIR [49551]
      consists of two domains of this fold
      1. Achromobacter cycloclastes [TaxId: 223] [49552] (10)
      2. Alcaligenes faecalis, strain s-6 [TaxId: 511] [49553] (83)
        SQ P38501
      3. Alcaligenes xylosoxidans [TaxId: 85698] [49554] (78)
        SQ O68601 25-360 ! SQ O68601 26-359 ! SQ O68601
      4. Neisseria gonorrhoeae, AniA [TaxId: 485] [69193] (2)
      5. Rhodobacter sphaeroides [TaxId: 1063] [110101] (13)
        SQ Q53239
    2. multi-copper oxidase CueO [69194]
      1. Escherichia coli [TaxId: 562] [69195] (15)
    3. Spore coat protein A, CotA [89219]
      1. Bacillus subtilis [TaxId: 1423] [89220] (22)
        SQ P07788
    4. Ascorbate oxidase [49555]
      consists of three domains of this fold
      1. Zucchini (Cucurbita pepo var. medullosa) [TaxId: 3663] [49556] (4)
    5. Laccase [49557]
      consists of three domains of this fold
      1. Inky cap fungus (Coprinus cinereus) [TaxId: 5346] [49558] (2)
      2. Trametes versicolor, laccase 1 [TaxId: 5325] [74871] (1)
      3. Trametes versicolor, laccase 2 [TaxId: 5325] [74872] (1)
      4. Melanocarpus albomyces [TaxId: 204285] [74873] (19)
      5. Rigidoporus lignosus [TaxId: 219653] [110102] (1)
        SQ Q6H9H7 22-515
    6. Ceruloplasmin [49559]
      consists of 6 domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [49560] (6)
    7. Coagulation factor V [110103]
      1. Cow (Bos taurus) [TaxId: 9913] [110104] (1)
        SQ Q28107 29-324, 1566-2210
  5. Ephrin ectodomain [74874] (2)
    eukaryotic signaling domain probably related to cupredoxins but lacking the metal-binding site
    1. Ephrin-b2 ectodomain [74875]
      1. Mouse (Mus musculus) [TaxId: 10090] [74876] (3)
    2. Ephrin-a5 [110105]
      1. Mouse (Mus musculus) [TaxId: 10090] [110106] (3)
        SQ O08543
  6. Peptidylarginine deiminase Pad4, N-terminal domain [110107] (1)
    probably related to cupredoxins but lacking the metal-binding site
    1. Peptidylarginine deiminase Pad4, N-terminal domain [110108]
      1. Human (Homo sapiens) [TaxId: 9606] [110109] (7)
        SQ Q9UM07
  7. SO1698-like [141095] (1)
    probably related to cupredoxins but lacking the metal-binding site
    1. Hypothetical protein SO1698 [141096]
      1. Shewanella oneidensis [TaxId: 70863] [141097] (1)
        SQ Q8EGA7 6-116,117-124
2. Major surface antigen p30, SAG1 [74877] (1)
  SS-crosslinked beta-sandwich of distinct geometry but topologically similar to cupredoxins
  uperfamily
  1. Major surface antigen p30, SAG1 [74878] (1)
    1. Major surface antigen p30, SAG1 [74879]
      duplication: tandem repeat of two homologous domains
      1. Toxoplasma gondii [TaxId: 5811] [74880] (5)
Ctag/Cox11 [110110] (1)
sandwich; 7 strands in 2 sheets, greek-key; permutation of the immunoglobulin-like fold
1. Ctag/Cox11 [110111] (1)
  uperfamily
  1. Ctag/Cox11 [110112] (1)
    Pfam 04442
    1. Cytochrome C oxidase assembly protein CtaG [110113]
      1. Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382] [110114] (2)
        SQ Q92RG6
Atu1913-like [141098] (1)
sandwich; 7 strands in two sheets, greek-key/jelly-roll; forms segment swapped dimers, swapping is probably facilitated by the helix insertion after strand 3
1. Atu1913-like [141099] (1)
  uperfamily
  1. Atu1913-like [141100] (1)
    1. Hypothetical protein Atu1913 [141101]
      1. Agrobacterium tumefaciens [TaxId: 358] [141102] (1)
        SQ Q8UE48 4-104
C2 domain-like [49561] (5)
sandwich; 8 strands in 2 sheets; greek-key
1. C2 domain (Calcium/lipid-binding domain, CaLB) [49562] (2)
  two constituent families are related by circular permutation
  uperfamily
  1. PLC-like (P variant) [49563] (12)
    1. PI-specific phospholipase C isozyme D1 (PLC-D1), C-terminal domain [49564]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49565] (10)
    2. Domain from cytosolic phospholipase A2 [49566]
      1. Human (Homo sapiens) [TaxId: 9606] [49567] (3)
    3. Pten tumor suppressor (Phoshphoinositide phosphatase), C-terminal domain [49568]
      1. Human (Homo sapiens) [TaxId: 9606] [49569] (1)
    4. Phoshoinositide 3-kinase (PI3K) [49570]
      1. Pig (Sus scrofa) [TaxId: 9823] [49571] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [49572] (3)
    5. Domain from protein kinase C delta [49573]
      rudiment form lacking calcium-binding site
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49574] (1)
    6. Domain from protein kinase C epsilon [69196]
      Calcium-independent
      1. Rat (Rattus rattus) [TaxId: 10117] [69197] (1)
    7. E3 ubiquitin-protein ligase Itchy [141103]
      1. Human (Homo sapiens) [TaxId: 9606] [141104] (1)
        SQ Q96J02 13-145
    8. Unc-13 homolog A [141105]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141106] (6)
        SQ Q62768 1-128! SQ Q62768 2-150
    9. Multiple C2 and transmembrane domain-containing protein 2, MCTP2 [158940]
      1. Human (Homo sapiens) [TaxId: 9606] [158941] (1)
        SQ Q6DN12 504-629
    10. Fantom [158942]
      RPGR-interacting protein 1-like protein
      1. Human (Homo sapiens) [TaxId: 9606] [158943] (1)
        SQ Q68CZ1 596-737
    11. Phospholipase C-beta-2 [158944]
      1. Human (Homo sapiens) [TaxId: 9606] [158945] (2)
        SQ Q00722 678-799
  2. Synaptotagmin-like (S variant) [49575] (12)
    topologically similar to the C-terminal domain of PapD
    1. Synaptogamin I [49576]
      duplication: contains tandem repeat of two similar domains
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49577] (7)
        SQ P21707 271-419 ! SQ P21707 271-419
      2. Homo sapiens [TaxId: 9606] [158946] (2)
    2. Synaptotagmin III [109606]
      duplication: contains 2 C2 domains
      1. Rat (Rattus norvegicus) [TaxId: 10116] [109607] (1)
        SQ P40748 293-588
    3. Synaptotagmin IV [101562]
      duplication: contains 2 C2 domains
      1. Human (Homo sapiens) [TaxId: 9606] [101563] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [110115] (2)
        SQ P50232 288-425
    4. Regulating synaptic membrane exocytosis protein, rim2 [101564]
      1. Human (Homo sapiens) [TaxId: 9606] [101565] (2)
    5. Piccolo [101566]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [101567] (1)
    6. C2 domain from protein kinase c (alpha) [49578]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49579] (1)
    7. C2 domain from protein kinase c (beta) [49580]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49581] (1)
    8. C2b-domain of rabphilin [49582]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49583] (4)
    9. C2 domain protein At1g63220 [117082]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117083] (1)
        SQ Q9C8S6 2-125
    10. Synaptotagmin XIII [117084]
      1. Human (Homo sapiens) [TaxId: 9606] [117085] (1)
        SQ Q7L8C5 155-280
2. Periplasmic chaperone C-domain [49584] (1)
  uperfamily
  1. Periplasmic chaperone C-domain [49585] (5)
    1. PapD [49586]
      1. Escherichia coli [TaxId: 562] [49587] (12)
    2. FimC [49588]
      1. Escherichia coli [TaxId: 562] [49589] (6)
    3. SfaE [74881]
      1. Escherichia coli [TaxId: 562] [74882] (1)
    4. Caf1m [89221]
      chaperone of F1 capsule antigen Caf1
      1. Yersinia pestis [TaxId: 632] [89222] (9)
    5. Periplasmic chaperone SafB [158947]
      1. Salmonella typhimurium [TaxId: 90371] [158948] (2)
        SQ Q8ZRK3 152-236
3. PHL pollen allergen [49590] (1)
  uperfamily
  1. PHL pollen allergen [49591] (2)
    1. PHL P 2 [49592]
      1. Timothy grass (Phleum pratense) [TaxId: 15957] [49593] (3)
    2. PHL P 1 C-terminal domain [82001]
      1. Timothy grass (Phleum pratense) [TaxId: 15957] [82002] (1)
4. Rab geranylgeranyltransferase alpha-subunit, insert domain [49594] (1)
  uperfamily
  1. Rab geranylgeranyltransferase alpha-subunit, insert domain [49595] (1)
    1. Rab geranylgeranyltransferase alpha-subunit, insert domain [49596]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49597] (2)
5. Smr-associated domain-like [158949] (1)
  1. Smr-associated domain [158950] (1)
    Pfam 09640; DUF2027
    1. Putative DNA mismatch repair protein BT2179 [158951]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [158952] (1)
        SQ Q8A5Q9 81-227
TRAF domain-like [49598] (1)
sandwich; 8 strands in 2 sheets; greek-key
1. TRAF domain-like [49599] (2)
  has a circularly permuted immunoglobulin-fold topology with extra strand
  uperfamily
  1. MATH domain [49600] (4)
    1. TNF receptor associated factor 2 (TRAF2) [49601]
      1. Human (Homo sapiens) [TaxId: 9606] [49602] (10)
    2. TNF receptor associated factor 3 (TRAF3) [49603]
      1. Human (Homo sapiens) [TaxId: 9606] [49604] (5)
        SQ Q13114 377-568
    3. TNF receptor associated factor 6 (TRAF6) [74883]
      1. Human (Homo sapiens) [TaxId: 9606] [74884] (3)
    4. Speckle-type poz protein SPOP [141107]
      1. Human (Homo sapiens) [TaxId: 9606] [141108] (1)
        SQ O43791 28-173
  2. SIAH, seven in absentia homolog [69198] (1)
    1. SIAH, seven in absentia homolog [69199]
      1. Mouse (Mus musculus) [TaxId: 10090] [69200] (5)
Neurophysin II [49605] (1)
sandwich; 8 strands in 2 sheets; meander
1. Neurophysin II [49606] (1)
  duplication: composed of two structural repeats
  uperfamily
  1. Neurophysin II [49607] (1)
    1. Neurophysin II [49608]
      can be classified as disulfide-rich
      1. Cow (Bos taurus) [TaxId: 9913] [49609] (6)
N-utilization substance G protein NusG, insert domain [82003] (1)
sandwich; 8 strands in 2 sheets; meander
1. N-utilization substance G protein NusG, insert domain [82004] (1)
  uperfamily
  1. N-utilization substance G protein NusG, insert domain [82005] (1)
    1. N-utilization substance G protein NusG, insert domain [82006]
      found only in some NusG species
      1. Aquifex aeolicus [TaxId: 63363] [82007] (4)
        interrupted by an insert beta-sandwich domain
Nucleoplasmin-like/VP (viral coat and capsid proteins) [88632] (7)
sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands
characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
1. Nucleoplasmin-like core domain [69203] (1)
  oligomerizes into a pentameric ring structure
  uperfamily
  1. Nucleoplasmin-like core domain [69204] (3)
    1. Nucleoplasmin core [69205]
      1. Xenopus laevis [TaxId: 8355] [69206] (1)
    2. Chromatin decondensation protein 1 (Crp1, Nlp) [89223]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [89224] (1)
    3. Nucleophosmin (NO38) [117086]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [117087] (2)
        SQ P07222 16-122
2. Positive stranded ssRNA viruses [88633] (9)
  uperfamily
  1. Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [88634] (18)
    the order of the chains N-VP0-VP3-VP1-C is as in the polyprotein; VP0 is cleaved later upon capsid assembly to VP4 and VP2
    there is a different order in the shuffled genome of insect picorna-like proteins (Cricket paralysis virus)
    1. Human enterovirus B coat proteins [88635]
      1. Human coxsackievirus B3 [TaxId: 12072] [49681] (1)
      2. Human coxsackievirus A9 [TaxId: 12067] [49683] (1)
      3. Human echovirus 1 [TaxId: 46633] [49685] (1)
      4. Human echovirus 11 [TaxId: 12078] [74890] (4)
    2. Bovine enterovirus coat proteins [49676]
      1. Bovine enterovirus, VG-5-27 [TaxId: 12064] [49677] (1)
    3. Poliovirus coat proteins [49666]
      1. Poliovirus type 1, strain Mahoney [TaxId: 12080] [49667] (12)
      2. Poliovirus type 2, strain Lansing [TaxId: 12083] [49668] (1)
      3. Poliovirus type 3, strain Sabin [TaxId: 12086] [49669] (7)
    4. Rhinovirus coat proteins [49670]
      1. Human rhinovirus B 14 (HRV-14) [TaxId: 12131] [49671] (30)
      2. Human rhinovirus 16, (HRV-16) [TaxId: 31708] [49672] (9)
      3. Human rhinovirus A 1A (HRV-1A) [TaxId: 12134] [49673] (4)
      4. Human rhinovirus A 2 (HRV-2) [TaxId: 12130] [49674] (2)
      5. Human rhinovirus 3, (HRV-3) [TaxId: 44130] [49675] (1)
    5. Aphthovirus (Foot-and-mouth disease virus) coat proteins [49659]
      1. FMDV (Foot-and-mouth disease virus), strain bfs, 1860 [TaxId: 12110] [49660] (4)
    6. Theilovirus capsid proteins [49686]
      1. Theiler's murine encephalomyelitis virus, strain da [TaxId: 12124] [49687] (2)
    7. Mengo encephalomyocarditis virus coat proteins [49678]
      1. Mengovirus [TaxId: 12107] [49679] (2)
    8. Swine vesicular disease virus coat proteins [89225]
      1. Swine vesicular disease virus [TaxId: 12075] [89226] (2)
    9. Insect picorna-like virus coat proteins [49654]
      different genetic order of VP segments due to extensive genome shuffling
      1. Cricket paralysis virus [TaxId: 12136] [49655] (1)
  2. Comoviridae-like VP [88636] (3)
    duplication: mature coat protein consists of three similar domains that can be in a single chain or in two separate chains
    1. Nepovirus capsid protein [49629]
      duplication: cnosists of three very similar domains
      1. TRSV (Tobacco ringspot virus) [TaxId: 12282] [49630] (1)
    2. Comovirus coat proteins (VP37 and VP23) [49627]
      chain 1 is one-domain VP23; chain 2 is two-domain VP37
      1. CPMV (Cowpea mosaic virus) [TaxId: 12264] [89227] (4)
      2. BPMV (Bean pod mottle virus) [TaxId: 12260] [49628] (3)
  3. Caliciviridae-like VP [88637] (1)
    1. Calicivirus capsid protein [63691]
      includes the P (protruding) domain of complex beta-structure containing a beta-barrel similar to the second domain of EF-TU
      1. Norwalk virus [TaxId: 11983] [63692] (1)
  4. Nodaviridae-like VP [88638] (3)
    1. Alphanodavirus capsid protein [49648]
      1. Black beetle virus [TaxId: 12285] [49649] (1)
      2. Nodamura virus [TaxId: 12288] [49650] (1)
      3. Pariacoto virus [TaxId: 103782] [49651] (1)
  5. Tetraviridae-like VP [101568] (1)
    1. Tetraomegavirus capsid protein [101569]
      contains an insert beta-sandwich domain
      1. Nudaurelia capensis omega virus [TaxId: 12541] [101570] (1)
  6. Bromoviridae-like VP [88639] (4)
    1. Cucumovirus coat protein [88640]
      1. CMV (Cucumber mosaic virus), strain fny [TaxId: 12305] [49646] (1)
      2. TAV (Tomato aspermy virus) [TaxId: 12315] [82012] (1)
      3. BMV (Brome mosaic virus) [TaxId: 12302] [74886] (31)
      4. Cowpea chlorotic mottle virus [TaxId: 12303] [49636] (1)
  7. Tymoviridae-like VP [88641] (3)
    1. Tymovirus coat protein [88642]
      1. PHMV (Physalis mottle virus) [TaxId: 72539] [49642] (2)
      2. DYMV (Desmodium yellow mottle tymovirus) [TaxId: 70821] [49644] (1)
      3. TYMV (Turnip yellow mosaic virus) [TaxId: 12154] [49640] (2)
        SQ P03608
  8. Tombusviridae-like VP [88643] (7)
    1. Necrovirus coat protein [49637]
      1. TNV (Tobacco necrosis virus) [TaxId: 12054] [49638] (1)
    2. Tombusvirus coat protein [49633]
      1. TBSV (Tomato bushy stunt virus) [TaxId: 12145] [49634] (1)
    3. Carmovirus coat protein [89228]
      1. CarMV (Carnation mottle virus) [TaxId: 11986] [89229] (1)
    4. Sobemovirus coat protein [88644]
      1. SMV (Sesbania mosaic virus) [TaxId: 12558] [49624] (7)
        SQ Q9EB06
      2. SBMV (Southern bean mosaic virus), cow pea strain [TaxId: 12139] [49632] (1)
      3. RYMV (Rice yellow mottle virus) [TaxId: 31744] [49626] (1)
      4. Cocksfoot mottle virus [TaxId: 40979] [82010] (1)
  9. Birnaviridae-like VP [141109] (1)
    dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses; includes Pfam 01766; Birnavirus VP2 protein
    1. Birnavirus VP2 [141110]
      Link between +sRNA and dsRNA viruses two domains - the first similar to scop_sf 88633 and the second, insert domain is similar to scop_sf 49818. dsRNA virus but unlike the other dsRNA viruses has a genomic arrangement and genomic replication strategy similar to +sRNA viruses
      1. Infectious bursal disease virus [TaxId: 10995] [141111] (41)
        SQ P15480 11-431! SQ P61825 8-440! SQ Q6S9I7 11-429
3. ssDNA viruses [88645] (3)
  uperfamily
  1. Microviridae-like VP [49612] (3)
    1. Microvirus capsid proteins [49613]
      include capsid protein F and spike protein G
      1. Bacteriophage phi-X174 [TaxId: 10847] [49614] (4)
      2. Bacteriophage G4 [TaxId: 10843] [49615] (1)
      3. Bacteriophage alpha3 [TaxId: 10849] [82008] (2)
  2. Parvoviridae-like VP [88646] (7)
    1. Parvovirus (panleukopenia virus) capsid protein [49661]
      1. Feline panleukopenia virus, strain b [TaxId: 10786] [49689] (1)
      2. Canine parvovirus [TaxId: 10788] [49662] (7)
      3. Feline parvovirus [TaxId: 10785] [49663] (3)
      4. Porcine parvovirus [TaxId: 10796] [69201] (1)
      5. Murine minute virus, strain i [TaxId: 10794] [49665] (2)
      6. Human parvovirus B19 [TaxId: 10798] [110116] (1)
        SQ Q9JGS0 246-781
    2. Dependovirus capsid protein [74887]
      1. Adeno-associated virus, aav-2 [TaxId: 272636] [74888] (1)
        a vector for human genome therapy
  3. Densovirinae-like VP [88647] (1)
    1. Densovirus capsid protein [49652]
      1. Galleria mellonella densovirus [TaxId: 37138] [49653] (1)
4. Group I dsDNA viruses [88648] (1)
  uperfamily
  1. Papovaviridae-like VP [88649] (3)
    1. Polyomavirus coat proteins [49657]
      1. Murine polyomavirus, strain small-plaque 16 [TaxId: 10634] [49658] (5)
      2. Simian virus 40, Sv40 [TaxId: 10633] [49691] (1)
    2. Papillomavirus L1 protein [49692]
      1. Human papillomavirus type 16 [TaxId: 333760] [49693] (1)
5. Group II dsDNA viruses VP [49749] (3)
  duplication: consists of two domains of this fold packed together like the nucleoplasmin subunits
  trimeric; in the trimers, the domains are arranged around pseudo six-fold axis
  uperfamily
  1. Coat protein p3 [49750] (1)
    1. Coat protein p3 [63403]
      1. Bacteriophage prd1 [TaxId: 10658] [49752] (3)
  2. Major capsid protein vp54 [82013] (1)
    1. Major capsid protein vp54 [82014]
      1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82015] (2)
        a large, lipid-containing, DNA virus
  3. Adenovirus hexon [49753] (2)
    each domain is heavily decorated with many insertions
    1. Adenovirus hexon [63404]
      1. Human adenovirus type 2 [TaxId: 10515] [49755] (1)
      2. Human adenovirus type 5 [TaxId: 28285] [49756] (25)
6. Satellite viruses [88650] (1)
  uperfamily
  1. Satellite viruses [88651] (3)
    1. SPMV coat protein [49617]
      1. Satellite panicum mosaic virus [TaxId: 154834] [49618] (1)
    2. STMV coat protein [49619]
      1. Satellite tobacco mosaic virus [TaxId: 12881] [49620] (1)
    3. STNV coat protein [49621]
      1. Satellite tobacco necrosis virus [TaxId: 12881] [49622] (1)
7. PHM/PNGase F [49742] (2)
  members of this superfamily bind peptide substrates
  duplication: consists of two domains of this fold packed together like the adjacent nucleoplasmin subunits
  uperfamily
  1. Glycosyl-asparaginase [49743] (1)
    1. Peptide:N-glycosidase F, PNGase F [49744]
      1. Flavobacterium meningosepticum [TaxId: 238] [49745] (3)
  2. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [49746] (1)
    1. Peptidylglycine alpha-hydroxylating monooxygenase, PHM [63402]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49748] (12)
gamma-Crystallin-like [49694] (1)
sandwich; 8 strands in 2 sheets; greek-key
duplication: has internal pseudo twofold symmetry
1. gamma-Crystallin-like [49695] (6)
  uperfamily
  1. Crystallins/Ca-binding development proteins [49696] (13)
    1. gamma-Crystallin [49697]
      duplication consists of two domains of this fold
      1. Cow (Bos taurus), isoform II (B) [TaxId: 9913] [49698] (6)
      2. Cow (Bos taurus), isoform IIIb (D) [TaxId: 9913] [49699] (1)
      3. Human (Homo sapiens), isoform D [TaxId: 9606] [89230] (6)
      4. Cow (Bos taurus), isoform S [TaxId: 9913] [49700] (1)
      5. Human (Homo sapiens) [TaxId: 9606] [69202] (1)
      6. Cow (Bos taurus), isoform F [TaxId: 9913] [49701] (1)
      7. Cow (Bos taurus), isoform E [TaxId: 9913] [101571] (1)
    2. beta-Crystallin [49702]
      duplication consists of two domains of this fold
      1. Cow (Bos taurus) [TaxId: 9913] [49703] (4)
      2. Rat (Rattus norvegicus), isoform E [TaxId: 10116] [49704] (10)
      3. Mouse (Mus musculus) [TaxId: 10090] [49705] (1)
      4. Human (Homo sapiens) [TaxId: 9606] [101572] (1)
    3. Protein S [49706]
      duplication consists of two domains of this fold
      1. Myxococcus xanthus [TaxId: 34] [49707] (3)
    4. Spherulin 3a (S3a) [49708]
      1. Physarum polycephalum [TaxId: 5791] [49709] (2)
  2. Yeast killer toxin [49710] (1)
    1. Yeast killer toxin [49711]
      1. Williopsis mrakii [TaxId: 4963] [49712] (1)
  3. Streptomyces metalloproteinase inhibitor, SMPI [49713] (1)
    1. Streptomyces metalloproteinase inhibitor, SMPI [49714]
      1. Streptomyces nigrescens [TaxId: 1920] [49715] (1)
  4. Killer toxin-like protein SKLP [49716] (1)
    1. Killer toxin-like protein SKLP [49717]
      1. Streptomyces sp. [TaxId: 1931] [49718] (1)
  5. Antifungal protein AFP1 [63693] (1)
    shares putative chitin-binding site with SKLP
    1. Antifungal protein AFP1 [63694]
      1. Streptomyces tendae, tu901 [TaxId: 1932] [63695] (2)
  6. Plant antimicrobial protein MIAMP1 [49719] (1)
    1. Plant antimicrobial protein MIAMP1 [49720]
      1. Macadamia nut (Macadamia integrifolia) [TaxId: 60698] [49721] (1)
Lipase/lipooxygenase domain (PLAT/LH2 domain) [49722] (1)
sandwich; 8 strands in 2 sheets; complex topology
duplication: has weak internal pseudo twofold symmetry
1. Lipase/lipooxygenase domain (PLAT/LH2 domain) [49723] (3)
  uperfamily
  1. Lipoxigenase N-terminal domain [49724] (3)
    1. Plant lipoxigenase [49725]
      1. Soybean (Glycine max), isozyme L1 [TaxId: 3847] [49726] (14)
      2. Soybean (Glycine max), isozyme L3 [TaxId: 3847] [49727] (9)
        SQ P09186
    2. 15-Lipoxygenase [49728]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [49729] (3)
  2. Colipase-binding domain [49730] (6)
    1. Pancreatic lipase, C-terminal domain [49731]
      1. Horse (Equus caballus) [TaxId: 9796] [49732] (1)
      2. Pig (Sus scrofa) [TaxId: 9823] [49733] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [49734] (3)
      4. Guinea pig (Cavia porcellus) [TaxId: 10141] [49735] (1)
      5. Dog (Canis familiaris) [TaxId: 9615] [49736] (1)
        pancreatic lipase related protein 1
      6. Rat (Rattus norvegicus) [TaxId: 10116] [49737] (1)
        pancreatic lipase related protein 2
  3. Alpha-toxin, C-terminal domain [49738] (2)
    1. Alpha-toxin, C-terminal domain [49739]
      1. Clostridium perfringens, different strains [TaxId: 1502] [49740] (5)
      2. Clostridium absonum [TaxId: 29369] [101573] (1)
Calpain large subunit, middle domain (domain III) [49757] (1)
sandwich; 8 strands in 2 sheets; jelly-roll
1. Calpain large subunit, middle domain (domain III) [49758] (1)
  uperfamily
  1. Calpain large subunit, middle domain (domain III) [49759] (3)
    1. Calpain large subunit, middle domain (domain III) [49760]
      1. Human (Homo sapiens), M-type [TaxId: 9606] [49761] (2)
      2. Rat (Rattus norvegicus), M-type [TaxId: 10116] [49762] (2)
      3. Rat (Rattus norvegicus), mu-type [TaxId: 10116] [101574] (1)
Supernatant protein factor (SPF), C-terminal domain [101575] (1)
sandwich; 8 strands in 2 sheets; jelly-roll; similarity to the Nucleoplasmin-like/VP fold
1. Supernatant protein factor (SPF), C-terminal domain [101576] (1)
  uperfamily
  1. Supernatant protein factor (SPF), C-terminal domain [101577] (1)
    1. Supernatant protein factor (SPF), C-terminal domain [101578]
      1. Human (Homo sapiens) [TaxId: 9606] [101579] (2)
        SQ O76054
Hypothetical protein TM1070 [89231] (1)
sandwich; 8 strands in 2 sheets; jelly-roll
1. Hypothetical protein TM1070 [89232] (1)
  uperfamily
  1. Hypothetical protein TM1070 [89233] (1)
    1. Hypothetical protein TM1070 [89234]
      1. Thermotoga maritima [TaxId: 2336] [89235] (1)
Olfactory marker protein [63696] (1)
sandwich; 8 strands in 2 sheets; jelly-roll
1. Olfactory marker protein [63697] (1)
  uperfamily
  1. Olfactory marker protein [63698] (2)
    1. Olfactory marker protein [63699]
      1. Mouse (Mus musculus) [TaxId: 10090] [63700] (3)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [69207] (2)
HSP20-like chaperones [49763] (1)
sandwich; 8 strands in 2 sheets; greek-key
1. HSP20-like chaperones [49764] (4)
  uperfamily
  1. HSP20 [49765] (2)
    1. Small heat shock protein [49766]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [49767] (1)
      2. Wheat (Triticum aestivum) [TaxId: 4565] [69208] (49)
  2. Co-chaperone p23-like [49768] (2)
    1. Co-chaperone p23 [49769]
      1. Human (Homo sapiens) [TaxId: 9606] [49770] (1)
    2. Hypothetical protein At3g03773 [117088]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117089] (1)
        SQ Q6ID70
  3. GS domain [101580] (2)
    Pfam 04969
    1. Suppressor of G2 allele of skp1 homolog, gst1 [101581]
      1. Human (Homo sapiens) [TaxId: 9606] [101582] (1)
    2. Ubiquitin carboxyl-terminal hydrolase 19, USP19 [117090]
      1. Human (Homo sapiens) [TaxId: 9606] [117091] (1)
        SQ O94966 326-446
  4. Nuclear movement domain [117092] (2)
    Pfam 03593
    1. Nuclear migration protein nudC [117093]
      1. Mouse (Mus musculus) [TaxId: 10090] [117094] (1)
        SQ O35685 171-288
    2. NudC domain containing protein 3, NUDCD3 (KIAA1068) [117095]
      1. Human (Homo sapiens) [TaxId: 9606] [117096] (1)
        SQ Q8IVD9 176-286
Heat shock protein 70kD (HSP70), peptide-binding domain [100919] (1)
beta-sandwich: 8 strands in 2 sheets
1. Heat shock protein 70kD (HSP70), peptide-binding domain [100920] (1)
  uperfamily
  1. Heat shock protein 70kD (HSP70), peptide-binding domain [100921] (4)
    1. DnaK [100922]
      1. Escherichia coli [TaxId: 562] [100923] (7)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [56782] (3)
      3. Cow (Bos taurus) [TaxId: 9913] [158953] (1)
    2. Chaperone protein hscA (Hsc66) [117097]
      1. Escherichia coli [TaxId: 562] [117098] (1)
        SQ P0A6Z1 390-615
Ecotin, trypsin inhibitor [49771] (1)
sandwich; 8 strands in 2 sheets; complex topology with the crossing loops
1. Ecotin, trypsin inhibitor [49772] (1)
  uperfamily
  1. Ecotin, trypsin inhibitor [49773] (1)
    1. Ecotin, trypsin inhibitor [49774]
      1. Escherichia coli [TaxId: 562] [49775] (17)
        SQ P23827 23-162
PEBP-like [49776] (1)
sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
1. PEBP-like [49777] (2)
  uperfamily
  1. Phosphatidylethanolamine binding protein [49778] (5)
    1. Phosphatidylethanolamine binding protein, PEBP [49779]
      1. Human (Homo sapiens) [TaxId: 9606] [49780] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [49781] (2)
      3. Mouse (Mus musculus), PEBP-2 [TaxId: 10090] [74891] (1)
    2. Centroradialis protein Cen [49782]
      1. Garden snapdragon (Antirrhinum majus) [TaxId: 4151] [49783] (1)
    3. Carboxypeptidase Y inhibitor [158954]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [158955] (1)
        SQ P14306 1-219
  2. Prokaryotic PEBP-like proteins [63701] (2)
    1. Hypothetical protein YbhB [63702]
      1. Escherichia coli [TaxId: 562] [63703] (2)
    2. Hypothetical protein YbcL [63704]
      1. Escherichia coli [TaxId: 562] [63705] (1)
Ganglioside M2 (gm2) activator [63706] (1)
sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
1. Ganglioside M2 (gm2) activator [63707] (1)
  uperfamily
  1. Ganglioside M2 (gm2) activator [63708] (1)
    1. Ganglioside M2 (gm2) activator [63709]
      1. Human (Homo sapiens) [TaxId: 9606] [63710] (10)
        SQ P17900 31-193
Nicotinic receptor ligand binding domain-like [63711] (1)
sandwich; 8 strands in 2 sheets; greek-key: partial topological similarity to immunoglobulin-like folds
1. Nicotinic receptor ligand binding domain-like [63712] (1)
  uperfamily
  1. Nicotinic receptor ligand binding domain-like [63713] (1)
    1. Acetylcholine binding protein (ACHBP) [63714]
      1. Great pond snail (Lymnaea stagnalis) [TaxId: 6523] [63715] (9)
Beta-galactosidase LacA, domain 3 [117099] (1)
sandwich; 8 strands in 2 sheets
1. Beta-galactosidase LacA, domain 3 [117100] (1)
  uperfamily
  1. Beta-galactosidase LacA, domain 3 [117101] (1)
    1. Beta-galactosidase LacA, domain 3 [117102]
      1. Penicillium sp. [TaxId: 5081] [117103] (2)
        SQ Q700S9 41-1011
Galactose-binding domain-like [49784] (1)
sandwich; 9 strands in 2 sheets; jelly-roll
1. Galactose-binding domain-like [49785] (32)
  uperfamily
  1. Galactose-binding domain [49786] (4)
    1. Galactose oxidase, N-terminal domain [49787]
      1. Dactylium dendroides [TaxId: 5132] [49788] (4)
        SQ Q01745 42-680
      2. Fungi (Fusarium sp.) [TaxId: 29916] [69209] (5)
        sequence identical to that of Dactylium dendroides
      3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [158956] (3)
    2. Sialidase, C-terminal domain [49789]
      1. Micromonospora viridifaciens [TaxId: 1881] [49790] (8)
        SQ Q02834 47-647
  2. Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) [49791] (4)
    1. C2 domain of factor V [49792]
      1. Human (Homo sapiens) [TaxId: 9606] [49793] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [110117] (1)
        SQ Q28107 29-324,1566-2210
    2. C2 domain of factor VIII [49794]
      1. Human (Homo sapiens) [TaxId: 9606] [49795] (4)
    3. B1 domain of neuropilin-1 [82016]
      1. Human (Homo sapiens) [TaxId: 9606] [82017] (4)
  3. APC10-like [69210] (3)
    Pfam 03256
    1. APC10/DOC1 subunit of the anaphase-promoting complex [69211]
      1. Human (Homo sapiens) [TaxId: 9606] [69212] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74892] (1)
    2. Placental protein 25, pp25 [117104]
      1. Human (Homo sapiens) [TaxId: 9606] [117105] (2)
        SQ Q9Y547
  4. delta-Endotoxin, C-terminal domain [49796] (4)
    1. delta-Endotoxin, C-terminal domain [49797]
      1. Bacillus thuringiensis tenebrionis, CRYIIIA (BT13) [TaxId: 1444] [49798] (1)
      2. Bacillus thuringiensis, CRY3bb1 [TaxId: 1428] [63716] (1)
      3. Bacillus thuringiensis, CRYIA (A) [TaxId: 1428] [49799] (1)
      4. Bacillus thuringiensis subsp. kurstaki, CRY2AA [TaxId: 29339] [63717] (1)
  5. Ephrin receptor ligand binding domain [49800] (2)
    1. Ligand-binding domain of the ephb2 receptor tyrosine kinase [49801]
      1. Mouse (Mus musculus) [TaxId: 10090] [49802] (3)
        SQ P54763 27-207
    2. Ephrin type-B receptor 4 [158957]
      1. Human (Homo sapiens) [TaxId: 9606] [158958] (2)
        SQ P54760 17-196
  6. beta-Galactosidase/glucuronidase, N-terminal domain [49803] (5)
    1. beta-Galactosidase [49804]
      1. Escherichia coli [TaxId: 562] [49805] (25)
        SQ P00722
      2. Arthrobacter sp. c2-2 [TaxId: 192168] [141112] (6)
        SQ Q8KRF6 4-219
    2. beta-Glucuronidase [49806]
      1. Human (Homo sapiens) [TaxId: 9606] [49807] (1)
    3. Beta-mannosidase [158959]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [158960] (18)
        SQ Q8AAK6 28-219
    4. Exochitosanase CsxA [158961]
      1. Amycolatopsis orientalis [TaxId: 31958] [158962] (2)
        SQ Q56F26 42-225
  7. Chondroitin ABC lyase I, N-terminal domain [89236] (1)
    1. Chondroitin ABC lyase I, N-terminal domain [89237]
      1. Proteus vulgaris [TaxId: 585] [89238] (1)
  8. CBM4/9 [74893] (3)
    1. Cellulose-binding domain of cellulase C [49809]
      1. Cellulomonas fimi [TaxId: 1708] [49810] (4)
    2. Carbohydrate binding module from a thermostable xylanase [74894]
      1. Rhodothermus marinus [TaxId: 29549] [74895] (2)
    3. Carbohydrate binding module from laminarinase 16A [82018]
      1. Thermotoga maritima [TaxId: 2336] [82019] (1)
  9. Family 6 carbohydrate binding module, CBM6 [69213] (4)
    1. Carbohydrate binding module from xylanase U [69214]
      1. Clostridium thermocellum [TaxId: 1515] [69215] (2)
    2. Cellulase B (lichenase 5a) [101583]
      1. Cellvibrio mixtus [TaxId: 39650] [101584] (6)
    3. Putative xylanase [89239]
      1. Clostridium stercorarium [TaxId: 1510] [89240] (8)
        SQ P33558 243-374, 384-512
    4. Hypothetical protein BH0236 [117106]
      1. Bacillus halodurans [TaxId: 86665] [117107] (3)
        SQ Q9KG76 790-923
  10. CBM15 [69216] (1)
    1. Xylan-binding module from xylanase 10c [69217]
      1. Cellvibrio japonicus [TaxId: 155077] [69218] (3)
        synonym: Pseudomonas cellulosa
  11. Family 17 carbohydrate binding module, CBM17 [69219] (1)
    1. Endo-1,4-beta glucanase EngF [69220]
      1. Clostridium cellulovorans [TaxId: 1493] [69221] (2)
  12. CBM22 [49811] (1)
    CBM family 22, formerly x6b domain
    1. Xylan-binding domain [49812]
      1. Clostridium thermocellum [TaxId: 1515] [49813] (3)
  13. Family 27 carbohydrate binding module, CBM27 [89241] (2)
    1. Beta-mannosidase, C-terminal domain [89242]
      1. Thermotoga maritima [TaxId: 2336] [89243] (3)
    2. Beta-1,4-mannanase ManA [110118]
      1. Caldicellulosiruptor saccharolyticus [TaxId: 44001] [110119] (2)
        SQ P77847 36-220
  14. Family 29 carbohydrate binding module, CBM29 [89244] (1)
    1. Non-catalytic protein 1, Ncp1 [89245]
      1. Piromyces equi [TaxId: 99929] [89246] (4)
        SQ Q9C171 337-477
  15. Fucose binding lectin [74896] (1)
    1. Fucose binding lectin [74897]
      1. European eel (Anguilla anguilla) [TaxId: 7936] [74898] (1)
  16. N-terminal domain of xrcc1 [49814] (1)
    1. N-terminal domain of xrcc1 [49815]
      the single-strand break repair protein
      1. Human (Homo sapiens) [TaxId: 9606] [49816] (2)
  17. F-box associated region, FBA [101585] (1)
    1. F-box only protein 2 [101586]
      1. Mouse (Mus musculus) [TaxId: 10090] [101587] (3)
  18. Allantoicase repeat [101588] (1)
    1. Allantoicase [101589]
      duplication: tandem repeat of two similar domains
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101590] (2)
        Yir029w
  19. PepX C-terminal domain-like [69222] (4)
    1. Bacterial cocaine esterase, C-terminal domain [69223]
      1. Rhodococcus sp. mb1 [TaxId: 51612] [69224] (4)
    2. Alpha-amino acid ester hydrolase [89247]
      1. Xanthomonas citri [TaxId: 346] [89248] (1)
      2. Acetobacter pasteurianus [TaxId: 438] [101591] (29)
    3. X-Prolyl dipeptidyl aminopeptidase PepX [82020]
      1. Lactococcus lactis [TaxId: 1358] [82021] (1)
  20. PA-IL, galactose-binding lectin 1 [82022] (1)
    a truncated form of this fold lacking one of the N-terminal strands
    1. PA-IL, galactose-binding lectin 1 [82023]
      1. Pseudomonas aeruginosa [TaxId: 287] [82024] (27)
  21. Proprotein convertase P-domain [89249] (3)
    a truncated form of this fold lacking one of the N-terminal strands
    1. Kexin, C-terminal domain [89250]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89251] (4)
    2. Furin, C-terminal domain [89252]
      1. Mouse (Mus musculus) [TaxId: 10090] [89253] (1)
    3. Alkaline serine protease kp-43, C-terminal domain [110120]
      1. Bacillus sp. KSM-KP43 [TaxId: 109322] [110121] (3)
        SQ Q93UV9 207-640
  22. Family 28 carbohydrate binding module, CBM28 [110122] (1)
    1. Endoglucanase (alkaline cellulase) [110123]
      1. Bacillus sp. 1139 [TaxId: 1411] [110124] (1)
        SQ P06564 578-761
  23. Family 30 carbohydrate binding module, CBM30 (PKD repeat) [110125] (1)
    1. Endoglucanase CelJ [110126]
      1. Clostridium thermocellum [TaxId: 1515] [110127] (7)
        SQ P71140 34-228 # chain B coverage
  24. Rhamnogalacturonase B, RhgB, C-terminal domain [110128] (1)
    1. Rhamnogalacturonase B, RhgB, C-terminal domain [110129]
      1. Aspergillus aculeatus [TaxId: 5053] [110130] (1)
        SQ Q00019
  25. Hypothetical protein AT3g04780/F7O18_27 [117108] (1)
    Pfam 06201; DUF1000
    1. Hypothetical protein AT3g04780/F7O18_27 [117109]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117110] (1)
        SQ Q93Z56
  26. Beta-galactosidase LacA, domains 4 and 5 [117111] (1)
    duplication: tandem repeat of two similar domains; some sequence similarity to the beta-Galactosidase/glucuronidase N-terminal domain (scop_fa 49803)
    1. Beta-galactosidase LacA, domains 4 and 5 [117112]
      1. Penicillium sp. [TaxId: 5081] [117113] (2)
        SQ Q700S9 41-1011
  27. Family 36 carbohydrate binding module, CBM36 [117114] (1)
    1. Endo-1,4-beta-xylanase D [117115]
      1. Paenibacillus polymyxa [TaxId: 1406] [117116] (2)
        SQ P45796 516-635
  28. Extended PAW domain [141113] (1)
    single domain; the N-terminal half is covered by Pfam 04721; DUF750 (Smart 00613; PAW), the C-terminal half by PfamB 028386
    1. Peptide:N-glycanase, PNGase, C-terminal domain [141114]
      1. Mouse (Mus musculus) [TaxId: 10090] [141115] (4)
        SQ Q9JI78 454-561! SQ Q9JI78 472-651
  29. CBM11 [141116] (1)
    Pfam 03425; Carbohydrate binding domain (family 11)
    1. Endoglucanase H [141117]
      1. Clostridium thermocellum [TaxId: 1515] [141118] (1)
        SQ P16218 655-821
  30. beta-mannanase CBM [141119] (1)
    1. Endo-beta-1,4-mannanase C-terminal domain [141120]
      1. Bacillus sp. JAMB-602 [TaxId: 244966] [141121] (1)
        SQ Q4W8M3 340-490
  31. YxiM N-terminal domain-like [158963] (1)
    PfamB 038265
    1. Hypothetical protein YxiM [158964]
      1. Bacillus subtilis [TaxId: 1423] [158965] (1)
        SQ P42304 29-174
  32. NPCBM-like [158966] (2)
    Pfam 08305
    1. Uncharacterized Protein CPF2129 [158967]
      1. Clostridium perfringens [TaxId: 1502] [158968] (3)
        SQ Q0TP83 906-1050
    2. Uncharacterized protein CPE0329 [158969]
      1. Clostridium perfringens [TaxId: 1502] [158970] (5)
        SQ Q8XNK4 34-204
Viral protein domain [49817] (1)
sandwich; 9 strands in 2 sheets; jelly-roll; form trimers
1. Viral protein domain [49818] (3)
  forms homotrimers
  uperfamily
  1. Top domain of virus capsid protein [49819] (4)
    this domain is inserted into a multihelical domain
    1. BTV vp7, central (top) domain [49820]
      1. Bluetongue virus [TaxId: 40051] [49821] (2)
    2. RDV p8, central (top) domain [100924]
      1. Rice dwarf virus [TaxId: 10991] [101592] (1)
      2. African horse sickness virus [TaxId: 40050] [49822] (1)
    3. vp6, the major capsid protein of group A rotavirus [63718]
      1. Bovine rotavirus [TaxId: 10927] [63719] (1)
  2. Influenza hemagglutinin headpiece [49823] (1)
    1. Hemagglutinin [49824]
      includes rudiment esterase domain
      1. Influenza A virus, different strains [TaxId: 11320] [49825] (49)
  3. Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [49826] (1)
    1. Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [49827]
      includes irregular N- and C-terminal extensions
      1. Influenza C virus [TaxId: 11552] [49828] (1)
Calcium-mediated lectin [82025] (1)
sandwich; 9 strands in 2 sheets; greek-key
1. Calcium-mediated lectin [82026] (1)
  uperfamily
  1. Calcium-mediated lectin [82027] (2)
    1. Fucose-binding lectin II (PA-LII) [82028]
      1. Pseudomonas aeruginosa [TaxId: 287] [82029] (32)
        SQ Q9HYN5 # PA3361
    2. Mannose-specific lectin RS-IIL [101593]
      1. Ralstonia solanacearum [TaxId: 305] [101594] (2)
Dextranase, N-terminal domain [101595] (1)
sandwich; 9 strands in 2 sheets; greek-key
1. Dextranase, N-terminal domain [101596] (1)
  uperfamily
  1. Dextranase, N-terminal domain [101597] (1)
    1. Dextranase, N-terminal domain [101598]
      1. Penicillium minioluteum [TaxId: 28574] [101599] (2)
Smp-1-like [101600] (1)
sandwich; 9 strands in 2 sheets; greek-key/jelly-roll
1. Smp-1-like [101601] (1)
  uperfamily
  1. Smp-1-like [101602] (2)
    1. Unnamed hypothetical protein [101603]
      similar to calpain-like protein fragment from Trypanosoma brucei and the L2230.07 gene product from Leishmania major
      1. Leishmania major [TaxId: 5664] [101604] (1)
    2. Small myristoylated protein 1, Smp-1 [158971]
      1. Leishmania major [TaxId: 5664] [158972] (1)
        SQ Q5SDH5 1-131
Superantigen (mitogen) Ypm [101605] (1)
sandwich; 9 strands in 2 sheets; jelly-roll
1. Superantigen (mitogen) Ypm [101606] (1)
  uperfamily
  1. Superantigen (mitogen) Ypm [101607] (1)
    1. Superantigen (mitogen) Ypm [101608]
      1. Yersinia pseudotuberculosis [TaxId: 633] [101609] (2)
ENV polyprotein, receptor-binding domain [49829] (1)
sandwich; 9 strands in 2 sheets; greek-key; contains a few helices in loop regions
1. ENV polyprotein, receptor-binding domain [49830] (1)
  uperfamily
  1. ENV polyprotein, receptor-binding domain [49831] (2)
    1. F-MuLV receptor-binding domain [49832]
      1. Friend murine leukemia virus [TaxId: 11795] [49833] (1)
    2. FLV receptor-binding domain [89254]
      1. Feline leukemia virus, strain b/lambda-b1 [TaxId: 11768] [89255] (1)
BTV NS2-like ssRNA-binding domain [110131] (1)
sandwich; 9 strands in 2 sheets; unusual topology with 2 crossover loops
1. BTV NS2-like ssRNA-binding domain [110132] (1)
  uperfamily
  1. BTV NS2-like ssRNA-binding domain [110133] (1)
    N-terminal half of Pfam 04514
    1. Nonstructural protein NS2 [110134]
      1. Bluetongue virus [TaxId: 40051] [110135] (1)
        SQ P23065 8-160
WSSV envelope protein-like [158973] (1)
beta-sandwich; 9 strands in 2 sheets; greek-key
1. WSSV envelope protein-like [158974] (1)
  1. WSSV envelope protein-like [158975] (2)
    1. Envelope protein VP28 [158976]
      1. White spot syndrome virus, WSSV [TaxId: 92652] [158977] (12)
        SQ Q9ICB7 32-201
    2. Envelope protein VP26 [158978]
      1. White spot syndrome virus, WSSV [TaxId: 92652] [158979] (1)
        SQ Q9ICG6 41-201
Virus attachment protein globular domain [49834] (1)
sandwich, 10 strands in 2 sheets; greek-key
1. Virus attachment protein globular domain [49835] (3)
  uperfamily
  1. Adenovirus fiber protein "knob" domain [49836] (7)
    1. Adenovirus fiber protein "knob" domain [49837]
      1. Human adenovirus type 5 [TaxId: 28285] [49838] (1)
      2. Human adenovirus type 2 [TaxId: 10515] [49839] (2)
      3. Human adenovirus type 3 [TaxId: 45659] [63720] (1)
      4. Human adenovirus type 12 [TaxId: 28282] [49840] (4)
      5. Human adenovirus type 37 [TaxId: 52275] [110136] (4)
        SQ Q64823 182-365 ! SQ Q64823 181-365
      6. Human adenovirus type 11P [TaxId: 343462] [158980] (2)
        SQ P35774 129-325
      7. Canine adenovirus 2 [TaxId: 10514] [158981] (18)
        SQ Q65914 361-542
  2. Reovirus attachment protein sigma 1 head domain [69225] (1)
    1. Reovirus attachment protein sigma 1 head domain [69226]
      1. Reovirus [TaxId: 10891] [69227] (1)
  3. Lactophage receptor-binding protein head domain [141122] (2)
    1. Baseplate protein (bpp), C-terminal domain [141123]
      1. Lactococcus phage tp901-1 [TaxId: 35345] [141124] (3)
        SQ Q9G096 63-163
    2. receptor binding protein, rbp, C-terminal domain [141125]
      1. Lactococcus lactis phage p2 [TaxId: 100641] [141126] (6)
        SQ Q71AW2 162-264
TNF-like [49841] (1)
sandwich, 10 strands in 2 sheets; jelly-roll
1. TNF-like [49842] (1)
  uperfamily
  1. TNF-like [49843] (18)
    1. Extracellular domain of CD40 ligand [49844]
      1. Human (Homo sapiens) [TaxId: 9606] [49845] (2)
    2. 30 kDa adipocyte complement-related protein [49846]
      1. Mouse (Mus musculus) [TaxId: 10090] [49847] (2)
    3. Tumor necrosis factor (TNF) [49848]
      1. Human (Homo sapiens) [TaxId: 9606] [49849] (10)
      2. Mouse (Mus musculus) [TaxId: 10090] [49850] (1)
    4. Apoptosis-2 ligand, apo2l/TRAIL [49851]
      1. Human (Homo sapiens) [TaxId: 9606] [49852] (5)
    5. TRANCE/RANKL cytokine [63721]
      1. Mouse (Mus musculus) [TaxId: 10090] [63722] (5)
    6. Soluble part of TALL-1, sTALL-1 (BAFF) [69228]
      1. Human (Homo sapiens) [TaxId: 9606] [69229] (6)
        also includes the PDB entry (1otz) that together with the entry (1p0t) provides the multimeric structure of the complex of this protein with its receptor, BAFF-R. In these entries protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
    7. Ectodysplasin A, Eda-a1 [101610]
      1. Human (Homo sapiens) [TaxId: 9606] [101611] (2)
    8. Collagen NC1 trimerisation domain [69230]
      1. Human (Homo sapiens), isoform X [TaxId: 9606] [69231] (1)
      2. Mouse (Mus musculus), isoform VIII [TaxId: 10090] [101612] (1)
    9. Complement c1q globular head, A chain [101613]
      hetrotrimer of A, B and C chains
      1. Human (Homo sapiens) [TaxId: 9606] [101614] (5)
    10. Complement c1q globular head, B chain [101615]
      hetrotrimer of A, B and C chains
      1. Human (Homo sapiens) [TaxId: 9606] [101616] (5)
    11. Complement c1q globular head, C chain [101617]
      hetrotrimer of A, B and C chains
      1. Human (Homo sapiens) [TaxId: 9606] [101618] (5)
    12. A proliferation-inducing ligand, APRIL [117117]
      1. Mouse (Mus musculus) [TaxId: 10090] [117118] (5)
        SQ Q9D777 105-251 ! SQ Q9D777 105-241
    13. Tumor necrosis factor ligand superfamily member 4, OX40L [141127]
      1. Human (Homo sapiens) [TaxId: 9606] [141128] (1)
        SQ P23510 58-183
      2. Mouse (Mus musculus) [TaxId: 10090] [141129] (3)
        SQ P43488 58-185
    14. Glucocorticoid-induced TNF-related ligand, TNFSF18 [158982]
      1. Mouse (Mus musculus) [TaxId: 10090] [158983] (6)
        SQ Q7TS55 51-173! SQ Q80YG2 49-173
      2. Human (Homo sapiens) [TaxId: 9606] [158984] (10)
        SQ Q9UNG2 55-177! SQ Q9UNG2 57-172! SQ Q9UNG2 57-176
CUB-like [49853] (3)
sandwich, 10 strands in 2 sheets; jelly-roll
1. Spermadhesin, CUB domain [49854] (1)
  uperfamily
  1. Spermadhesin, CUB domain [49855] (6)
    1. Acidic seminal fluid protein (ASFP) [49856]
      1. Cow (Bos taurus) [TaxId: 9913] [49857] (1)
    2. Major seminal plasma glycoprotein PSP-I [49858]
      1. Pig (Sus scrofa) [TaxId: 9823] [49859] (1)
    3. Major seminal plasma glycoprotein PSP-II [49860]
      1. Pig (Sus scrofa) [TaxId: 9823] [49861] (1)
    4. Mannose-binding protein associated serine protease 2, MASP2 [89256]
      duplication: contains two CUB domains separated by an EGF-like domain
      1. Rat (Rattus norvegicus) [TaxId: 10116] [89257] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [110137] (2)
        SQ O00187 17-181
    5. Complement C1S component [89258]
      1. Human (Homo sapiens) [TaxId: 9606] [89259] (1)
2. Collagen-binding domain [89260] (1)
  N-terminal strand appears only in calcium-free form
  uperfamily
  1. Collagen-binding domain [89261] (1)
    1. Class 1 collagenase [89262]
      1. Bacteria (Clostridium histolyticum) [TaxId: 1498] [89263] (4)
3. Acetamidase/Formamidase-like [141130] (1)
  decorated fold with additional structures; contains extra C-terminal alpha+beta subdomain: beta(2)-alpha(2)-beta(2): antiparallel beta-sheet, order 1243
  uperfamily
  1. Acetamidase/Formamidase-like [141131] (1)
    Pfam 03069
    1. Putative acetamidase TM0119 [141132]
      1. Thermotoga maritima [TaxId: 2336] [141133] (4)
        SQ Q9WXX3 1-283
Hyaluronate lyase-like, C-terminal domain [49862] (1)
sandwich, 10 strands in 2 sheets; "folded meander"
1. Hyaluronate lyase-like, C-terminal domain [49863] (1)
  uperfamily
  1. Hyaluronate lyase-like, C-terminal domain [49864] (6)
    1. Chondroitinase AC [49865]
      1. Pedobacter heparinus (Flavobacterium heparinum) [TaxId: 984] [49866] (5)
      2. Arthrobacter aurescens [TaxId: 43663] [101619] (6)
    2. Hyaluronate lyase [49867]
      1. Streptococcus pneumoniae [TaxId: 1313] [49868] (19)
        SQ Q54873 287-1007
      2. Streptococcus agalactiae [TaxId: 1311] [69232] (3)
    3. Xanthan lyase [89264]
      1. Bacillus sp. gl1 [TaxId: 84635] [89265] (7)
    4. Chondroitin ABC lyase I [89266]
      domain 4
      1. Proteus vulgaris [TaxId: 585] [89267] (1)
Cytolysin/lectin [63723] (1)
sandwich, 10 strands in 2 sheets;
1. Cytolysin/lectin [63724] (2)
  some topological similarity to osmotin
  uperfamily
  1. Anemone pore-forming cytolysin [63725] (2)
    Pfam 06369
    1. Equinatoxin II (eqtII, tenebrosin C) [63726]
      1. European sea anemone (Actinia equina) [TaxId: 6106] [63727] (3)
        SQ P61914 40-214
    2. Sticholysin II [89268]
      1. Carribean sea anemone (Stoichactis helianthus) [TaxId: 6123] [89269] (3)
  2. Fungal fruit body lectin [117119] (2)
    Pfam 07367
    1. Lectin xcl [117120]
      1. Xerocomus chrysenteron [TaxId: 5386] [117121] (1)
        SQ Q8WZC9
    2. TF antigen-binding lectin [117122]
      1. Common mushroom (Agaricus bisporus) [TaxId: 5341] [117123] (5)
        SQ Q00022
Putative glucosidase YicI, C-terminal domain [117124] (1)
sandwich; 10 strands in two sheets
1. Putative glucosidase YicI, C-terminal domain [117125] (1)
  uperfamily
  1. Putative glucosidase YicI, C-terminal domain [117126] (1)
    1. Putative glucosidase YicI, C-terminal domain [117127]
      1. Escherichia coli [TaxId: 562] [117128] (15)
        SQ P31434
CsrA-like [117129] (1)
sandwich; 10 strands in 2 sheets; intertwined dimer (segment-swapped, 5-stranded greek-key sandwich?)
1. CsrA-like [117130] (1)
  uperfamily
  1. CsrA-like [117131] (1)
    Pfam 02599
    1. Carbon storage regulator homolog, CsrA [117132]
      1. Pseudomonas aeruginosa [TaxId: 287] [117133] (1)
        SQ O69078
Osmotin, thaumatin-like protein [49869] (1)
sandwich; 11 strands in 2 sheets
1. Osmotin, thaumatin-like protein [49870] (1)
  has two smaller insertion domains
  uperfamily
  1. Osmotin, thaumatin-like protein [49871] (4)
    1. Osmotin [101620]
      antifungal protein
      1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [101621] (1)
    2. Pathogenesis-related protein 5d [49872]
      1. Common tobacco (Nicotiana tabacum) [TaxId: 4097] [49873] (1)
    3. Zeamatin [49874]
      antifungal protein
      1. Maize (Zea mays) [TaxId: 4577] [49875] (1)
    4. Thaumatin [49876]
      1. Ketemfe (Thaumatococcus daniellii) [TaxId: 4621] [49877] (19)
        SQ P02883
SMAD/FHA domain [49878] (1)
sandwich; 11 strands in 2 sheets; greek-key
1. SMAD/FHA domain [49879] (4)
  has a few short helices inserted in loops
  uperfamily
  1. SMAD domain [49880] (4)
    1. Smad4 tumor suppressor C-terminal domain [49881]
      1. Human (Homo sapiens) [TaxId: 9606] [49882] (6)
        SQ Q13485 314-546
    2. Smad3 MH2 domain [82030]
      1. Human (Homo sapiens) [TaxId: 9606] [82031] (4)
        SQ P84022 228-425
    3. Smad2 MH2 domain [49883]
      1. Human (Homo sapiens) [TaxId: 9606] [49884] (2)
    4. Smad1 [69233]
      1. Human (Homo sapiens) [TaxId: 9606] [69234] (1)
  2. FHA domain [49885] (12)
    1. Phosphotyrosine binding domain of Rad53 [49886]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [49887] (18)
    2. Cell cycle checkpoint protein Chfr [74899]
      1. Human (Homo sapiens) [TaxId: 9606] [74900] (2)
    3. Chk2 kinase [74901]
      1. Human (Homo sapiens) [TaxId: 9606] [74902] (1)
    4. Kinase associated protein phosphatase [101622]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101623] (1)
    5. FHA domain containing protein At4G14490 [101624]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [101625] (1)
    6. Antigen ki-67 [101626]
      1. Human (Homo sapiens) [TaxId: 9606] [101627] (2)
    7. Polynucleotide kinase 3'-phosphatase [101628]
      1. Mouse (Mus musculus) [TaxId: 10090] [101629] (5)
      2. Human (Homo sapiens) [TaxId: 9606] [141134] (1)
        SQ Q96T60 8-108
    8. Afadin [141135]
      1. Mouse (Mus musculus) [TaxId: 10090] [141136] (1)
        SQ Q9QZQ1 382-487
    9. Kinesin-like protein kif1c [141137]
      1. Human (Homo sapiens) [TaxId: 9606] [141138] (1)
        SQ O43896 498-599
    10. Probable regulatory protein EmbR, C-terminal domain [141139]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141140] (3)
        SQ P66799 284-382
    11. Ubiquitin ligase protein RNF8 [141141]
      1. Human (Homo sapiens) [TaxId: 9606] [141142] (2)
        SQ O76064 8-139
  3. Interferon regulatory factor 3 (IRF3), transactivation domain [101630] (1)
    weak sequence similarity to SMAD domain
    1. Interferon regulatory factor 3 (IRF3), transactivation domain [101631]
      1. Human (Homo sapiens) [TaxId: 9606] [101632] (2)
  4. EssC N-terminal domain-like [141143] (1)
    PfamB 051221 covers two consecutive domains; the first one is of canonical topology, whereas the second domain has a cirular permutation, beginnig at strand 2 and ending at strand 1 of the canonical fold
    1. Protein EssC [141144]
      SAV0287; similar to DNA segregation ATPase and related proteins
      1. Staphylococcus aureus [TaxId: 1280] [141145] (2)
        SQ Q8NYF3 1-78! SQ Q8NYF3 79-186
Soluble secreted chemokine inhibitor, VCCI [49888] (1)
sandwich; 11 strands in 2 sheets; greek-key
1. Soluble secreted chemokine inhibitor, VCCI [49889] (1)
  uperfamily
  1. Soluble secreted chemokine inhibitor, VCCI [49890] (1)
    1. Soluble secreted chemokine inhibitor, VCCI [49891]
      1. Cowpox virus [TaxId: 10243] [49892] (1)
Baculovirus p35 protein [49893] (1)
sandwich; 14 strands in 2 sheets; greek-key
1. Baculovirus p35 protein [49894] (1)
  has a few helices inserted in loops
  uperfamily
  1. Baculovirus p35 protein [49895] (1)
    1. Baculovirus p35 protein [49896]
      Apoptotic caspase inhibitor
      1. AcMNPV (Autographa californica nuclear polyhedrosis virus) [TaxId: 46015] [49897] (6)
Concanavalin A-like lectins/glucanases [49898] (1)
sandwich; 12-14 strands in 2 sheets; complex topology
1. Concanavalin A-like lectins/glucanases [49899] (25)
  uperfamily
  1. Legume lectins [49900] (28)
    1. Concanavalin A [49901]
      natural circle permutation: the "old" N- and C-termini are linked with a peptide bond, whereas the "new" ones correspond to a cleaved loop
      1. Jack bean (Canavalia ensiformis) [TaxId: 3823] [49902] (52)
        SQ P81461
      2. Brazilian jackbean (Canavalia brasiliensis) [TaxId: 61861] [49903] (1)
    2. Legume lectin [49904]
      1. Garden pea (Pisum sativum) [TaxId: 3888] [49905] (6)
        two-chain protein resulted from a single-chain precursor
      2. Common lentil (Lens culinaris) [TaxId: 3864] [49906] (4)
        two-chain protein resulted from a single-chain precursor
      3. West-central african legume (Griffonia simplicifolia) [TaxId: 3850] [49907] (3)
      4. Griffonia simplicifolia, lectin I-b4 [TaxId: 3850] [69235] (2)
      5. Coral tree (Erythrina corallodendron) [TaxId: 3843] [49908] (8)
        SQ P16404
      6. Cockspur coral tree (Erythrina crista-galli) [TaxId: 49817] [74903] (5)
        SQ Q6YD91
      7. Winged bean (Psophocarpus tetragonolobus), basic agglutinin [TaxId: 3891] [49909] (50)
      8. Winged bean (Psophocarpus tetragonolobus), acidic lectin [TaxId: 3891] [63728] (2)
      9. Lathyrus ochrus, isolectin I [TaxId: 3858] [49910] (7)
      10. Lathyrus ochrus, isolectin II [TaxId: 3858] [49911] (2)
      11. Peanut (Arachis hypogaea) [TaxId: 3818] [49912] (44)
        SQ P02872 24-255
      12. Soybean (Glycine max) [TaxId: 3847] [49913] (5)
      13. Field bean (Dolichos lablab), Fril [TaxId: 35936] [49914] (1)
        a legume lectin that delays hematopoietic progenitor maturation
      14. Horse gram (Dolichos biflorus), different isoforms [TaxId: 3840] [49915] (5)
      15. Mucana (Dioclea grandiflora) [TaxId: 3837] [49916] (1)
        natural circle permutation resulting from a post-translational modification of precursor
      16. Duke (Dioclea guianensis) [TaxId: 99571] [63729] (2)
        natural circle permutation resulting from a post-translational modification of precursor
      17. Cratylia mollis, isoform 1 [TaxId: 252530] [101633] (1)
        natural circle permutation resulting from a post-translational modification of precursor
      18. Furze (Ulex europaeus), UEA-I [TaxId: 3902] [49917] (2)
      19. Furze (Ulex europaeus), UEA-II [TaxId: 3902] [49918] (5)
      20. Bloodwood tree (Pterocarpus angolensis) [TaxId: 182271] [82032] (51)
      21. Maackia amurensis, leukoagglutinin [TaxId: 37501] [49919] (1)
      22. Black locust (Robinia pseudoacacia) [TaxId: 35938] [63730] (2)
      23. Hairy vetch (Vicia villosa), isolectin b4 [TaxId: 3911] [82033] (1)
    3. Phytohemagglutinin-L, PHA-L, also arcelin [49920]
      single-chain subunit has "generic" topology
      1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49921] (4)
      2. Kidney bean (Phaseolus vulgaris), G02771, arcelin-5a [TaxId: 3885] [49922] (1)
    4. alpha-Amylase inhibitor [49923]
      1. Kidney bean (Phaseolus vulgaris) [TaxId: 3885] [49924] (1)
  2. Lectin leg-like [74904] (3)
    mammalian protein related to legume lectins
    1. Carbohydrate-recognition domain of P58/ERGIC-53 [74905]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [74906] (2)
    2. Emp47p N-terminal domain [141146]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141147] (8)
        SQ P43555 35-255! SQ P43555 36-259
    3. Emp46p N-terminal domain [141148]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141149] (6)
        SQ Q12396 54-271! SQ Q12396 55-272
  3. Glycosyl hydrolases family 16 [49925] (8)
    Pfam 00722
    beta-Glucanase-like
    1. Bacillus 1-3,1-4-beta-glucanase [49926]
      1. Bacillus licheniformis [TaxId: 1402] [49927] (1)
      2. synthetic, hybrid between Bacillus amyloliquefaciens and Bacillus macerans proteins [49928] (3)
      3. Bacillus macerans [TaxId: 44252] [49929] (6)
      4. Fibrobacter succinogenes [TaxId: 833] [89270] (3)
        a natural circularly permuted protein
    2. kappa-Carrageenase, catalytic [49930]
      1,3-alpha-1,4-beta-D-galactose-4-sulfate-3,6-anhydro-D-galactose 4 galactohydrolase
      1. Pseudoalteromonas carrageenovora [TaxId: 227] [49931] (1)
    3. Xyloglucan endotransglycosylase [101634]
      1. European aspen (Populus tremula) [TaxId: 113636] [101635] (2)
    4. beta-Agarase A [101636]
      1. Zobellia galactanivorans [TaxId: 63186] [101637] (3)
    5. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, catalytic domain [117134]
      1. Clostridium perfringens [TaxId: 1502] [117135] (1)
        SQ Q934G8 17-420
  4. Galectin (animal S-lectin) [49932] (11)
    1. Galectin-1 [100925]
      1. Cow (Bos taurus) [TaxId: 9913] [49934] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [101638] (6)
        SQ P09382
      3. Chicken (Gallus gallus) [TaxId: 9031] [49936] (1)
        galectin-1 homologue CG-16
      4. Toad (Bufo arenarum) [TaxId: 38577] [49937] (2)
    2. Galectin-7 [100926]
      1. Human (Homo sapiens) [TaxId: 9606] [49935] (5)
    3. S-lac lectin, L-14-II [100927]
      1. Human (Homo sapiens) [TaxId: 9606] [100928] (1)
    4. Charcot-Leyden crystal (CLC) protein [49938]
      1. Human (Homo sapiens) [TaxId: 9606] [49939] (4)
    5. Galectin-2 [101639]
      1. Inky cap fungus (Coprinopsis cinerea) [TaxId: 5346] [101640] (6)
    6. Galectin-3 CRD [49940]
      1. Human (Homo sapiens) [TaxId: 9606] [49941] (6)
    7. Congerin I [49942]
      1. Conger eel (Conger myriaster) [TaxId: 7943] [49943] (2)
    8. Congerin II [82034]
      1. Conger eel (Conger myriaster) [TaxId: 7943] [82035] (4)
  5. Laminin G-like module [49944] (7)
    1. Sex hormone-binding globulin [49945]
      1. Human (Homo sapiens) [TaxId: 9606] [49946] (9)
    2. Laminin alpha2 chain [49947]
      1. Mouse (Mus musculus) [TaxId: 10090] [49948] (3)
    3. Ligand-binding domain of neurexin 1beta [49949]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [49950] (16)
      2. Homo sapiens [TaxId: 9606] [158985] (2)
    4. Growth-arrest-specific protein Gas6 [82036]
      1. Human (Homo sapiens) [TaxId: 9606] [82037] (1)
    5. Agrin [101641]
      alternative splicing
      1. Chicken (Gallus gallus) [TaxId: 9031] [101642] (4)
    6. Thrombospondin 1 N-terminal domain [141150]
      1. Human (Homo sapiens) [TaxId: 9606] [141151] (8)
        SQ P07996 28-233! SQ P07996 29-233
  6. Thrombospondin C-terminal domain [101643] (1)
    Pfam 05735
    1. Thrombospondin C-terminal domain [101644]
      1. Human (Homo sapiens) [TaxId: 9606] [101645] (1)
  7. Pentraxin (pentaxin) [49951] (2)
    1. Serum amyloid P component (SAP) [49952]
      1. Human (Homo sapiens) [TaxId: 9606] [49953] (38)
    2. C-reactive protein (CRP) [49954]
      1. Human (Homo sapiens) [TaxId: 9606] [49955] (3)
  8. Calnexin/calreticulin [69236] (1)
    1. Calnexin [69237]
      1. Dog (Canis familiaris) [TaxId: 9615] [69238] (1)
  9. vp4 sialic acid binding domain [74907] (1)
    1. vp4 sialic acid binding domain [74908]
      1. Rhesus rotavirus [TaxId: 10969] [74909] (4)
  10. Hypothetical protein YesU [101646] (1)
    1. Hypothetical protein YesU [101647]
      1. Bacillus subtilis [TaxId: 1423] [101648] (1)
  11. Alginate lyase [101649] (3)
    members have same function and similar structures but low sequence similarity
    1. Alginate lyase [101650]
      1. Alteromonas sp. [TaxId: 232] [101651] (1)
    2. Alginate lyase PA1167 [110138]
      1. Pseudomonas aeruginosa [TaxId: 287] [110139] (1)
        SQ Q9I4H0
    3. Polyguluronate lyase [110140]
      1. Corynebacterium sp. ALY-1 [TaxId: 101519] [110141] (1)
        SQ Q9RB42
  12. Clostridium neurotoxins, the second last domain [49956] (3)
    1. Tetanus neurotoxin [49957]
      1. Clostridium tetani [TaxId: 1513] [49958] (10)
    2. Botulinum neurotoxin [49959]
      1. Clostridium botulinum, serotype A [TaxId: 1491] [49960] (1)
      2. Clostridium botulinum, serotype B [TaxId: 1491] [49961] (17)
  13. Exotoxin A, N-terminal domain [49962] (1)
    1. Exotoxin A, N-terminal domain [49963]
      1. Pseudomonas aeruginosa [TaxId: 287] [49964] (2)
  14. Vibrio cholerae sialidase, N-terminal and insertion domains [49965] (1)
    1. Vibrio cholerae sialidase, N-terminal and insertion domains [49966]
      both domains have this fold
      rest of protein is beta-propeller of six sheets
      1. Vibrio cholerae [TaxId: 666] [49967] (3)
        SQ P37060
  15. Leech intramolecular trans-sialidase, N-terminal domain [49968] (1)
    1. Leech intramolecular trans-sialidase, N-terminal domain [49969]
      1. North american leech (Macrobdella decora) [TaxId: 6405] [49970] (5)
  16. Trypanosoma sialidase, C-terminal domain [82038] (2)
    1. Trypanosoma sialidase, C-terminal domain [82039]
      1. Trypanosoma rangeli [TaxId: 5698] [82040] (10)
        SQ O44049 20-653
      2. Parasitic flagellate protozoan (Trypanosoma cruzi) [TaxId: 5693] [89271] (12)
        SQ Q26966
  17. Glycosyl hydrolase family 7 catalytic core [49971] (6)
    contains many insertions in the common fold
    1. Cellobiohydrolase I (cellulase, Endoglucanase I, CBH1) [68900]
      1. Trichoderma reesei, Cel7A [TaxId: 51453] [68898] (13)
      2. Trichoderma reesei, Endoglucanase I [TaxId: 51453] [68899] (1)
      3. Fusarium oxysporum [TaxId: 5507] [49976] (4)
      4. Humicola insolens, Cel7b [TaxId: 34413] [49977] (6)
      5. Phanerochaete chrysosporium, Cel7d [TaxId: 5306] [69239] (5)
      6. Talaromyces emersonii [TaxId: 68825] [117136] (1)
        SQ Q8TFL9
  18. Glycosyl hydrolases family 32 C-terminal domain [101652] (2)
    Pfam 08244
    flat sheet beta-sandwich lacking the characteristic beta-bulge in the C-terminal strand
    1. Beta-fructosidase (invertase), C-terminal domain [101653]
      1. Thermotoga maritima [TaxId: 2336] [101654] (7)
    2. Exo-inulinase [117137]
      1. Aspergillus awamori [TaxId: 105351] [117138] (3)
        SQ Q96TU3 20-536
  19. Xylanase/endoglucanase 11/12 [49978] (24)
    1. Xylanase II [49979]
      Partial overlap with common fold and the active sites of the other endoglucanases
      1. Bacillus circulans [TaxId: 1397] [49980] (10)
      2. Bacillus subtilis [TaxId: 1423] [49981] (7)
      3. Bacillus agaradhaerens [TaxId: 76935] [49982] (4)
      4. Bacillus subtilis, B230 [TaxId: 1423] [74910] (1)
      5. Streptomyces sp. s38, xyl1 [TaxId: 181109] [69240] (1)
      6. Trichoderma harzianum [TaxId: 5544] [49983] (1)
      7. Trichoderma reesei, xynI [TaxId: 51453] [49984] (1)
      8. Trichoderma reesei, xynII [TaxId: 51453] [49985] (10)
      9. Thermomyces lanuginosus [TaxId: 5541] [49986] (1)
      10. Aspergillus niger [TaxId: 5061] [49987] (1)
      11. Aspergillus kawachii [TaxId: 40384] [49988] (2)
        SQ P55328 29-210 # 100% sequence identity; Aspergillus awamori TaxID: 105351
      12. Paecilomyces variotii, Bainier 1907 [TaxId: 45996] [49989] (1)
      13. Dictyoglomus thermophilum [TaxId: 14] [49990] (1)
      14. Chaetomium thermophilum [TaxId: 209285] [89272] (3)
        endoxylanase 11a
      15. Nonomuraea flexuosa [TaxId: 103836] [89273] (1)
      16. Penicillium funiculosum [TaxId: 28572] [110142] (1)
        SQ Q9HFH0
      17. Trichoderma longibrachiatum [TaxId: 5548] [158986] (1)
    2. Family 12 endo-1,4-beta-glucanase (cellulase) catalytic domain [49991]
      1. Streptomyces lividans, CelB2 [TaxId: 1916] [49992] (2)
      2. Streptomyces sp. 11ag8 [TaxId: 133452] [89274] (1)
      3. Rhodothermus marinus [TaxId: 29549] [89275] (7)
      4. Trichoderma reesei, Cel12A [TaxId: 51453] [63731] (3)
      5. Humicola grisea [TaxId: 5527] [101655] (5)
        SQ Q8NJY3 31-254
      6. Hypocrea schweinitzii [TaxId: 36924] [89276] (1)
      7. Aspergillus niger [TaxId: 5061] [82041] (2)
  20. Peptidase A4 [101656] (2)
    circular permutation of the canonical fold
    1. Scytalidopepsin B [101657]
      1. Fungus (Scytalidium lignicola) [TaxId: 5539] [101658] (5)
    2. Aspergillopepsin II [141152]
      1. Aspergillus niger [TaxId: 5061] [141153] (1)
        SQ P24665 60-91,112-282
  21. Alpha-L-arabinofuranosidase B, N-terminal domain [110143] (1)
    1. Alpha-L-arabinofuranosidase B, N-terminal domain [110144]
      1. Aspergillus kawachii [TaxId: 40384] [110145] (4)
        SQ Q8NK89 19-499
  22. SPRY domain [141154] (5)
    Pfam 00622
    1. LD34464p [141155]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141156] (1)
        SQ Q7JUY1 103-319
        Cg2944-pf, isoform f
    2. Similar to Ret finger protein-like 1 [141157]
      1. Human (Homo sapiens) [TaxId: 9606] [141158] (4)
    3. SPRY domain-containing SOCS box protein 2 [141159]
      1. Mouse (Mus musculus) [TaxId: 10090] [141160] (1)
        SQ O88838 12-224
    4. 52 kDa Ro protein [158987]
      1. Human (Homo sapiens) [TaxId: 9606] [158988] (2)
        SQ P19474 287-465
    5. Cg2944-PF (gus) [158989]
      isoform F
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [158990] (2)
        SQ A1Z6E2 31-234
  23. Beta-D-xylosidase C-terminal domain-like [141161] (4)
    1. Beta-D-xylosidase C-terminal domain [141162]
      1. Bacillus subtilis [TaxId: 1423] [141163] (4)
        SQ P94489 325-533
      2. Clostridium acetobutylicum [TaxId: 1488] [141164] (8)
        SQ Q97DM1 323-532
      3. Geobacillus stearothermophilus [TaxId: 1422] [141165] (16)
        SQ Q68HB3 325-535
      4. Bacillus halodurans [TaxId: 86665] [141166] (2)
        SQ Q9K6P5 321-525
  24. SO2946-like [141167] (1)
    1. Hypothetical protein SO2946 [141168]
      1. Shewanella oneidensis [TaxId: 70863] [141169] (3)
        SQ Q8ED25 24-262
  25. MAM domain [141170] (1)
    Pfam 00629
    1. Receptor-type tyrosine-protein phosphatase mu [141171]
      1. Human (Homo sapiens) [TaxId: 9606] [141172] (1)
        SQ P28827 21-183
Supersandwich [49993] (3)
sandwich; 18 strands in 2 sheets
1. Galactose mutarotase-like [74650] (11)
  probable carbohydrate-binding domain in enzymes acting on sugars
  uperfamily
  1. Aldose 1-epimerase (mutarotase) [74911] (4)
    1. Galactose mutarotase [74912]
      1. Lactococcus lactis [TaxId: 1358] [74913] (19)
      2. Human (Homo sapiens) [TaxId: 9606] [101659] (2)
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141173] (1)
        SQ P04397 358-699
        C-terminal domain of Gal10 bifunctional protein
    2. Aldose 1-epimerase homologue [89277]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89278] (1)
        5C981 (C01B4.6 or YK2391) gene product
  2. Hypothetical protein HI1317 [89279] (1)
    1. Hypothetical protein HI1317 [89280]
      1. Haemophilus influenzae [TaxId: 727] [89281] (1)
  3. beta-Galactosidase, domain 5 [49995] (2)
    1. beta-Galactosidase, domain 5 [49996]
      1. Escherichia coli [TaxId: 562] [49997] (25)
        SQ P00722
      2. Arthrobacter sp. c2-2 [TaxId: 192168] [141174] (6)
        SQ Q8KRF6 722-1023
  4. Hyaluronate lyase-like, central domain [50006] (6)
    1. Chondroitinase AC [50007]
      1. Pedobacter heparinus (Flavobacterium heparinum) [TaxId: 984] [50008] (5)
      2. Arthrobacter aurescens [TaxId: 43663] [101660] (6)
    2. Hyaluronate lyase [50009]
      1. Streptococcus pneumoniae [TaxId: 1313] [50010] (19)
        SQ Q54873 287-1007
      2. Streptococcus agalactiae [TaxId: 1311] [69241] (3)
    3. Xanthan lyase [89282]
      1. Bacillus sp. gl1 [TaxId: 84635] [89283] (7)
    4. Chondroitin ABC lyase I [89284]
      domain 3
      1. Proteus vulgaris [TaxId: 585] [89285] (1)
  5. Glycosyltransferase family 36 N-terminal domain [63733] (2)
    overall domain organization is similar to Bacterial glucoamylase
    1. Lactobacillus maltose phosphorylase, N-terminal domain [63734]
      1. Lactobacillus brevis [TaxId: 1580] [63735] (1)
    2. Chitobiose phosphorylase ChbP [110146]
      1. Vibrio proteolyticus [TaxId: 671] [110147] (3)
        SQ Q76IQ9
  6. Bacterial glucoamylase N-terminal domain-like [82042] (2)
    overall domain organization is similar to Lactobacillus maltose phosphorylase
    1. Bacterial glucoamylase, N-terminal domain [82043]
      1. Thermoanaerobacterium thermosaccharolyticum [TaxId: 1517] [82044] (2)
    2. Glucodextranase, domain N [101661]
      1. Arthrobacter globiformis [TaxId: 1665] [101662] (2)
  7. 4-alpha-glucanotransferase, C-terminal domain [89286] (1)
    family 57 glycoside hydrolase; overall domain organization is similar to that of the alpha-mannosidase family
    1. 4-alpha-glucanotransferase, C-terminal domain [89287]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [89288] (3)
  8. alpha-mannosidase, C-terminal domain [88656] (2)
    family 38 glycoside hydrolase; overall domain organization is similar to that of the 4-alpha-glucanotransferase family
    the supersandwich domain is elaborated with additional beta-strands and beta-sandwich subdomains
    1. Golgi alpha-mannosidase II [88657]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [88658] (46)
        SQ Q24451 94-1107
    2. Lysosomal alpha-mannosidase [89289]
      the single-chain precursor is processed into 5 peptides; heavily glycosylated
      1. Cow (Bos taurus) [TaxId: 9913] [89290] (1)
  9. MdoG-like [110148] (1)
    Pfam 04349; Pfam coverage extends to the C-terminal immunoglobulin-like domain
    1. Glucans biosynthesis protein G (MdoG, OpgG), N-terminal domain [110149]
      1. Escherichia coli [TaxId: 562] [110150] (1)
        SQ P33136 23-511
  10. Rhamnogalacturonase B, RhgB, N-terminal domain [110151] (1)
    1. Rhamnogalacturonase B, RhgB, N-terminal domain [110152]
      1. Aspergillus aculeatus [TaxId: 5053] [110153] (1)
        SQ Q00019
  11. YicI N-terminal domain-like [117139] (2)
    1. Putative glucosidase YicI, N-terminal domain [117140]
      1. Escherichia coli [TaxId: 562] [117141] (15)
        SQ P31434
    2. Alpha-galactosidase GalA N-terminal domain [141175]
      rudiment, partly refolded form of supersandwich fold
      1. Thermotoga maritima [TaxId: 2336] [141176] (1)
        SQ O33835 1-177
2. V-region of surface antigen I/II (SA I/II, PAC) [74914] (1)
  uperfamily
  1. V-region of surface antigen I/II (SA I/II, PAC) [74915] (1)
    1. V-region of surface antigen I/II (SA I/II, PAC) [74916]
      1. Streptococcus mutans [TaxId: 1309] [74917] (1)
3. Amine oxidase catalytic domain [49998] (1)
  uperfamily
  1. Amine oxidase catalytic domain [49999] (5)
    1. Copper amine oxidase, domain 3 [50000]
      1. Escherichia coli [TaxId: 562] [50001] (11)
      2. Pea seedling (Pisum sativum) [TaxId: 3888] [50002] (2)
        SQ Q43077
      3. Arthrobacter globiformis [TaxId: 1665] [50003] (53)
        SQ P46881 9-628
      4. Yeast (Hansenula polymorpha) [TaxId: 4905] [50004] (14)
    2. Lysyl oxidase PplO, domain 3 [101663]
      1. Yeast (Pichia pastoris) [TaxId: 4922] [101664] (3)
        SQ Q96X16 43-777
Leukotriene A4 hydrolase N-terminal domain [63736] (1)
duplication: two beta-sandwiches of similar topologies are fused together in a single three beta-sheet domain
1. Leukotriene A4 hydrolase N-terminal domain [63737] (1)
  uperfamily
  1. Leukotriene A4 hydrolase N-terminal domain [63738] (1)
    1. Leukotriene A4 hydrolase N-terminal domain [63739]
      1. Human (Homo sapiens) [TaxId: 9606] [63740] (15)
        SQ P09960
EV matrix protein [50011] (1)
consists of two beta-sandwich domains of similar topologies
1. EV matrix protein [50012] (1)
  uperfamily
  1. EV matrix protein [50013] (1)
    1. EV matrix protein [50014]
      1. Ebola virus [TaxId: 205488] [50015] (3)
Viral chemokine binding protein m3 [82045] (1)
consists of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds
1. Viral chemokine binding protein m3 [82046] (1)
  uperfamily
  1. Viral chemokine binding protein m3 [82047] (1)
    1. Viral chemokine binding protein m3 [82048]
      1. Murid herpesvirus 4, MuHV-4 [TaxId: 33708] [82049] (7)
gp9 [50016] (1)
consists of two different beta-sandwich domains unrelated to other beta-sandwich folds
1. gp9 [50017] (1)
  uperfamily
  1. gp9 [50018] (1)
    1. gp9 [50019]
      the trigger of tail contraction and the long tail fibers connector
      1. Bacteriophage T4 [TaxId: 10665] [50020] (20)
Flagellar hook protein flgE [117142] (1)
consists of two different domains; d1: [complex fold made of bifurcated beta-sheets]; d2 (inserted into d1): [beta-sandwich; 8 strands in 2 sheets]
1. Flagellar hook protein flgE [117143] (1)
  uperfamily
  1. Flagellar hook protein flgE [117144] (1)
    1. Flagellar hook protein flgE [117145]
      1. Salmonella typhimurium [TaxId: 90371] [117146] (1)
        SQ P16322 71-363
ISP domain [50021] (1)
consists of two all-beta subdomains: conserved small domain has a rubredoxin-like fold; larger domain consists of 6 beta-stands packed in either sandwich of two 3-stranded sheets or closed barrel (n=6; S=8)
1. ISP domain [50022] (3)
  uperfamily
  1. Rieske iron-sulfur protein (ISP) [50023] (11)
    1. ISP subunit of the mitochondrial cytochrome bc1-complex, water-soluble domain [50024]
      1. Cow (Bos taurus) [TaxId: 9913] [50025] (10)
      2. Chicken (Gallus gallus) [TaxId: 9031] [50026] (6)
        SQ P13272 79-274 ! SQ P13272 # precursor of chains I,E and V,R
      3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63741] (9)
    2. ISP subunit from the cytochrome b6f complex, soluble domain [101665]
      1. Mastigocladus laminosus [TaxId: 83541] [101666] (6)
      2. Chlamydomonas reinhardtii [TaxId: 3055] [101667] (1)
    3. ISP subunit from chloroplast cytochrome bf complex [50027]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [50028] (1)
    4. Arsenite oxidase Rieske subunit [50029]
      1. Alcaligenes faecalis [TaxId: 511] [50030] (2)
    5. Rieske protein II (SoxF) [74918]
      1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [74919] (1)
    6. Soluble Rieske protein [89291]
      1. Thermus thermophilus [TaxId: 274] [89292] (1)
    7. Rieske-type ferredoxin associated with biphenyl dioxygenase [50031]
      1. Burkholderia cepacia [TaxId: 292] [50032] (1)
    8. Toluene-4-monooxygenase system protein C, TmoC [110154]
      1. Pseudomonas mendocina [TaxId: 300] [110155] (3)
        SQ Q00458
  2. Ring hydroxylating alpha subunit ISP domain [50033] (7)
    1. Naphthalene 1,2-dioxygenase alpha subunit, N-domain [50034]
      1. Pseudomonas putida [TaxId: 303] [50035] (16)
      2. Rhodococcus sp. ncimb12038 [TaxId: 92694] [141177] (6)
        SQ Q9X3R9 1-162
    2. Biphenyl dioxygenase large subunit BphA1, N-terminal domain [110156]
      1. Rhodococcus sp. (strain RHA1) [TaxId: 101510] [110157] (2)
        SQ Q53122 17-451
    3. 2-oxo-1,2-dihydroquinoline 8-monooxygenase, oxygenase component OxoO [141178]
      1. Pseudomonas putida [TaxId: 303] [141179] (1)
        SQ O05935 16-163
    4. Nitrobenzene dioxygenase alpha subunit, NBDO-alpha [141180]
      1. Comamonas sp. JS765 [TaxId: 58226] [141181] (3)
        SQ Q8RTL4 3-152
    5. Large subunit of cumene dioxygenase cumA1 [141182]
      1. Pseudomonas fluorescens [TaxId: 294] [141183] (1)
        SQ Q51743 19-180
    6. Terminal oxygenase component of carbazole CarAa [141184]
      1. Janthinobacterium sp. j3 [TaxId: 213804] [141185] (10)
        SQ Q84II6 1-142
  3. NirD-like [158991] (3)
    retains the common fold but lacks the Fe-S cluster
    1. NADH-nitrite reductase small subunit NirD [158992]
      1. Escherichia coli [TaxId: 562] [158993] (1)
        SQ P0A9I8 1-108
      2. Erwinia carotovora [TaxId: 554] [158994] (1)
        SQ Q6CZS1 1-122
      3. Vibrio parahaemolyticus [TaxId: 670] [158995] (8)
        SQ Q87HB1 4-111
Trm112p-like [158996] (1)
similar to the small domain of the ISP (scop_cf 50021)
1. Trm112p-like [158997] (1)
  possibly have evolved from a metal ion (or cofactor)-binding protein of a rubredoxin-like fold; in the known members, from one to three of the four metal-binding positions are occupied by cysteine residues
  1. Trm112p-like [158998] (3)
    Pfam 03966; previously DUF343
    1. Uncharacterized protein Cgl1405/cg1592 [158999]
      1. Corynebacterium glutamicum [TaxId: 1718] [159000] (1)
        SQ Q8NQM9 1-59
    2. Hypothetical protein CV3345 [159001]
      annotated in PDB 2HF1 as Tetraacyldisaccharide-1-P 4-kinase LpxK
      1. Chromobacterium violaceum [TaxId: 536] [159002] (2)
        SQ Q7NSS5 2-60
    3. Uncharacterized protein PFL1779 [159003]
      1. Pseudomonas fluorescens [TaxId: 294] [159004] (2)
        SQ Q4KFT4 3-61
YopX-like [159005] (1)
consists of two domains: the N-terminal dimerisation domain of variable structure and the C-terminal domain with similarity to the SH3-like fold
1. YopX-like [159006] (1)
  conmrises proteins of plasmid and phage origins
  1. YopX-like [159007] (3)
    Pfam 09643
    1. Hypothetical protein EF1440 [159008]
      1. Enterococcus faecalis [TaxId: 1351] [159009] (4)
        SQ Q835D7 1-143
    2. Hypothetical protein YopX [159010]
      1. Bacillus subtilis [TaxId: 1423] [159011] (3)
        SQ O34401 1-134
    3. Orf041 product [159012]
      1. Staphylococcus phage 37 [TaxId: 320840] [159013] (1)
        SQ Q4ZC86 1-133
Obg-fold [82050] (1)
this fold is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich
these regions form six left-handed collagen-like helices packed and H-bonded together
1. Obg GTP-binding protein N-terminal domain [82051] (1)
  uperfamily
  1. Obg GTP-binding protein N-terminal domain [82052] (2)
    1. Obg GTP-binding protein N-terminal domain [82053]
      1. Bacillus subtilis [TaxId: 1423] [82054] (1)
      2. Thermus thermophilus [TaxId: 274] [101668] (1)
        TT1381
SH3-like barrel [50036] (21)
barrel, partly opened; n*=4, S*=8; meander
the last strand is interrupted by a turn of 3-10 helix
1. C-terminal domain of transcriptional repressors [50037] (3)
  the N-terminal domains of these repressors bind DNA
  uperfamily
  1. Biotin repressor (BirA) [50038] (2)
    1. Biotin repressor/biotin holoenzyme synthetase, C-terminal domain [50039]
      1. Escherichia coli [TaxId: 562] [50040] (5)
    2. Biotin--[acetyl-CoA-carboxylase] ligase C-terminal domain [141186]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141187] (28)
        SQ O57883 189-235
  2. FeoA-like [50041] (4)
    1. Diphtheria toxin repressor (DtxR) [50042]
      1. Corynebacterium diphtheriae [TaxId: 1717] [50043] (15)
        SQ P33120
    2. Iron-dependent regulator IdeR [63742]
      1. Mycobacterium tuberculosis [TaxId: 1773] [63743] (2)
        SQ Q50495
    3. Ferrous iron transport protein A, FeoA [159014]
      1. Klebsiella pneumoniae [TaxId: 573] [159015] (1)
        SQ A6TF31 1-75
    4. Hypothetical protein PA4359 [159016]
      1. Pseudomonas aeruginosa [TaxId: 287] [159017] (1)
        SQ Q9HW42 1-75
  3. Transcriptional repressor protein KorB [69242] (1)
    1. Transcriptional repressor protein KorB [69243]
      1. Escherichia coli [TaxId: 562] [69244] (2)
2. SH3-domain [50044] (1)
  uperfamily
  1. SH3-domain [50045] (48)
    1. C-Crk, N-terminal SH3 domain [50046]
      1. Mouse (Mus musculus) [TaxId: 10090] [50047] (9)
    2. Fyn proto-oncogene tyrosine kinase, SH3 domain [50048]
      1. Human (Homo sapiens) [TaxId: 9606] [50049] (11)
    3. SH3 domain from nebulin [50050]
      1. Human (Homo sapiens) [TaxId: 9606] [50051] (2)
    4. Abl tyrosine kinase, SH3 domain [50052]
      1. Mouse (Mus musculus) [TaxId: 10090] [50053] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [50054] (5)
    5. Phosphatidylinositol 3-kinase (p85-alpha subunit, pi3k), SH3 domain [50055]
      1. Human (Homo sapiens) [TaxId: 9606] [50056] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [50057] (2)
    6. alpha-Spectrin, SH3 domain [50058]
      1. Chicken (Gallus gallus) [TaxId: 9031] [50059] (21)
    7. IL-2 inducible T-cell (Itc) kinase [50060]
      1. Mouse (Mus musculus) [TaxId: 10090] [50061] (1)
    8. Hemapoetic cell kinase Hck [50062]
      1. Human (Homo sapiens) [TaxId: 9606] [50063] (6)
    9. Carboxyl-terminal src kinase (csk) [74654]
      1. Human (Homo sapiens) [TaxId: 9606] [74658] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [74655] (1)
    10. c-src protein tyrosine kinase [50064]
      1. Human (Homo sapiens) [TaxId: 9606] [50065] (5)
      2. Chicken (Gallus gallus) [TaxId: 9031] [50066] (9)
      3. Avian sarcoma virus [TaxId: 11876] [50067] (2)
        v-src
    11. Bruton's tyrosine kinase [50068]
      1. Human (Homo sapiens) [TaxId: 9606] [50069] (3)
      2. Mus musculus [TaxId: 10090] [159018] (2)
    12. tyrosine kinase tec [69246]
      1. Mouse (Mus musculus) [TaxId: 10090] [69247] (1)
    13. Growth factor receptor-bound protein 2 (GRB2), N- and C-terminal domains [50070]
      1. Human (Homo sapiens) [TaxId: 9606] [50071] (6)
      2. Mouse (Mus musculus) [TaxId: 10090] [50072] (5)
      3. Caenorhabditis elegans, SEM-5 [TaxId: 6239] [50073] (5)
        Sex muscle abnormal protein 5
    14. Grb2-related adaptor protein 2 (Mona/Gads) [89293]
      1. Mouse (Mus musculus) [TaxId: 10090] [89294] (5)
    15. Phospholipase C, SH3 domain [50074]
      1. Human (Homo sapiens) [TaxId: 9606] [50075] (2)
    16. p56-lck tyrosine kinase, SH3 domain [50076]
      1. Human (Homo sapiens) [TaxId: 9606] [50077] (10)
    17. 53BP2 [50078]
      1. Human (Homo sapiens) [TaxId: 9606] [50079] (1)
    18. Amphiphysin 2 [50080]
      synonyms: Myc box dependent interacting protein 1, bin1
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50081] (4)
    19. EPS8 SH3 domain [50082]
      1. Mouse (Mus musculus) [TaxId: 10090] [50083] (3)
    20. Vav N-terminal SH3 domain [63744]
      1. Mouse (Mus musculus) [TaxId: 10090] [63745] (3)
    21. Melanoma inhibitory activity protein [63746]
      1. Human (Homo sapiens) [TaxId: 9606] [63747] (3)
    22. Psd-95 [69248]
      associates with a guanylate kinase domain
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69249] (3)
    23. Actin binding protein ABP1 [74920]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74921] (2)
    24. p47pox (neutrophil cytosolic factor 1) [89295]
      1. Human (Homo sapiens) [TaxId: 9606] [89296] (5)
    25. p67phox [74922]
      1. Human (Homo sapiens) [TaxId: 9606] [74923] (1)
    26. Peroxisomal membrane protein Pex13p [82055]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82056] (5)
    27. Intersectin 2 (KIAA1256) [101669]
      1. Human (Homo sapiens) [TaxId: 9606] [101670] (5)
        SQ Q9NZM3 761-841, 897-957, 982-1037, 1055-1121, 1102-1186
    28. Hypothetical protein Baa76854.1 (KIAA1010) [101671]
      1. Human (Homo sapiens) [TaxId: 9606] [101672] (2)
    29. Olygophrenin-1 like protein (KIAA0621) [101673]
      1. Human (Homo sapiens) [TaxId: 9606] [101674] (1)
    30. Signal transducing adaptor molecule Stam2 [101675]
      1. Mouse (Mus musculus) [TaxId: 10090] [101676] (1)
    31. Rac/CDC42 GEF 6 [101677]
      1. Human (Homo sapiens) [TaxId: 9606] [101678] (1)
    32. Hypothetical protein YFR024c [101679]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101680] (2)
    33. Fyn-binding protein (T-cell adapter protein adap) [101681]
      1. Human (Homo sapiens) [TaxId: 9606] [101682] (1)
    34. SH3-like domain of the L-type calcium channel [110158]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [110159] (4)
        SQ P54288
      2. Rat (Rattus norvegicus) [TaxId: 10116] [110160] (3)
        SQ P54287 38-362
    35. BAI1-associated protein 2-like 1 (RIKEN cDNA 1300006m19) [110161]
      1. Mouse (Mus musculus) [TaxId: 10090] [110162] (1)
        SQ Q9DBJ3 343-401
    36. Kalirin-9a [117147]
      1. Mouse (Mus musculus) [TaxId: 10090] [117148] (1)
        SQ Q8BTT9 594-651
    37. RIM binding protein 2, RIMBP2 [117149]
      1. Human (Homo sapiens) [TaxId: 9606] [117150] (1)
        SQ O15034 160-242
    38. BZZ1 [141188]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141189] (1)
        SQ P38822 497-552
    39. Nck-2 [159019]
      1. Human (Homo sapiens) [TaxId: 9606] [159020] (1)
        SQ O43639 192-262
        unclassified SH3 domains of this protein species are: 1WX6, 2B86, 2FRW, 2FRY
3. Prokaryotic SH3-related domain [82057] (4)
  uperfamily
  1. GW domain [82058] (1)
    1. Internalin B, C-terminal domains [82059]
      duplication: tandem repeat of three SH3-like GW domains
      1. Listeria monocytogenes [TaxId: 1639] [82060] (1)
  2. PhnA-like [141190] (2)
    Pfam 03831
    1. Hypothetical protein PA0128, C-terminal domain [141191]
      1. Pseudomonas aeruginosa [TaxId: 287] [141192] (1)
        SQ Q9I704 40-113
    2. Hypothetical protein RPA4501 [141193]
      1. Rhodopseudomonas palustris [TaxId: 1076] [141194] (1)
        SQ Q6N1A7 1-72
  3. Spr N-terminal domain-like [141195] (1)
    1. Cell wall-associated hydrolase Spr N-terminal domain [141196]
      1. Nostoc punctiforme [TaxId: 272131] [141197] (3)
        SQ Q8YRR4 13-86
  4. Ply C-terminal domain-like [141198] (1)
    duplication: tandem repeat of two SH3-like domains swapped with the N-terminal strands; non-overlapping parts of sequence are covered by PfamB 062324 and PfamB 020199
    1. Endolysin Ply, C-terminal domain [141199]
      1. Bacteriophage Psa [TaxId: 171618] [141200] (1)
        SQ Q8W5Y8 181-314
4. Myosin S1 fragment, N-terminal domain [50084] (1)
  uperfamily
  1. Myosin S1 fragment, N-terminal domain [50085] (4)
    1. Myosin S1 fragment, N-terminal domain [50086]
      1. Chicken (Gallus gallus), pectoral muscle [TaxId: 9031] [50087] (4)
      2. Chicken (Gallus gallus), Va isoform [TaxId: 9031] [101683] (3)
      3. Bay scallop (Aequipecten irradians) [TaxId: 31199] [50088] (11)
        SQ P24733 3-836 ! SQ P24733 6-837
      4. Dictyostelium discoideum [TaxId: 44689] [50089] (21)
5. Tudor/PWWP/MBT [63748] (4)
  uperfamily
  1. Tudor domain [63749] (7)
    Pfam 00567
    1. Survival motor neuron protein 1, smn [63750]
      1. Human (Homo sapiens) [TaxId: 9606] [63751] (2)
    2. p53-binding protein 1, 53BP1 [110163]
      duplication; contains two Tudor domains in tandem
      1. Human (Homo sapiens) [TaxId: 9606] [110164] (6)
        SQ Q12888 1485-1602 ! SQ Q12888 1484-1606
    3. Tudor domain-containing protein 3, TDRD3 [141201]
      1. Mouse (Mus musculus) [TaxId: 10090] [141202] (1)
        SQ Q91W18 553-612
    4. Jumonji domain-containing protein 2A [141203]
      contains tandem repeat of two segment-swapped Tudor domains
      1. Human (Homo sapiens) [TaxId: 9606] [141204] (20)
        SQ O75164 897-955! SQ O75164 956-1011
    5. Tudor and KH domain-containing protein TDRKH [141205]
      1. Human (Homo sapiens) [TaxId: 9606] [141206] (1)
        SQ Q9Y2W6 329-425
    6. P100 co-activator, SND1 [141207]
      1. Human (Homo sapiens) [TaxId: 9606] [141208] (2)
        SQ Q7KZF4 705-794
    7. Lamin-b receptor [141209]
      1. Human (Homo sapiens) [TaxId: 9606] [141210] (1)
        SQ Q14739 1-55
  2. PWWP domain [69250] (6)
    includes the C-terminal all-alpha subdomain
    1. DNA methyltransferase DNMT3B [69251]
      1. Mouse (Mus musculus) [TaxId: 10090] [69252] (1)
    2. Hypothetical protein SPBC215.07c [89297]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [89298] (1)
    3. Hepatoma-derived growth factor, related protein 3 [101684]
      1. Mouse (Mus musculus) [TaxId: 10090] [101685] (1)
    4. Hepatoma-derived growth factor, HDGF [117151]
      1. Human (Homo sapiens) [TaxId: 9606] [117152] (3)
        SQ P51858 1-100
      2. Rat (Rattus norvegicus) [TaxId: 10116] [141211] (1)
        SQ Q8VHK7 1-110
    5. Histone-lysine N-methyltransferase NSD3 [141212]
      WHSC1L1
      1. Human (Homo sapiens) [TaxId: 9606] [141213] (1)
        SQ Q9BZ95 957-1053
  3. MBT repeat [89299] (4)
    Pfam 02820
    contains extended 'arm', N-terminal to the common fold core
    1. Scml2 protein [89300]
      duplication: contains tandem repeat of two MBT repeats
      1. Human (Homo sapiens) [TaxId: 9606] [89301] (7)
    2. Lethal(3)malignant brain tumor-like protein [101686]
      1. Human (Homo sapiens) [TaxId: 9606] [101687] (3)
    3. Lethal(3)malignant brain tumor-like 3 protein, L3MBTL3 (KIAA1798) [117153]
      1. Human (Homo sapiens) [TaxId: 9606] [117154] (2)
        SQ Q96JM7 259-372, 469-562
    4. Scm-like with four MBT domains protein 2, SFMBT2 (KIAA1617) [117155]
      1. Human (Homo sapiens) [TaxId: 9606] [117156] (1)
        SQ Q5VUG0 181-285
  4. CPH domain [159021] (1)
    1. Cullin-7 [159022]
      1. Human (Homo sapiens) [TaxId: 9606] [159023] (1)
        SQ Q14999 360-435
6. Chromo domain-like [54160] (3)
  SH3-like barrel is capped by a C-terminal helix
  uperfamily
  1. "Histone-like" proteins from archaea [54161] (2)
    1. DNA-binding protein [54162]
      1. Archaeon Sulfolobus solfataricus, Sso7d [TaxId: 2287] [54163] (8)
        SQ P61991
      2. Archaeon Sulfolobus acidocaldarius, Sac7d [TaxId: 2285] [54164] (10)
        SQ P13123
  2. Chromo domain [54165] (10)
    lacks the SH3-like barrel first strand that can be complemented by bound peptide ligand; in shadow chromo domain the corresponding site is altered by insertion; similarity to the IL8-like fold
    1. Heterochromatin protein 1, HP1 [54166]
      duplication: consists of two homologous domains, N-terminal chromo domain and C-terminal chromo shadow domain
      1. Mouse (Mus musculus), HP1 beta (MOD1, M31) [TaxId: 10090] [54167] (8)
      2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [75343] (3)
        SQ P05205 23-74
      3. Fission yeast (Schizosaccharomyces pombe), SWI6 [TaxId: 4896] [54169] (1)
    2. Polycomb protein, Pc [101688]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101689] (2)
    3. Histone methyltransferase clr4, chromo domain [64217]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [64218] (1)
    4. Chromobox protein homolog 8 [141214]
      Polycomb 3 homolog, Pc3
      1. Mouse (Mus musculus) [TaxId: 10090] [141215] (1)
        SQ Q9QXV1 7-58
    5. CpSRP43 [141216]
      Signal recognition particle 43 kDa protein, chloroplast precursor (CAO)
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141217] (6)
        SQ O22265 265-319! SQ O22265 320-373! SQ O22265 84-128
    6. Chromodomain protein, Y-like isoform [141218]
      1. Human (Homo sapiens) [TaxId: 9606] [141219] (1)
        SQ Q32NC5 1-66
    7. ATP-dependent helicase CHD1 (Chromo domain protein 1) [141220]
      1. Human (Homo sapiens) [TaxId: 9606] [141221] (25)
        SQ O14646 269-366! SQ O14646 270-355! SQ O14646 366-445! SQ O14646 367-443! SQ O14646 367-445
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141222] (2)
        SQ P32657 172-252! SQ P32657 249-347
  3. Chromo barrel domain [117157] (3)
    typical SH3-like barrel fold; similar sequence motif to the canonical chromo domain
    1. Probable histone acetyltransferase MYST1 [117158]
      1. Mouse (Mus musculus) [TaxId: 10090] [117159] (1)
        SQ Q9D1P2 49-169
    2. Putative histone acetyltransferase MOF [141223]
      Males-absent on the first protein
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [141224] (1)
        SQ O02193 367-454
    3. Mortality factor 4-like protein 1, MRG15 [141225]
      MORF-related gene 15 isoform 1
      1. Human (Homo sapiens) [TaxId: 9606] [141226] (7)
        SQ Q9UBU8 6-88
7. BAH domain [82061] (1)
  uperfamily
  1. BAH domain [82062] (1)
    1. Origin-recognition complex protein 120kDa subunit, Orc1p [82063]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82064] (3)
8. PAZ domain [101690] (1)
  uperfamily
  1. PAZ domain [101691] (5)
    1. Argonaute 2 [101692]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101693] (4)
        SQ Q9VUQ5 602-717 ! SQ Q9VUQ5 602-720
    2. Argonaute 1 [101694]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101695] (1)
    3. Eukaryotic translation initiation factor 2C 1, EIF2C1 [110165]
      1. Human (Homo sapiens) [TaxId: 9606] [110166] (2)
        SQ Q9UL18 225-349
    4. Argonaute homologue PF0537 [110167]
      includes the N-terminal domain
      1. Pyrococcus furiosus [TaxId: 2261] [110168] (3)
        SQ Q8U3D2
    5. Argonaute homologue Aq_1447 [141227]
      includes the N-terminal domain
      1. Aquifex aeolicus [TaxId: 63363] [141228] (6)
        SQ O67434 4-314
9. Cap-Gly domain [74924] (1)
  uperfamily
  1. Cap-Gly domain [74925] (12)
    Pfam 01302
    1. Cytoskeleton-associated protein F53F4.3 [74926]
      1. Caenorhabditis elegans [TaxId: 6239] [74927] (2)
        SQ Q20728 132-229
    2. Cylindromatosis tumour-suppressor Cyld [82065]
      1. Human (Homo sapiens) [TaxId: 9606] [82066] (3)
        SQ Q9NQC7 125-206, 228-304, 460-550
    3. Tubulin-specific chaperone B (SKAP1) [117160]
      1. Mouse (Mus musculus) [TaxId: 10090] [117161] (1)
        SQ Q9D1E6 134-233
    4. CLIP170-related 59kda protein CLIPR-59 (1500005P14Rik) [117162]
      1. Mouse (Mus musculus) [TaxId: 10090] [117163] (1)
        SQ Q9DB67 19-107
      2. Human (Homo sapiens) [TaxId: 9606] [141229] (1)
        SQ Q96DZ5 285-366
    5. Restin-like protein 2, Rsnl2 [117164]
      1. Mouse (Mus musculus) [TaxId: 10090] [117165] (2)
        SQ Q8CI96 266-354; 617-696
    6. CLIP-115 [141230]
      1. Human (Homo sapiens) [TaxId: 9606] [141231] (4)
        SQ Q9UDT6 219-289! SQ Q9UDT6 68-149
    7. Centrosome-associated protein 350 [141232]
      1. Human (Homo sapiens) [TaxId: 9606] [141233] (1)
        SQ Q5VT06 2473-2581
    8. Dynactin 1 [141234]
      1. Human (Homo sapiens) [TaxId: 9606] [141235] (6)
        SQ Q14203 1-99! SQ Q14203 25-98
    9. Restin [141236]
      1. Human (Homo sapiens) [TaxId: 9606] [141237] (3)
        SQ P30622 1-128! SQ P30622 181-340
      2. Mouse (Mus musculus) [TaxId: 10090] [141238] (1)
        SQ Q922J3 58-128
    10. Kinesin-like protein kif13b [141239]
      1. Human (Homo sapiens) [TaxId: 9606] [141240] (1)
        SQ Q9NQT8 1684-1771
10. Electron transport accessory proteins [50090] (4)
  uperfamily
  1. R67 dihydrofolate reductase [50091] (1)
    1. R67 dihydrofolate reductase [50092]
      1. Escherichia coli, plasmid PLZ1 [TaxId: 562] [50093] (6)
  2. Photosystem I accessory protein E (PsaE) [50094] (4)
    1. Photosystem I accessory protein E (PsaE) [50095]
      1. Cyanobacterium (Synechococcus sp.), pcc 7002 [TaxId: 1131] [50096] (2)
      2. Cyanobacterium (Synechocystis sp.), pcc 6803 [TaxId: 1143] [89302] (1)
      3. Cyanobacterium (Nostoc sp.), strain pcc8009 [TaxId: 1180] [50097] (2)
      4. Synechococcus elongatus [TaxId: 32046] [63752] (1)
  3. Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain [50098] (1)
    1. Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain [50099]
      1. Synechocystis sp. [TaxId: 1143] [50100] (6)
  4. Nitrile hydratase beta chain [50101] (3)
    contains irregular array of helices in the N-terminal extension
    1. Iron-containing nitrile hydratase [50102]
      1. Rhodococcus erythropolis [TaxId: 1833] [50103] (16)
        also Rhodococcus sp. R312
    2. Cobalt-containing nitrile hydratase [82067]
      1. Pseudonocardia thermophila [TaxId: 1848] [82068] (5)
        SQ Q7SID3
      2. Bacillus smithii [TaxId: 1479] [117166] (1)
        SQ Q84FS6 # 85% sequence identity; Bacillus sp. RAPc8 TaxID: 218609
11. Translation proteins SH3-like domain [50104] (7)
  many known members contain KOW motif
  uperfamily
  1. Ribosomal proteins L24p and L21e [50105] (5)
    1. Ribosomal proteins L24 (L24p) [50106]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [50107] (44)
        SQ P10972
      2. Escherichia coli [TaxId: 562] [141241] (30)
        SQ P60624 1-102
      3. Deinococcus radiodurans [TaxId: 1299] [159024] (7)
        SQ Q9RXJ1 4-113
      4. Thermus thermophilus [TaxId: 274] [159025] (11)
        SQ Q72I15 2-102
    2. Ribosomal proteins L21e [50108]
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [50109] (40)
        SQ P12734
  2. eIF5a N-terminal domain-like [50110] (7)
    1. Eukaryotic initiation translation factor 5a (eIF5a) [50111]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50112] (2)
      2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50113] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82069] (1)
      4. Leishmania infantum [TaxId: 5671] [110169] (1)
        SQ Q9N9V6
      5. Leishmania mexicana [TaxId: 5665] [117167] (1)
        SQ Q9N9V6 97% sequence identity
    2. Woronin body major protein (Hex1) [82070]
      1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82071] (1)
    3. Elongation factor P N-terminal domain [110170]
      1. Thermus thermophilus HB8 [TaxId: 300852] [110171] (1)
        SQ Q76G20
  3. C-terminal domain of ribosomal protein L2 [50114] (5)
    1. C-terminal domain of ribosomal protein L2 [50115]
      1. Bacillus stearothermophilus [TaxId: 1422] [50116] (2)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [50117] (40)
        SQ P20276
      3. Thermus thermophilus [TaxId: 274] [159026] (5)
        SQ Q72I07 126-272
      4. Escherichia coli [TaxId: 562] [159027] (27)
        SQ P60422 125-269
      5. Deinococcus radiodurans [TaxId: 1299] [159028] (5)
        SQ Q9RXJ9 128-272
  4. N-utilization substance G protein NusG, C-terminal domain [82072] (2)
    1. N-utilization substance G protein NusG, C-terminal domain [82073]
      1. Aquifex aeolicus [TaxId: 63363] [82074] (3)
      2. Thermus thermophilus [TaxId: 274] [101696] (1)
  5. SPT5 KOW domain-like [141242] (1)
    part of Pfam 00467
    1. Transcription elongation factor SPT5 [141243]
      1. Human (Homo sapiens) [TaxId: 9606] [141244] (1)
        SQ O00267 462-523
  6. Ribosomal protein L19 [141245] (3)
    Pfam 01245
    1. Ribosomal protein L19 [141246]
      1. Escherichia coli [TaxId: 562] [141247] (9)
        SQ P0A7K6 1-114
      2. Deinococcus radiodurans [TaxId: 1299] [159029] (6)
        SQ Q9RWB4 2-109
      3. Thermus thermophilus [TaxId: 274] [159030] (4)
        SQ P60490 1-138
  7. Ribosomal protein L14e [159031] (1)
    PfamB 032577
    1. Ribosomal protein L14e [159032]
      1. Sulfolobus solfataricus [TaxId: 2287] [159033] (1)
        SQ Q980C1 1-96
12. Cell growth inhibitor/plasmid maintenance toxic component [50118] (3)
  contains insert beta-sheet subdomain and C-terminal helix
  uperfamily
  1. CcdB [50119] (1)
    1. CcdB [50120]
      topoisomerase poison
      1. Escherichia coli [TaxId: 562] [50121] (6)
  2. Kid/PemK [82075] (3)
    1. Kid toxin protein (ParD) [82076]
      1. Plasmid R1, from Escherichia coli [TaxId: 2482] [82077] (3)
    2. MazF protein [89303]
      1. Escherichia coli [TaxId: 562] [89304] (1)
    3. PemK-like protein YdcE [82078]
      1. Bacillus subtilis [TaxId: 1423] [82079] (1)
  3. Rv2302-like [141248] (1)
    different orientation for the extra C-terminal helix relative the SH3-like barrel
    1. Hypothetical protein Rv2302/MT2359 [141249]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141250] (1)
        SQ P64983 1-80
13. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63433] (1)
  uperfamily
  1. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63434] (1)
    contains 5 short helices in the loop between the third and fourth strands
    1. Fumarylacetoacetate hydrolase, FAH, N-terminal domain [63435]
      1. Mouse (Mus musculus) [TaxId: 10090] [63436] (6)
14. DNA-binding domain of retroviral integrase [50122] (1)
  uperfamily
  1. DNA-binding domain of retroviral integrase [50123] (3)
    1. DNA-binding domain of retroviral integrase [50124]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [50125] (4)
      2. Rous sarcoma virus RSV [TaxId: 11886] [50126] (2)
      3. Simian immunodeficiency virus [TaxId: 11723] [50127] (1)
15. Hypothetical protein YfhH [101697] (1)
  contains extra N-terminal all-alpha subdomain
  uperfamily
  1. Hypothetical protein YfhH [101698] (1)
    1. Hypothetical protein YfhH [101699]
      1. Bacillus subtilis [TaxId: 1423] [101700] (1)
16. Kinase-associated protein B-like [141251] (1)
  contains extra C-terminal alpha-hairpin
  uperfamily
  1. Kinase-associated protein B-like [141252] (1)
    1. Kinase-associated protein B [141253]
      1. Bacillus cereus [TaxId: 1396] [141254] (2)
        SQ Q816F1 4-127
        BC4909
17. YccV-like [141255] (1)
  contains extra C-terminal helix packed against barrel
  uperfamily
  1. YccV-like [141256] (1)
    1. Hypothetical protein YccV [141257]
      1. Escherichia coli [TaxId: 562] [141258] (1)
        SQ P0AB20 21-114
18. CarD-like [141259] (1)
  uperfamily
  1. CarD-like [141260] (1)
    Pfam 02559
    1. Transcription-repair coupling factor, RRCF, middle domain [141261]
      1. Escherichia coli [TaxId: 562] [141262] (2)
        SQ P30958 466-545
19. Mib/herc2 domain-like [159034] (1)
  1. Mib/herc2 domain [159035] (1)
    Pfam 06701
    1. E3 ubiquitin-protein ligase hectd1 [159036]
      1. Human (Homo sapiens) [TaxId: 9606] [159037] (1)
        SQ Q9ULT8 1268-1340
20. YorP-like [159038] (1)
  1. YorP-like [159039] (1)
    Pfam 09629
    1. Uncharacterized protein YorP [159040]
      1. Bacillus subtilis [TaxId: 1423] [159041] (1)
        SQ O31898 1-71
21. Plus3-like [159042] (1)
  1. Plus3 [159043] (1)
    Pfam 03126
    1. RNA polymerase-associated protein RTF1 homolog [159044]
      1. Human (Homo sapiens) [TaxId: 9606] [159045] (2)
        SQ Q92541 307-442! SQ Q92541 313-444
GroES-like [50128] (2)
contains barrel, partly opened; n*=4, S*=8; meander
1. GroES-like [50129] (2)
  uperfamily
  1. GroES [50130] (5)
    1. Chaperonin-10 (GroES) [50131]
      1. Escherichia coli [TaxId: 562] [50132] (31)
      2. Mycobacterium tuberculosis [TaxId: 1773] [63753] (2)
      3. Mycobacterium leprae [TaxId: 1769] [50133] (1)
      4. Thermus thermophilus [TaxId: 274] [110172] (3)
        SQ P61493 ! SQ P61492
    2. GP31 co-chaperonin [50134]
      1. Bacteriophage T4 [TaxId: 10665] [50135] (8)
  2. Alcohol dehydrogenase-like, N-terminal domain [50136] (27)
    C-terminal domain is alpha/beta (classical Rossmann-fold)
    1. Alcohol dehydrogenase [50137]
      contains a Zn-finger subdomain, residues 94-117
      1. Horse (Equus caballus) [TaxId: 9796] [50138] (38)
        SQ P00327
      2. Human (Homo sapiens), different isozymes [TaxId: 9606] [50139] (26)
        SQ P00326 ! SQ P00325 ! SQ P07327
      3. Mouse (Mus musculus), class II [TaxId: 10090] [50140] (3)
      4. Frog (Rana perezi) [TaxId: 8403] [89305] (2)
      5. Cod (Gadus callarias) [TaxId: 8053] [50141] (1)
      6. Archaeon Sulfolobus solfataricus [TaxId: 2287] [82080] (4)
      7. Archaeon Aeropyrum pernix [TaxId: 56636] [101701] (1)
      8. Pseudomonas aeruginosa [TaxId: 287] [101702] (1)
      9. Bacillus stearothermophilus [TaxId: 1422] [101703] (1)
    2. Hypothetical protein TM0436 [101704]
      1. Thermotoga maritima [TaxId: 2336] [101705] (1)
    3. Hypothetical protein YhdH [101706]
      1. Escherichia coli [TaxId: 562] [101707] (2)
        SQ P26646
    4. Hypothetical protein YahK [101708]
      1. Escherichia coli [TaxId: 562] [101709] (1)
    5. Benzyl alcohol dehydrogenase [89306]
      1. Acinetobacter calcoaceticus [TaxId: 471] [89307] (1)
    6. Bacterial secondary alcohol dehydrogenase [50142]
      1. Clostridium beijerinckii [TaxId: 1520] [50143] (3)
      2. Thermoanaerobacter brockii [TaxId: 29323] [50144] (10)
    7. Ketose reductase (sorbitol dehydrogenase) [50145]
      1. Silverleaf whitefly (Bemisia argentifolii) [TaxId: 77855] [50146] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [101710] (3)
    8. Formaldehyde dehydrogenase [82081]
      1. Pseudomonas putida [TaxId: 303] [82082] (1)
    9. Quinone oxidoreductase [50147]
      1. Escherichia coli [TaxId: 562] [50148] (1)
      2. Thermus thermophilus [TaxId: 274] [89308] (2)
      3. Human (Homo sapiens) [TaxId: 9606] [117168] (1)
        SQ Q08257
    10. 2,4-dienoyl-CoA reductase [89309]
      1. Yeast (Candida tropicalis) [TaxId: 5482] [89310] (5)
    11. Putative zinc-binding alcohol dehydrogenase [101711]
      1. Mouse (Mus musculus) [TaxId: 10090] [101712] (1)
    12. Cinnamyl alcohol dehydrogenase, ADH6 [110173]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110174] (3)
        SQ Q04894
    13. Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase [110175]
      1. Guinea pig (Cavia porcellus) [TaxId: 10141] [110176] (5)
        SQ Q9EQZ5
    14. B. subtilis YhfP homologue [117169]
      1. Bacillus stearothermophilus [TaxId: 1422] [117170] (1)
        SQ Q5L022; 96% sequence identity; Geobacillus kaustophilus TaxID:1462
    15. Hypothetical protein YhfP [117171]
      1. Bacillus subtilis [TaxId: 1423] [117172] (2)
        SQ O07615
2. SacY-like RNA-binding domain [50151] (1)
  uperfamily
  1. BglG-like antiterminator proteins [50152] (2)
    1. SacY [50153]
      1. Bacillus subtilis [TaxId: 1423] [50154] (1)
    2. LicT [74928]
      1. Bacillus subtilis [TaxId: 1423] [74929] (1)
PDZ domain-like [50155] (1)
contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix
1. PDZ domain-like [50156] (6)
  peptide-binding domain
  uperfamily
  1. PDZ domain [50157] (55)
    Pfam 00595
    1. Discs large protein homolog [50158]
      1. Human (Homo sapiens) [TaxId: 9606] [50159] (4)
    2. Cask/Lin-2 [50160]
      1. Human (Homo sapiens) [TaxId: 9606] [50161] (1)
    3. Synapse-associated protein 102 [101713]
      1. Human (Homo sapiens) [TaxId: 9606] [101714] (2)
    4. Synaptic protein PSD-95 [50162]
      Synonym: synapse associated protein 90, sap90
      duplication: contains three PDZ domains
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50163] (9)
        SQ P31016 62-154
      2. Human (Homo sapiens) [TaxId: 9606] [74932] (1)
    5. Syntrophin [50164]
      1. Mouse (Mus musculus) [TaxId: 10090] [50165] (3)
    6. Syntenin 1 [89311]
      1. Human (Homo sapiens) [TaxId: 9606] [89312] (26)
    7. Segment polarity protein dishevelled homolog Dvl-2 [89313]
      1. African clawed frog (Xenopus laevis) [TaxId: 8355] [89314] (5)
      2. Mouse (Mus musculus) [TaxId: 10090] [101715] (1)
    8. Neuronal nitric oxide synthase, NNOS [50166]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50167] (3)
    9. Phosphatase hPTP1e [50168]
      1. Human (Homo sapiens) [TaxId: 9606] [50169] (3)
      2. Mouse (Mus musculus) [TaxId: 10090] [74930] (3)
    10. Na+/H+ exchanger regulatory factor, NHERF [63754]
      1. Human (Homo sapiens) [TaxId: 9606] [63755] (4)
    11. Inad [63756]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63757] (1)
    12. Glutamate receptor interacting protein [82083]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82084] (3)
      2. Mouse (Mus musculus) [TaxId: 10090] [110177] (1)
        SQ Q925T6 461-570
    13. Erbin [82085]
      1. Human (Homo sapiens) [TaxId: 9606] [82086] (5)
    14. GTPase-binding domain of the cell polarity protein par6 (Par-6B) [89315]
      1. Mouse (Mus musculus) [TaxId: 10090] [89316] (1)
      2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101716] (3)
        SQ O97111 156-253; Cg5884-pa
    15. Glutamate receptor-interacting protein 1, GRIP1 [101717]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [101718] (2)
    16. Membrane associated guanylate kinase inverted-2 (MAGI-2, KIAA0705) [101719]
      1. Human (Homo sapiens) [TaxId: 9606] [101720] (5)
        SQ Q86UL8 412-522, 600-682, 774-865, 913-1015, 1141-1230
    17. KIAA1526 protein [101721]
      1. Human (Homo sapiens) [TaxId: 9606] [101722] (3)
    18. Hypothetical protein KIAA1095 [101723]
      1. Human (Homo sapiens) [TaxId: 9606] [101724] (2)
        SQ Q9UPQ7 246-339, 404-512
    19. Discs large 5 protein KIAA0583 [101725]
      1. Human (Homo sapiens) [TaxId: 9606] [101726] (1)
    20. Hypothetical protein KIAA0559 [101727]
      1. Human (Homo sapiens) [TaxId: 9606] [101728] (1)
    21. Hypothetical protein KIAA1849 [101729]
      1. Human (Homo sapiens) [TaxId: 9606] [101730] (1)
    22. Scribble (KIAA0147) [101731]
      1. Human (Homo sapiens) [TaxId: 9606] [101732] (3)
        SQ Q14160 680-951, 1096-1193 # structure of 1st PDZ domain is also known, 1XQ5
    23. Shank1, PDZ domain [101733]
      SH3 and multiple ankyrin repeat domains protein 1
      1. Rat (Rattus norvegicus) [TaxId: 10116] [101734] (2)
    24. Zasp (Cypher, Oracle 1) [101735]
      1. Human (Homo sapiens) [TaxId: 9606] [101736] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [117173] (1)
        SQ Q9D130 1-83
    25. Alpha-actinin-2 associated LIM protein [110178]
      1. Mouse (Mus musculus) [TaxId: 10090] [110179] (1)
        SQ O70209 4-93
    26. Glutamate receptor interacting protein 2, GRIP2 (KIAA1719) [110180]
      1. Human (Homo sapiens) [TaxId: 9606] [110181] (2)
        SQ Q9C0E4 238-341
    27. Harmonin [110182]
      1. Mouse (Mus musculus) [TaxId: 10090] [110183] (1)
        SQ Q9ES64 741-850
      2. Human (Homo sapiens) [TaxId: 9606] [141263] (1)
        SQ Q9Y6N9 201-301
    28. Rhophilin-2 [110184]
      1. Mouse (Mus musculus) [TaxId: 10090] [110185] (1)
        SQ Q8BWR8 506-603
    29. PDZ-LIM protein mystique [110186]
      1. Mouse (Mus musculus) [TaxId: 10090] [110187] (1)
        SQ Q8R1G6 3-83
    30. Enigma homolog ENH [117174]
      1. Mouse (Mus musculus) [TaxId: 10090] [117175] (1)
        SQ Q8CI51 5-94
    31. DNA Regulating synaptic membrane exocytosis protein 2, RIMS2 [117176]
      1. Human (Homo sapiens) [TaxId: 9606] [117177] (1)
        SQ Q9UQ26 637-754; the structure of the 1st C2 domain (807-934) is also known (scop_sp 101565)
    32. Partitioning-defective 3-like protein, PAR3-L (RIKEN cDNA 2810455b10) [117178]
      1. Mouse (Mus musculus) [TaxId: 10090] [117179] (1)
        SQ Q5SV53 478-591
    33. Regulator of G-protein signaling 3, RGS3 [117180]
      1. Mouse (Mus musculus) [TaxId: 10090] [117181] (1)
        SQ Q9DC04 18-94
      2. Human (Homo sapiens) [TaxId: 9606] [141264] (2)
        SQ P49796 300-376
    34. PDZ domain containing protein 11, Pdzk11 [117182]
      1. Mouse (Mus musculus) [TaxId: 10090] [117183] (1)
        SQ Q9CZG9 37-127
    35. hypothetical PDZ domain containing protein Uqcrc2 (4930408O21Rik) [117184]
      1. Mouse (Mus musculus) [TaxId: 10090] [117185] (1)
        SQ Q9CR71 8-120
    36. Tight junction protein ZO-2, Tjp2 [141265]
      1. Mouse (Mus musculus) [TaxId: 10090] [141266] (1)
        SQ Q9Z0U1 1-104
    37. Multiple PDZ domain protein [141267]
      1. Human (Homo sapiens) [TaxId: 9606] [141268] (4)
        SQ Q5VZ62 1138-1243! SQ Q5VZ62 1955-2042
    38. Afadin [141269]
      1. Human (Homo sapiens) [TaxId: 9606] [141270] (3)
        SQ P55196 985-1079! SQ P55196 987-1077
    39. Syntaxin binding protein 4 [141271]
      1. Mouse (Mus musculus) [TaxId: 10090] [141272] (1)
        SQ Q9WV89 12-107
    40. Channel associated protein of synapse-110 [141273]
      Discs large homolog 2, PSD-93
      1. Human (Homo sapiens) [TaxId: 9606] [141274] (1)
        SQ Q15700 190-283
    41. Maguk p55 subfamily member 5 [141275]
      1. Mouse (Mus musculus) [TaxId: 10090] [141276] (1)
        SQ Q9JLB2 236-335
        Structure of the second L27 domain is known (scop_sp 101293)
    42. Neurabin-i [141277]
      1. Human (Homo sapiens) [TaxId: 9606] [141278] (1)
        SQ Q9ULJ8 500-593
    43. Regulating synaptic membrane exocytosis protein 1, RIMS1 [141279]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141280] (1)
        SQ Q9JIR4 597-705
      2. Human (Homo sapiens) [TaxId: 9606] [141281] (1)
        SQ Q86UR5 585-694
    44. Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11) [141282]
      1. Human (Homo sapiens) [TaxId: 9606] [141283] (7)
        SQ Q02410 656-740! SQ Q02410 657-743! SQ Q02410 657-745! SQ Q02410 743-822! SQ Q02410 745-823! SQ Q02410 746-839
        structure of the PTB domain is also known (scop_sp 50757)
    45. Presynaptic protein sap97 [141284]
      PSD-95 homologue
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141285] (1)
        SQ Q62696 221-313
    46. Tyrosine-protein phosphatase non-receptor type 4, PTPN4 [141286]
      1. Human (Homo sapiens) [TaxId: 9606] [141287] (1)
        SQ P29074 507-612
  2. Tail specific protease PDZ domain [68933] (2)
    1. Photosystem II D1 C-terminal processing protease [68934]
      1. Algae (Scenedesmus obliquus) [TaxId: 3088] [50171] (4)
    2. Tricorn protease [69253]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69254] (4)
  3. HtrA-like serine proteases [74933] (4)
    1. Protease Do (DegP, HtrA), C-terminal domains [74934]
      duplication: tandem repeat of two PDZ domains
      1. Escherichia coli [TaxId: 562] [74935] (27)
    2. Mitochondrial serine protease HtrA2 [74936]
      1. Human (Homo sapiens) [TaxId: 9606] [74937] (3)
    3. Stress sensor protease DegS, C-terminal domain [110188]
      1. Escherichia coli [TaxId: 562] [110189] (7)
        SQ P31137 37-354 ! SQ P31137
    4. Protease PepD [141288]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141289] (6)
        SQ O53896 375-462
        Rv0983
  4. Interleukin 16 [50172] (1)
    1. Interleukin 16 [50173]
      1. Human (Homo sapiens) [TaxId: 9606] [50174] (2)
  5. EpsC C-terminal domain-like [159046] (1)
    PfamB 005596
    1. General secretion pathway protein C, EpsC [159047]
      1. Vibrio cholerae [TaxId: 666] [159048] (3)
        SQ P45777 204-305! SQ P45777 219-305
  6. MTH1368 C-terminal domain-like [159049] (1)
    middle part of Pfam 02163
    1. Uncharacterized protein MTH1368 [159050]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [159051] (1)
        SQ O27421 208-310
N-terminal domains of the minor coat protein g3p [50175] (1)
core: barrel, in some members open; n*=4, S*=8; meander
1. N-terminal domains of the minor coat protein g3p [50176] (1)
  uperfamily
  1. N-terminal domains of the minor coat protein g3p [50177] (2)
    1. N-terminal domains of the minor coat protein g3p [50178]
      duplication: the two domains share a common fold
      1. Bacteriophage M13 [TaxId: 10870] [50179] (2)
      2. Bacteriophage fd [TaxId: 10864] [50180] (2)
Sm-like fold [50181] (5)
core: barrel, open; n*=4, S*=8; meander; SH3-like topology
1. Sm-like ribonucleoproteins [50182] (6)
  uperfamily
  1. Sm motif of small nuclear ribonucleoproteins, SNRNP [50183] (13)
    forms homo and heteroheptameric ring structures
    1. D1 core SNRNP protein [50184]
      1. Human (Homo sapiens) [TaxId: 9606] [50185] (1)
    2. D2 core SNRNP protein [50186]
      1. Human (Homo sapiens) [TaxId: 9606] [50187] (1)
    3. D3 core SNRNP protein [50188]
      1. Human (Homo sapiens) [TaxId: 9606] [50189] (1)
    4. B core SNRNP protein [50190]
      1. Human (Homo sapiens) [TaxId: 9606] [50191] (1)
    5. Small nuclear ribonucleoprotein F, Smf [82087]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82088] (2)
    6. Archaeal homoheptameric Sm protein [63758]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [63759] (5)
        MTH649, smap1
      2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [63760] (2)
        smap1
      3. Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234] [63761] (2)
      4. Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234] [74938] (1)
      5. Archaeon Pyrococcus abyssi [TaxId: 29292] [82089] (2)
      6. Sulfolobus solfataricus [TaxId: 2287] [141290] (14)
        SQ Q97ZQ0 1-76
        SnRNP-2
    7. Sm-Like archaeal protein Smap3 [89317]
      contains additional C-terminal alpha+beta domain
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [89318] (1)
    8. U6 snRNA-associated sm-like protein LSM5 [141291]
      1. Cryptosporidium parvum [TaxId: 5807] [141292] (2)
        SQ Q5CXX3 24-115
  2. Pleiotropic translational regulator Hfq [74939] (3)
    forms homohexameric ring structures
    1. Pleiotropic translational regulator Hfq [74940]
      1. Staphylococcus aureus [TaxId: 1280] [74941] (2)
      2. Escherichia coli [TaxId: 562] [89319] (1)
      3. Pseudomonas aeruginosa [TaxId: 287] [141293] (12)
        SQ Q9HUM0 6-71
  3. Mechanosensitive channel protein MscS (YggB), middle domain [82090] (1)
    1. Mechanosensitive channel protein MscS (YggB), middle domain [82091]
      forms homoheptameric ring structure very similar to those of the archaeal and eukaryotic Sm proteins
      1. Escherichia coli [TaxId: 562] [82092] (14)
  4. PF1955-like [141294] (1)
    homohexadecameric assembly: two stacked octameric rings
    1. Hypothetical protein PF1955 [141295]
      1. Pyrococcus furiosus [TaxId: 2261] [141296] (4)
        SQ Q8TZN2 5-70
  5. LSM14 N-terminal domain-like [141297] (1)
    1. LSM14 homolog A (Lsm14a) [141298]
      1. Zebrafish (Danio rerio) [TaxId: 7955] [141299] (2)
        SQ Q6P111 6-85
  6. YgdI/YgdR-like [159052] (6)
    Pfam 06004; DUF903, putative lipoprotein; both homohexameric and homoheptameric ring assemblies are observed in the crystals
    1. Uncharacterized protein SO0963 [159053]
      1. Shewanella oneidensis [TaxId: 70863] [159054] (2)
        SQ Q8EI81 25-76
    2. Uncharacterized protein YgdI [159055]
      1. Salmonella typhimurium [TaxId: 90371] [159056] (6)
        SQ Q7CPV8 23-75
    3. Uncharacterized protein ECA1013 [159057]
      1. Erwinia carotovora [TaxId: 554] [159058] (7)
        SQ Q6D8G1 21-73
    4. Putative outer membrane lipoprotein STM1585 [159059]
      1. Salmonella typhimurium [TaxId: 90371] [159060] (3)
        SQ Q7CQI7 22-73
    5. Uncharacterized protein PSPPH2109 [159061]
      1. Pseudomonas syringae [TaxId: 317] [159062] (1)
        SQ Q48JU9 23-74
    6. Hypothetical lipoprotein YgdR [159063]
      1. Escherichia coli [TaxId: 562] [159064] (1)
        SQ P65294 23-72
2. YhbC-like, C-terminal domain [74942] (1)
  uperfamily
  1. YhbC-like, C-terminal domain [74943] (1)
    1. Hypothetical protein SP14.3 (SP0552) [74944]
      1. Streptococcus pneumoniae [TaxId: 1313] [74945] (1)
3. GatD N-terminal domain-like [141300] (1)
  uperfamily
  1. GatD N-terminal domain-like [141301] (2)
    PfamB 010580
    1. Glutamyl-tRNA(Gln) amidotransferase subunit D, GatD [141302]
      1. Pyrococcus abyssi [TaxId: 29292] [141303] (2)
        SQ Q9V0T9 2-75
      2. Methanobacterium thermoautotrophicum [TaxId: 145262] [141304] (2)
        SQ O26802 2-73
4. Dom34/Pelota N-terminal domain-like [159065] (1)
  1. Dom34/Pelota N-terminal domain-like [159066] (2)
    Warning: Pfam incorrectly assigns this domain to the same family as the structurally unrelated N-terminal domain of eRF1 (Pfam 03463)
    1. Cell division protein pelota [159067]
      1. Thermoplasma acidophilum [TaxId: 2303] [159068] (1)
        SQ Q9HJ74 1-126
    2. Dom34 [159069]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159070] (3)
        SQ P33309 1-135
5. TrmB C-terminal domain-like [159071] (1)
  sugar-binding domain; permuted OB-fold?
  1. TrmB C-terminal domain-like [159072] (1)
    C-terminal part of PfamB 004822
    1. Transcriptional regulator TrmB [159073]
      1. Thermococcus litoralis [TaxId: 2265] [159074] (1)
        SQ Q7LYW4 247-338
SspB-like [101737] (1)
core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
1. SspB-like [101738] (2)
  uperfamily
  1. Stringent starvation protein B, SspB [101739] (2)
    1. Stringent starvation protein B, SspB [101740]
      a specificity-enhancing factor for the ClpXP proteolytic machine
      1. Escherichia coli [TaxId: 562] [101741] (6)
      2. Haemophilus influenzae [TaxId: 727] [101742] (7)
        SQ P45206 5-110
  2. AGR_C_3712p-like [159075] (1)
    Pfam 07031; DUF1321
    1. Uncharacterized protein AGR_C_3712p [159076]
      1. Agrobacterium tumefaciens [TaxId: 358] [159077] (2)
        SQ Q8U561 3-119
Rof/RNase P subunit-like [101743] (1)
core: barrel, open; n*=4, S*=8; meander; SH3-like topology; some similarity to the Sm-like fold
1. Rof/RNase P subunit-like [101744] (2)
  uperfamily
  1. RNase P subunit p29-like [101745] (3)
    two available NMR structures display similar topologies but different barrel shapes
    the barrel shape of the full-length X-ray structures of AF1917 differs from both earlier NMR structures
    1. Hypothetical protein AF1917 [101746]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [101747] (3)
        SQ O28362
    2. Hypothetical protein MTH11 [101748]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101749] (1)
    3. Hypothetical protein PH1771 [117186]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [117187] (1)
        SQ O59425
  2. Rof-like [141305] (1)
    Pfam 07073; ROF
    1. Inhibitor of Rho Rof [141306]
      formerly hypothetical protein YaeO
      1. Escherichia coli [TaxId: 562] [141307] (1)
        SQ P0AFW8 1-86
Hydrophobin II, HfbII [101750] (1)
core: barrel, closed; n=4, S=8; complex topology; helix-containing crossover connection
1. Hydrophobin II, HfbII [101751] (1)
  uperfamily
  1. Hydrophobin II, HfbII [101752] (1)
    a self-assembling amphiphile
    1. Hydrophobin II, HfbII [101753]
      1. Trichoderma reesei [TaxId: 51453] [101754] (13)
Ribosomal protein L14 [50192] (1)
barrel, closed; n=5, S=8, meander
1. Ribosomal protein L14 [50193] (1)
  uperfamily
  1. Ribosomal protein L14 [50194] (5)
    1. Ribosomal protein L14 [50195]
      1. Bacillus stearothermophilus [TaxId: 1422] [50196] (5)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [50197] (42)
        SQ P22450
      3. Thermus thermophilus [TaxId: 274] [141308] (9)
        SQ Q5SHP8 1-122
      4. Escherichia coli [TaxId: 562] [159078] (29)
        SQ P02411 2-122
      5. Deinococcus radiodurans [TaxId: 1299] [159079] (6)
        SQ Q9RXJ2 1-134
OB-fold [50198] (16)
barrel, closed or partly opened n=5, S=10 or S=8; greek-key
1. Staphylococcal nuclease [50199] (1)
  uperfamily
  1. Staphylococcal nuclease [50200] (1)
    barrel, closed; n=5, S=10
    1. Staphylococcal nuclease [50201]
      1. Staphylococcus aureus [TaxId: 1280] [50202] (68)
        SQ P00644 89-223
2. Bacterial enterotoxins [50203] (2)
  uperfamily
  1. Bacterial AB5 toxins, B-subunits [50204] (9)
    1. Heat-labile toxin [50205]
      1. Escherichia coli, type IB [TaxId: 562] [50206] (29)
      2. Escherichia coli, type IIB [TaxId: 562] [50207] (3)
    2. Cholera toxin [50208]
      barrel, partly opened; n*=5, S*=10
      1. Vibrio cholerae [TaxId: 666] [50209] (33)
        SQ P01556 22-124
    3. Verotoxin-1/shiga-toxin, B-pentamer [50210]
      phage-borne toxin; bacteriophages H30 and H19B
      1. Escherichia coli [TaxId: 562] [50211] (22)
      2. Shigella dysenteriae, toxin I [TaxId: 622] [50212] (3)
        identical sequence with verotoxin-1 B
      3. Shigella dysenteriae, toxin II [TaxId: 622] [101755] (6)
    4. Pertussis toxin S2/S3 subunits, C-terminal domain [50213]
      N-terminal domain in S2/S3 has C-lectin-like fold
      1. Bordetella pertussis [TaxId: 520] [50214] (3)
    5. Pertussis toxin S4 subunit [50215]
      1. Bordetella pertussis [TaxId: 520] [50216] (3)
    6. Pertussis toxin S5 subunit [50217]
      1. Bordetella pertussis [TaxId: 520] [50218] (3)
  2. Superantigen toxins, N-terminal domain [50219] (15)
    1. Staphylococcal enterotoxin A, SEA [50220]
      1. Staphylococcus aureus [TaxId: 1280] [50221] (6)
    2. Staphylococcal enterotoxin C2, SEC2 [50222]
      1. Staphylococcus aureus [TaxId: 1280] [50223] (8)
    3. Toxic shock syndrome toxin-1 (TSST-1) [50224]
      1. Staphylococcus aureus [TaxId: 1280] [50225] (13)
    4. Staphylococcal enterotoxin B, SEB [50226]
      1. Staphylococcus aureus [TaxId: 1280] [50227] (12)
    5. Staphylococcal enterotoxin C3, SEC3 [50228]
      1. Staphylococcus aureus [TaxId: 1280] [50229] (11)
        SQ P23313
    6. Staphylococcal enterotoxin H, SEH [50230]
      1. Staphylococcus aureus [TaxId: 1280] [50231] (4)
    7. Superantigen-like protein SET3 [74946]
      1. Staphylococcus aureus [TaxId: 1280] [74947] (3)
    8. Streptococcal superantigen Spe-C [50232]
      1. Streptococcus pyogenes [TaxId: 1314] [50233] (3)
    9. Streptococcal superantigen Spe-H [50234]
      1. Streptococcus pyogenes [TaxId: 1314] [50235] (2)
    10. Streptococcal superantigen Smez-2 [50236]
      1. Streptococcus pyogenes [TaxId: 1314] [50237] (2)
    11. Streptococcal superantigen SSA [50238]
      1. Streptococcus pyogenes [TaxId: 1314] [50239] (10)
    12. Streptococcal pyrogenic exotoxin A1 [50240]
      1. Streptococcus pyogenes [TaxId: 1314] [50241] (8)
        SQ P08095
    13. Exotoxin 1 (SET1, Superantigen-like protein 7) [110190]
      1. Staphylococcus aureus [TaxId: 1280] [110191] (2)
        SQ Q9ZFS5 36-231
    14. Streptococcal pyrogenic exotoxin Spe-J [110192]
      1. Streptococcus pyogenes [TaxId: 1314] [110193] (2)
        SQ Q7BAE3
    15. Enterotoxin type I, SEI [159080]
      1. Staphylococcus aureus [TaxId: 1280] [159081] (1)
        SQ Q52T95 4-86
3. TIMP-like [50242] (3)
  uperfamily
  1. Tissue inhibitor of metalloproteinases, TIMP [50243] (3)
    contains an irregular alpha+beta subdomain in the C-terminal extension
    1. TIMP-1 [50244]
      1. Human (Homo sapiens) [TaxId: 9606] [50245] (6)
    2. TIMP-2 [50246]
      1. Human (Homo sapiens) [TaxId: 9606] [50247] (3)
      2. Cow (Bos taurus) [TaxId: 9913] [50248] (3)
  2. Netrin-like domain (NTR/C345C module) [89320] (2)
    Pfam 01759
    1. Procollagen c-proteinase enhancer protein PCOLCE [89321]
      1. Human (Homo sapiens) [TaxId: 9606] [89322] (1)
    2. Complement C5 domain [117188]
      1. Human (Homo sapiens) [TaxId: 9606] [117189] (1)
        SQ P01031 1530-1676 # structure of the C5a anaphylotoxin domain (679-751) is also known (scop_sp 47689)
  3. The laminin-binding domain of agrin [63767] (1)
    1. The laminin-binding domain of agrin [63768]
      1. Chicken (Gallus gallus) [TaxId: 9031] [63769] (3)
        SQ Q90685 # ! Fragment
4. Heme chaperone CcmE [82093] (1)
  uperfamily
  1. Heme chaperone CcmE [82094] (2)
    1. Heme chaperone CcmE [82095]
      1. Escherichia coli [TaxId: 562] [82096] (1)
      2. Shewanella putrefaciens [TaxId: 24] [82097] (2)
5. gp5 N-terminal domain-like [69255] (1)
  uperfamily
  1. gp4 N-terminal domain-like [69256] (2)
    1. Tail-associated lysozyme gp5, N-terminal domain [69257]
      1. Bacteriophage T4 [TaxId: 10665] [69258] (1)
    2. Hypothetical protein c3393 [159082]
      1. Escherichia coli o6 [TaxId: 217992] [159083] (1)
        SQ Q8FED2 378-468
6. Hypothetical protein YgiW [101756] (1)
  uperfamily
  1. Hypothetical protein YgiW [101757] (1)
    Pfam 04076, Domain of unknown function DUF388
    1. Hypothetical protein YgiW [101758]
      1. Escherichia coli [TaxId: 562] [101759] (1)
7. Nucleic acid-binding proteins [50249] (16)
  uperfamily
  1. Anticodon-binding domain [50250] (7)
    barrel, closed; n=5, S=10
    1. Aspartyl-tRNA synthetase (AspRS) [50251]
      this is N-terminal domain in prokaryotic enzymes and the first "visible" domain in eukaryotic enzymes
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50252] (3)
      2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [50253] (1)
      3. Thermus thermophilus, AspRS-2 [TaxId: 274] [89323] (1)
        non-discriminating and archaeal-type enzyme
      4. Escherichia coli [TaxId: 562] [50254] (3)
      5. Thermus thermophilus, AspRS-1 [TaxId: 274] [50255] (3)
    2. Lysyl-tRNA synthetase (LysRS) [50256]
      1. Escherichia coli, gene lysS [TaxId: 562] [50257] (4)
      2. Escherichia coli, gene lysU [TaxId: 562] [50258] (5)
  2. RecG "wedge" domain [69259] (1)
    1. RecG "wedge" domain [69260]
      1. Thermotoga maritima [TaxId: 2336] [69261] (1)
  3. DNA helicase RuvA subunit, N-terminal domain [50259] (3)
    barrel, closed; n=5, S=10
    1. DNA helicase RuvA subunit, N-terminal domain [50260]
      tetramer; binds Holliday junction
      1. Escherichia coli [TaxId: 562] [50261] (5)
      2. Mycobacterium leprae [TaxId: 1769] [50262] (1)
      3. Thermus thermophilus [TaxId: 274] [82098] (1)
  4. Single strand DNA-binding domain, SSB [50263] (17)
    barrel, closed; n=5, S=10
    1. ssDNA-binding protein [50264]
      1. Human (Homo sapiens), mitochondria [TaxId: 9606] [50265] (4)
        SQ Q04837
      2. Escherichia coli [TaxId: 562] [50266] (5)
        SQ P02339
      3. Mycobacterium tuberculosis [TaxId: 1773] [101760] (4)
      4. Deinococcus radiodurans [TaxId: 1299] [110194] (1)
        SQ Q9RY51
    2. Archaeal ssDNA-binding protein [89324]
      similar to the domains of the Replication protein A
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89325] (1)
    3. Replication protein A 70 KDa subunit (RPA70) [50267]
      duplication: consists of three domains of this fold; contains zinc-finger insert in the C-terminal domain, residues 479-511
      1. Human (Homo sapiens) [TaxId: 9606] [50268] (6)
    4. Replication protein A 32 KDa subunit (RPA32) fragment [50269]
      1. Human (Homo sapiens) [TaxId: 9606] [50270] (10)
    5. Replication protein A 14 KDa (RPA14) subunit [50271]
      1. Human (Homo sapiens) [TaxId: 9606] [50272] (10)
    6. CDC13 ssDNA-binding domain [74948]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74949] (2)
    7. Telomere end binding protein alpha subunit [50273]
      duplication: consists of three domains of this fold
      1. Oxytricha nova [TaxId: 200597] [50274] (18)
    8. Core domain of telomere end binding protein beta subunit [50275]
      1. Oxytricha nova [TaxId: 200597] [50276] (14)
    9. Protection of telomeres protein 1, Pot1 [101761]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [101762] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [117190] (1)
        SQ Q9NUX5 6-299
    10. OB-fold domains of BRCA2 [82099]
      duplication: tandem repeat of three OB-fold domains
      1. Mouse (Mus musculus) [TaxId: 10090] [82100] (2)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82101] (1)
    11. Primosomal replication protein N, PriB [117191]
      1. Escherichia coli [TaxId: 562] [117192] (4)
        SQ P07013
    12. Hypothetical protein At4g28440 (F20O9.120) [117193]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117194] (1)
        SQ O49453 14-145
  5. Myf domain [50277] (7)
    1. Domain B2 of PheRS-beta, PheT [50278]
      1. Thermus thermophilus [TaxId: 274] [50279] (9)
        identical sequence to Thermus aquaticus, TaxId: 271
    2. C-terminal domain of methionyl-tRNA synthetase, MetRS-CD [82102]
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [82103] (1)
    3. EMAP II [50280]
      domain of the p43 protein
      1. Human (Homo sapiens) [TaxId: 9606] [50281] (3)
    4. C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS [89326]
      EMAP II-like domain found in vertebrata and insect enzymes; free domain possesses a cytokine activity
      1. Human (Homo sapiens) [TaxId: 9606] [89327] (1)
    5. Structure-specific tRNA-binding protein TRBP111 [89328]
      1. Escherichia coli [TaxId: 562] [89329] (1)
        YgjH
      2. Aquifex aeolicus [TaxId: 63363] [101763] (1)
        aq_422; putative methionyl-tRNA synthetase beta subunit
    6. TRBP111 homolog CsaA [63770]
      possesses export-related chaperone and tRNA-binding activities
      1. Thermus thermophilus [TaxId: 274] [63771] (1)
  6. Cold shock DNA-binding domain-like [50282] (56)
    barrel, closed; n=5, S=8
    1. Major cold shock protein [50283]
      1. Escherichia coli [TaxId: 562] [50284] (2)
      2. Bacillus subtilis [TaxId: 1423] [50285] (6)
      3. Bacillus caldolyticus [TaxId: 1394] [50286] (8)
      4. Thermotoga maritima [TaxId: 2336] [69262] (1)
    2. Y-box protein 1 cold shock domain (YB1-CSD) [69263]
      1. Human (Homo sapiens) [TaxId: 9606] [69264] (1)
    3. S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase [50287]
      1. Escherichia coli [TaxId: 562] [50288] (1)
      2. Streptomyces antibioticus [TaxId: 1890] [50289] (1)
    4. S1 domain of NusA [69265]
      1. Thermotoga maritima [TaxId: 2336] [69266] (2)
      2. Mycobacterium tuberculosis [TaxId: 1773] [69267] (4)
    5. C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) [88670]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [88671] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117195] (7)
        SQ P34087
      3. Human (Homo sapiens) [TaxId: 9606] [141309] (4)
        SQ P62487 78-171
    6. Translational initiation factor 1, IF1 [50290]
      1. Escherichia coli [TaxId: 562] [50291] (3)
    7. Archaeal initiation factor-1a, aIF1a [63772]
      evolutionary link between IF1 and eIF1a
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [63773] (1)
    8. Translation initiation factor-1a, eIF1a [50292]
      1. Human (Homo sapiens) [TaxId: 9606] [50293] (1)
    9. Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain [74950]
      1. Human (Homo sapiens) [TaxId: 9606] [74951] (2)
        SQ P05198
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101764] (1)
      3. Sulfolobus solfataricus [TaxId: 2287] [141310] (1)
        SQ Q97Z79 1-84
    10. Viral structural mimic of eIF2alpha [74952]
      1. Vaccinia virus [TaxId: 10245] [74953] (1)
      2. Myxoma virus, m156r [TaxId: 10273] [74954] (1)
    11. Rho termination factor, RNA-binding domain [68910]
      1. Escherichia coli [TaxId: 562] [68911] (14)
        SQ P03002
    12. C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) [50296]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [50297] (2)
      2. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [50298] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [82104] (1)
      4. Leishmania infantum [TaxId: 5671] [110195] (1)
        SQ Q9N9V6
      5. Leishmania mexicana [TaxId: 5665] [117196] (1)
        SQ Q9N9V6 97% sequence identity
    13. C-terminal domain of eIF5a homologue (Hex1) [82105]
      1. Filamentous fungi (Neurospora crassa) [TaxId: 5141] [82106] (1)
    14. N-terminal domain of ribosomal protein L2 [50299]
      incomplete OB-fold lacking the last strand
      1. Bacillus stearothermophilus [TaxId: 1422] [50300] (2)
      2. Archaeon Haloarcula marismortui [TaxId: 2238] [50301] (40)
        SQ P20276
        includes the N-terminal tail
      3. Thermus thermophilus [TaxId: 274] [159084] (5)
        SQ Q72I07 1-125
      4. Deinococcus radiodurans [TaxId: 1299] [159085] (5)
        SQ Q9RXJ9 33-127
      5. Escherichia coli [TaxId: 562] [159086] (27)
        SQ P60422 3-124
    15. Ribosomal protein S12 [50302]
      1. Thermus thermophilus [TaxId: 274] [50303] (36)
        SQ P17293
      2. Escherichia coli [TaxId: 562] [159087] (25)
        SQ P0A7S3 1-123
    16. Ribosomal protein S17 [50304]
      1. Thermus thermophilus [TaxId: 274] [50305] (45)
        SQ P24321
      2. Bacillus stearothermophilus [TaxId: 1422] [50306] (1)
      3. Escherichia coli [TaxId: 562] [159088] (26)
        SQ P02373 3-82
    17. Ribosomal protein S28e [101765]
      incomplete OB-fold lacking the last strand
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101766] (1)
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101767] (1)
    18. Elongation factor P middle and C-terminal domains [110196]
      duplication: contains two domains of this fold
      1. Thermus thermophilus HB8 [TaxId: 300852] [110197] (1)
        SQ Q76G20
    19. S1-domain of Ribonuclease E [110198]
      1. Escherichia coli [TaxId: 562] [110199] (3)
        SQ P21513 35-125
    20. Probable GTPase EngC (YjeQ), N-terminal domain [110200]
      1. Thermotoga maritima [TaxId: 2336] [110201] (1)
        SQ Q9X242 # TM1717
      2. Bacillus subtilis [TaxId: 1423] [117197] (1)
        SQ O34530
    21. Cold shock domain protein E1 (UNR) [117198]
      1. Human (Homo sapiens) [TaxId: 9606] [117199] (1)
        SQ O75534 15-90
    22. S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) [117200]
      1. Human (Homo sapiens) [TaxId: 9606] [117201] (1)
        SQ Q14690 173-278
    23. Exoribonuclease 2, RNB [159089]
      RNase II; contains 3 S1-like domains in addition to an OB-fold embedded in the catalytic domain
      1. Escherichia coli [TaxId: 562] [159090] (18)
        SQ P30850 1-82! SQ P30850 4-82! SQ P30850 5-82! SQ P30850 558-643! SQ P30850 558-644! SQ P30850 83-172
    24. S1-domain of exosome component 3 (RRP40) [159091]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159092] (1)
        SQ Q08285 62-151
      2. Human (Homo sapiens) [TaxId: 9606] [159093] (1)
        SQ Q9NQT5 108-195
    25. Ribonuclease II family protein DR0020 [159094]
      1. Deinococcus radiodurans [TaxId: 1299] [159095] (4)
        SQ Q9RYD0 404-461
    26. S1-domain of Ribosomal RNA-processing protein 4, RRP4 [159096]
      1. Human (Homo sapiens) [TaxId: 9606] [159097] (1)
        SQ Q13868 73-167
    27. Exosome component 1, EXOSC1 [159098]
      3'-5' exoribonuclease CSL4 homolog
      1. Human (Homo sapiens) [TaxId: 9606] [159099] (1)
        SQ Q9Y3B2 61-185
    28. S1-domain of exosome complex RNA-binding protein 1, ECR1 [159100]
      1. Aeropyrum pernix [TaxId: 56636] [159101] (1)
        SQ Q9YC02 60-147
      2. Sulfolobus solfataricus [TaxId: 2287] [159102] (2)
        SQ Q9UXC4 66-152
      3. Archaeoglobus fulgidus [TaxId: 2234] [159103] (3)
        SQ O29758 53-135
    29. Exosome complex exonuclease RRP44 [159104]
      member or the RNase II family; contains 3 S1-like domains; two of them are in tandem N-terminally to the catalytic domain and one is C-terminally to the catalytic domain that also contains an OB-fold
      1. Saccharomyces cerevisiae [TaxId: 4932] [159105] (3)
        SQ Q08162 252-399! SQ Q08162 400-494! SQ Q08162 911-998
    30. Tex S1-domain [159106]
      1. Pseudomonas aeruginosa [TaxId: 287] [159107] (3)
        SQ Q9HTY8 637-730
  7. TRAM domain [101768] (3)
    Pfam 01938
    1. rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain [101769]
      1. Escherichia coli [TaxId: 562] [101770] (3)
    2. Hypothetical protein MM1357 [141311]
      1. Methanosarcina mazei [TaxId: 2209] [141312] (1)
        SQ Q8PX65 1-68
    3. Hypothetical protein MMP0076 [141313]
      1. Methanococcus maripaludis [TaxId: 39152] [141314] (1)
        SQ Q6M142 1-69
  8. Hypothetical protein MTH1 (MT0001), insert domain [74955] (1)
    1. Hypothetical protein MTH1 (MT0001), insert domain [74956]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [74957] (1)
  9. DNA ligase/mRNA capping enzyme postcatalytic domain [50307] (6)
    1. RNA guanylyltransferase (mRNA capping enzyme) [50308]
      1. Chlorella virus PBCV-1 [TaxId: 10506] [50309] (3)
    2. mRNA capping enzyme alpha subunit [89330]
      1. Yeast (Candida albicans) [TaxId: 5476] [89331] (1)
    3. ATP-dependent DNA ligase [50310]
      1. Bacteriophage T7 [TaxId: 10760] [50311] (1)
      2. Chlorella virus PBCV-1 [TaxId: 10506] [50312] (7)
    4. NAD+-dependent DNA ligase [50313]
      1. Thermus filiformis [TaxId: 276] [50314] (2)
    5. DNA ligase I (LIG1) [117202]
      1. Human (Homo sapiens) [TaxId: 9606] [117203] (1)
        SQ P18858 262-901
  10. Phage ssDNA-binding proteins [50315] (5)
    barrel, open; n*=5, S*=8; the members' structures vary greater that those from cellular organisms
    1. Gene V protein [50316]
      1. Enterobacteria phage M13, including coliphage f1 [TaxId: 10870] [50317] (19)
      2. Pseudomonas phage Pf3 [TaxId: 10872] [50318] (1)
    2. Gene 32 protein (gp32) core [50319]
      contains a Zn-finger subdomain, res. 63-111
      1. Bacteriophage T4 [TaxId: 10665] [50320] (1)
      2. Enterobacteria phage RB69 [TaxId: 12353] [159108] (3)
        SQ Q7Y265 32-241
    3. gp2.5 [63774]
      1. Bacteriophage T7 [TaxId: 10760] [63775] (1)
  11. DNA replication initiator (cdc21/cdc54) N-terminal domain [89332] (1)
    1. DNA replication initiator (cdc21/cdc54) N-terminal domain [89333]
      MCM complex protein; dodecamer assembly; includes the N-terminal all-alpha subdomain and inserted Zn-finger
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [89334] (1)
  12. RNA polymerase subunit RBP8 [50321] (1)
    duplication; contains tandem repeat of two incomplete OB-folds; forms a single barrel; n=8, S=10
    1. RNA polymerase subunit RBP8 [50322]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50323] (31)
        SQ P20436
  13. RecO N-terminal domain-like [117204] (1)
    N-terminal part of Pfam 02565
    1. Recombinational repair protein RecO, N-terminal domain [117205]
      1. Deinococcus radiodurans [TaxId: 1299] [117206] (1)
        SQ Q9RW50 # DR0819
  14. TIP49 domain [141315] (1)
    N-terminal part of Pfam 06068; the RuvA-like OB-fold domain in RuvB-like eukaryotic proteins
    1. RuvB-like 2 protein, RUVBL2 (TIP49b) [141316]
      1. Human (Homo sapiens) [TaxId: 9606] [141317] (1)
        SQ Q9Y230 131-212
  15. SSO2064-like [159109] (1)
    Pfam 01796; DUF35; contains extra N-terminal zinc finger subdomain of the rubredoxin-like fold
    1. Hypothetical protein SSO2064 [159110]
      1. Sulfolobus solfataricus [TaxId: 2287] [159111] (2)
        SQ Q97WQ4 8-144
  16. RNB domain-like [159112] (3)
    Pfam 00773; RNase II catalytic domain; decorated OB-fold domain with extra C-terminal structures forming the active site
    1. Exosome complex exonuclease RRP44 [159113]
      1. Saccharomyces cerevisiae [TaxId: 4932] [159114] (1)
        SQ Q08162 495-910
    2. Ribonuclease II family protein DR0020 [159115]
      Includes extra N-terminal all-alpha subdomain
      1. Deinococcus radiodurans [TaxId: 1299] [159116] (4)
        SQ Q9RYD0 3-403
    3. Exoribonuclease 2, RNB [159117]
      RNase II
      1. Escherichia coli [TaxId: 562] [159118] (6)
        SQ P30850 173-557
8. Inorganic pyrophosphatase [50324] (1)
  uperfamily
  1. Inorganic pyrophosphatase [50325] (6)
    barrel, closed; n=5, S=8
    1. Inorganic pyrophosphatase [50326]
      eukaryotic enzyme has additional secondary structures at both N- and C-termini
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50327] (16)
      2. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [50328] (1)
      3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101771] (1)
      4. Escherichia coli [TaxId: 562] [50329] (17)
      5. Thermus thermophilus [TaxId: 274] [50330] (1)
      6. Pyrococcus furiosus [TaxId: 2261] [117207] (1)
        SQ Q8U438
9. MOP-like [50331] (3)
  uperfamily
  1. Molybdate/tungstate binding protein MOP [50332] (2)
    1. Molybdate/tungstate binding protein MOP [50333]
      homohexamer: trimer of the C-terminal strand swapped dimers
      1. Sporomusa ovata [TaxId: 2378] [50334] (1)
      2. Clostridium pasteurianum, MOP II [TaxId: 1501] [69270] (5)
  2. BiMOP, duplicated molybdate-binding domain [50335] (2)
    duplication: tandem repeat of two OB-fold domains with swapped C-terminal strands
    1. Cytoplasmic molybdate-binding protein ModG [63776]
      1. Azotobacter vinelandii [TaxId: 354] [63777] (3)
    2. C-terminal domain of molybdate-dependent transcriptional regulator ModE [63405]
      1. Escherichia coli [TaxId: 562] [50337] (5)
  3. ABC-transporter additional domain [50338] (5)
    probably stems out from the biMOP domain
    1. Maltose transport protein MalK, C-terminal domain [63406]
      1. Archaeon Thermococcus litoralis [TaxId: 2265] [50340] (1)
      2. Escherichia coli [TaxId: 562] [101772] (13)
    2. Glucose transport protein GlcV, N-terminal domain [89335]
      1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [89336] (5)
    3. Hypothetical protein PH0022, C-terminal domain [117208]
      1. Pyrococcus horikoshii [TaxId: 53953] [117209] (2)
        SQ O57758
    4. Sulfate/molybdate ABC transporter, ATP-binding protein [159119]
      1. Methanosarcina acetivorans [TaxId: 2214] [159120] (2)
        SQ Q8TTZ3 230-348
10. CheW-like [50341] (1)
  uperfamily
  1. CheW-like [50342] (2)
    duplication: tandem repeat of two swapped domains, one with a canonical OB-fold topology and one with a circular permutation
    1. Histidine kinase CheA, C-terminal domain [50343]
      1. Thermotoga maritima [TaxId: 2336] [50344] (3)
    2. Chemotaxis protein CheW [69271]
      1. Thermotoga maritima [TaxId: 2336] [69272] (3)
11. TM0957-like [141318] (1)
  extra N-terminal region and large insertion after strand 3 together form an alpha-helical subdomain
  uperfamily
  1. TM0957-like [141319] (1)
    1. Hypothetical protein TM0957 [141320]
      1. Thermotoga maritima [TaxId: 2336] [141321] (4)
        SQ Q9X052 39-214
12. NfeD domain-like [141322] (1)
  close structural similarity to some members of the Nucleic acid-binding OB-fold proteins, possibly related to this superfamily
  uperfamily
  1. NfeD domain-like [141323] (1)
    C-terminal part of Pfam 01957
    1. Hypothetical protein PH0471 [141324]
      NfeD short homolog
      1. Pyrococcus horikoshii [TaxId: 53953] [141325] (1)
        SQ O58204 72-143
13. BC4932-like [159121] (1)
  1. BC4932-like [159122] (2)
    Pfam 06486; DUF1093
    1. Uncharacterized protein BC2438 [159123]
      1. Bacillus cereus [TaxId: 1396] [159124] (1)
        SQ Q813L1 22-129
    2. Uncharacterized protein BC4932 [159125]
      1. Bacillus cereus [TaxId: 1396] [159126] (1)
        SQ Q812L6 22-117
14. HupF/HypC-like [159127] (1)
  contains extra C-terminal helix packed against the beta-barrel side
  1. HupF/HypC-like [159128] (3)
    Pfam 01455
    1. Hydrogenase expression/formation protein HypC [159129]
      1. Escherichia coli [TaxId: 562] [159130] (1)
        SQ P0AAM3 1-90
      2. Shewanella oneidensis [TaxId: 70863] [159131] (2)
        SQ Q8EF93 1-76
      3. Thermococcus kodakaraensis [TaxId: 311400] [159132] (3)
        SQ Q5JII0 2-72
15. EutN/CcmL-like [159133] (1)
  homohexameric unit
  1. EutN/CcmL-like [159134] (3)
    Pfam 03319
    1. Ethanolamine utilization protein EutN [159135]
      1. Escherichia coli [TaxId: 562] [159136] (18)
        SQ P0AEJ9 1-95
    2. Carboxysome shell protein [159137]
      Unidentified carboxysome polypeptide
      1. Thiobacillus neapolitanus [TaxId: 927] [159138] (5)
        SQ O85043 1-82
    3. Carbon dioxide concentrating mechanism protein CcmL [159139]
      1. Synechocystis sp. (strain PCC 6803) [TaxId: 1148] [159140] (10)
        SQ P72759 1-96
16. HIN-2000 domain-like [159141] (1)
  duplication: tandem repeat of two OB-fold domains
  1. HIN-200/IF120x domain [159142] (1)
    Pfam 02760
    1. Gamma-interferon-inducible protein Ifi-16 [159143]
      1. Human (Homo sapiens) [TaxId: 9606] [159144] (8)
        SQ Q16666 199-301! SQ Q16666 302-389
PRC-barrel domain [50345] (1)
core: barrel, partly opened; n*=5, S*=8; meander
1. PRC-barrel domain [50346] (4)
  uperfamily
  1. MTH1895 [101773] (1)
    homodimeric protein; subunits are composed of a stand-alone copy of this domain
    1. MTH1895 [101774]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [101775] (1)
  2. Photosynthetic reaction centre, H-chain, cytoplasmic domain [50347] (3)
    1. Photosynthetic reaction centre [50348]
      1. Rhodopseudomonas viridis [TaxId: 1079] [50349] (11)
      2. Rhodobacter sphaeroides [TaxId: 1063] [50350] (39)
        SQ P11846
      3. Thermochromatium tepidum [TaxId: 1050] [50351] (1)
  3. RIKEN cDNA 2310057j16 protein (KIAA1543) [110202] (1)
    contains an N-terminal alpha-haipin and other fold decorations
    1. RIKEN cDNA 2310057j16 protein (KIAA1543) [110203]
      1. Mouse (Mus musculus) [TaxId: 10090] [110204] (1)
        SQ Q80VC9 1112-1240
  4. RimM C-terminal domain-like [141326] (1)
    1. 16S rRNA processing protein RimM, C-terminal domain [141327]
      1. Pseudomonas aeruginosa [TaxId: 287] [141328] (1)
        SQ Q9HXQ0 101-175
beta-Trefoil [50352] (8)
barrel, closed; n=6, S=12; and a hairpin triplet; meander
duplication: has internal pseudo threefold symmetry
1. Cytokine [50353] (2)
  uperfamily
  1. Fibroblast growth factors (FGF) [50354] (11)
    1. Basic FGF (FGF2) [50355]
      1. Human (Homo sapiens) [TaxId: 9606] [50356] (16)
    2. Acidic FGF (FGF1) [50357]
      1. Cow (Bos taurus) [TaxId: 9913] [50358] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [50359] (28)
        SQ P05230 16-152 ! SQ P05230
      3. Eastern newt (Notophthalmus viridescens) [TaxId: 8316] [63778] (1)
    3. Fibroblast growth factor 4 (FGF4) [63779]
      1. Human (Homo sapiens) [TaxId: 9606] [63780] (1)
    4. Keratinocyte growth factor, FGF7 [50360]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50361] (2)
    5. Fibroblast growth factor 9, FGF9 [63781]
      1. Human (Homo sapiens) [TaxId: 9606] [63782] (2)
    6. Fibroblast growth factor-10, FGF10 [82107]
      1. Human (Homo sapiens) [TaxId: 9606] [82108] (1)
    7. Fibrobast growth factor homologous factor 1 (FHF1b, FGF12b) [101776]
      1. Human (Homo sapiens) [TaxId: 9606] [101777] (1)
    8. Fibroblast growth factor-19 (FGF19) [101778]
      1. Human (Homo sapiens) [TaxId: 9606] [101779] (3)
    9. Fibroblast growth factor 8, FGF8 [159145]
      1. Human (Homo sapiens) [TaxId: 9606] [159146] (2)
        SQ P55075 52-198
  2. Interleukin-1 (IL-1) [50362] (6)
    1. Interleukin-1beta [50363]
      1. Human (Homo sapiens) [TaxId: 9606] [50364] (20)
        SQ P01584 117-269
      2. Mouse (Mus musculus) [TaxId: 10090] [50365] (2)
    2. Interleukin-1 receptor antagonist protein [50366]
      1. Human (Homo sapiens) [TaxId: 9606] [50367] (5)
    3. Interleukin-1alpha [50368]
      1. Human (Homo sapiens) [TaxId: 9606] [50369] (1)
    4. Interleukin-1F5 [101780]
      1. Mouse (Mus musculus) [TaxId: 10090] [101781] (1)
    5. Interleukin-18 [101782]
      1. Human (Homo sapiens) [TaxId: 9606] [101783] (1)
2. MIR domain [82109] (1)
  uperfamily
  1. MIR domain [82110] (2)
    Pfam 02815
    1. IP3 receptor type 1 binding core, domain 1 [82111]
      1. Mouse (Mus musculus) [TaxId: 10090] [82112] (1)
    2. Hypothetical protein R12E2.13 (1D10) [110205]
      1. Caenorhabditis elegans [TaxId: 6239] [110206] (1)
        SQ O61793
3. Ricin B-like lectins [50370] (3)
  uperfamily
  1. Ricin B-like [50371] (18)
    1. Plant cytotoxin B-chain (lectin) [50372]
      duplication: consists of two domains of this fold
      1. Castor bean (Ricinus communis), Ricin [TaxId: 3988] [50373] (2)
        SQ P06750 303-564
      2. Abrus precatorius [TaxId: 3816] [50374] (1)
      3. Mongolian snake-gourd (Trichosanthes kirilowii), Lectin 1 [TaxId: 3677] [89337] (1)
      4. European mistletoe (Viscum album) [TaxId: 3972] [50375] (18)
        different sequence variants
        SQ Q6ITZ3 266-520; SQ P81446 269-531 # 91% sequence identity
      5. Sambucus ebulus, ebulin [TaxId: 28503] [50376] (4)
    2. Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain) [50377]
      1. Streptomyces olivaceoviridis [TaxId: 1921] [50378] (11)
      2. Streptomyces lividans [TaxId: 1916] [74958] (3)
    3. Hemagglutinin component Ha1 [101784]
      1. Clostridium botulinum D phage [TaxId: 29342] [101785] (1)
      2. Clostridium botulinum [TaxId: 1491] [159147] (12)
    4. Cytolethal distending toxin subunit A [110207]
      1. Haemophilus ducreyi [TaxId: 730] [110208] (1)
        SQ O06522 57-223
      2. Actinobacillus actinomycetemcomitans [TaxId: 714] [141329] (2)
        SQ O87120 70-222
    5. Cytolethal distending toxin subunit C [110209]
      1. Haemophilus ducreyi [TaxId: 730] [110210] (1)
        SQ O06524 25-178
      2. Actinobacillus actinomycetemcomitans [TaxId: 714] [141330] (2)
        SQ Q7DK11 25-178
    6. Hemolytic lectin CEL-III, domains 1 and 2 [110211]
      1. Cucumaria echinata [TaxId: 40245] [110212] (9)
        SQ Q868M7 11-442
    7. Polypeptide N-acetylgalactosaminyltransferase 1, C-terminal domain [117210]
      1. Mouse (Mus musculus) [TaxId: 10090] [117211] (1)
        SQ O08912
    8. 29-kDa galactose-binding lectin [159148]
      duplication: tadem repeat of two Ricin B-like domains
      1. Lumbricus terrestris [TaxId: 6398] [159149] (4)
        SQ O96048 131-260
    9. Agglutinin-1 chain B [159150]
      1. Abrus precatorius [TaxId: 3816] [159151] (2)
        SQ Q9M6E9 287-420! SQ Q9M6E9 421-547
    10. Agglutinin MOA, N-terminal domain [159152]
      1. Fairy-ring mushroom (Marasmius oreades) [TaxId: 181124] [159153] (1)
        SQ Q8X123 2-155
  2. Cysteine rich domain [50379] (1)
    1. Mannose receptor [50380]
      1. Mouse (Mus musculus) [TaxId: 10090] [50381] (4)
  3. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [117212] (1)
    1. GlcNAc-alpha-1,4-Gal-releasing endo-beta-galactosidase, GngC, C-terminal domain [117213]
      1. Clostridium perfringens [TaxId: 1502] [117214] (1)
        SQ Q934G8 17-420
4. Agglutinin [50382] (1)
  this superfamily is distinct from the ricin B-like lectin superfamily
  uperfamily
  1. Agglutinin [50383] (1)
    1. Agglutinin [50384]
      duplication: the tandem repeat of beta-trefoil domains
      1. Love-lies-bleeding (Amaranthus caudatus) [TaxId: 3567] [50385] (2)
5. STI-like [50386] (2)
  uperfamily
  1. Kunitz (STI) inhibitors [50387] (7)
    1. Winged bean albumin 1 [50388]
      1. Goa bean (Psophocarpus tetragonolobus) [TaxId: 3891] [50389] (1)
    2. Erythrina cafra trypsin inhibitor [50390]
      1. Erythrina caffra [TaxId: 3842] [50391] (1)
    3. chymotrypsin inhibitor WCI [50392]
      1. Winged bean (Psophocarpus tetragonolobus) [TaxId: 3891] [50393] (6)
    4. Soybean trypsin inhibitor [50394]
      1. Soybean (Glycine max) [TaxId: 3847] [50395] (4)
    5. Amylase/subtilisin inhibitor [50396]
      1. Barley (Hordeum vulgare), seed [TaxId: 4513] [50397] (3)
    6. Serine protease inhibitor DrTI [110213]
      1. Royal poinciana (Delonix regia) [TaxId: 72433] [110214] (1)
        SQ P83667
    7. Two-chain trypsin inhibitor [110215]
      1. Balsam copaiba (Copaifera langsdorffii) [TaxId: 280048] [110216] (1)
        SQ P84144,P84145 # two chains probably resulted from a single chain precursor
  2. Clostridium neurotoxins, C-terminal domain [50399] (3)
    overall fold is very similar to that of the STI family
    1. Tetanus neurotoxin [50400]
      1. Clostridium tetani [TaxId: 1513] [50401] (10)
    2. Botulinum neurotoxin [50402]
      1. Clostridium botulinum, serotype A [TaxId: 1491] [50403] (1)
      2. Clostridium botulinum, serotype B [TaxId: 1491] [50404] (17)
6. Actin-crosslinking proteins [50405] (2)
  uperfamily
  1. Fascin [50406] (1)
    1. Fascin [50407]
      duplication: tandem repeat of four domains
      1. Human (Homo sapiens) [TaxId: 9606] [50408] (1)
  2. Histidine-rich actin-binding protein (hisactophilin) [50409] (1)
    1. Histidine-rich actin-binding protein (hisactophilin) [50410]
      1. Dictyostelium discoideum [TaxId: 44689] [50411] (2)
7. DNA-binding protein LAG-1 (CSL) [110217] (1)
  contains rudiment hairpin triplet lacking one hairpin
  uperfamily
  1. DNA-binding protein LAG-1 (CSL) [110218] (1)
    1. DNA-binding protein LAG-1 (CSL) [110219]
      1. Caenorhabditis elegans [TaxId: 6239] [110220] (4)
        SQ Q9TYY1 195-660
8. AbfB domain [110221] (1)
  uperfamily
  1. AbfB domain [110222] (1)
    Pfam 05270
    1. Alpha-L-arabinofuranosidase B (AbfB), C-terminal domain [110223]
      1. Aspergillus kawachii [TaxId: 40384] [110224] (4)
        SQ Q8NK89 19-499
Reductase/isomerase/elongation factor common domain [50412] (4)
barrel, closed; n=6, S=10; greek-key
1. Riboflavin synthase domain-like [63380] (3)
  uperfamily
  1. Riboflavin synthase [63783] (2)
    duplication: consists of two homologous domains
    1. Riboflavin synthase [63784]
      trimerizes via the additional C-terminal helix
      1. Escherichia coli [TaxId: 562] [63785] (4)
        SQ P29015 1-87
      2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82113] (1)
  2. Ferredoxin reductase FAD-binding domain-like [63381] (19)
    coupled with a NADP-binding domain of alpha/beta class
    1. Ferredoxin reductase (flavodoxin reductase) N-terminal domain [50415]
      1. Spinach (Spinacia oleracea) [TaxId: 3562] [50416] (7)
      2. Garden pea (Pisum sativum) [TaxId: 3888] [50417] (4)
      3. Paprika (Capsicum annuum) [TaxId: 4072] [50418] (1)
      4. Maize (Zea mays), leaf isoform [TaxId: 4577] [50419] (2)
      5. Maize (Zea mays), root isoform [TaxId: 4577] [63786] (1)
      6. Cyanobacterium (Anabaena sp.), pcc 7119 [TaxId: 1167] [50420] (25)
      7. Escherichia coli [TaxId: 562] [50421] (1)
      8. Azotobacter vinelandii [TaxId: 354] [50422] (1)
    2. NAD(P)H:flavin oxidoreductase [50423]
      1. Escherichia coli [TaxId: 562] [50424] (1)
    3. Nitrate reductase core domain [50425]
      1. Corn (Zea mays) [TaxId: 4577] [50426] (3)
    4. cytochrome b5 reductase [50427]
      1. Pig (Sus scrofa), liver [TaxId: 9823] [50428] (1)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [69273] (3)
        SQ P20070 33-300
      3. Human (Homo sapiens) [TaxId: 9606] [117215] (1)
        SQ P00387 30-300
    5. Phthalate dioxygenase reductase [50430]
      contains additional 2Fe-2S ferredoxin domain
      1. Pseudomonas cepacia, db01 [TaxId: 292] [50431] (1)
    6. Benzoate dioxygenase reductase [74959]
      1. Acinetobacter sp. [TaxId: 472] [74960] (1)
    7. Dihydroorotate dehydrogenase B, PyrK subunit [50433]
      1. Lactococcus lactis, isozyme B [TaxId: 1358] [50434] (3)
    8. Flavohemoglobin, central domain [50436]
      contains additional globin domain
      1. Alcaligenes eutrophus [TaxId: 106590] [50437] (1)
      2. Escherichia coli [TaxId: 562] [74961] (1)
    9. Methane monooxygenase component C, MmoC [117216]
      1. Methylococcus capsulatus [TaxId: 414] [117217] (1)
        SQ P22868 99-348 # structure of the N-terminal, 2Fe-2S ferredoxin domain is also known (1JQ4; scop_sp 69669)
  3. NADPH-cytochrome p450 reductase FAD-binding domain-like [50438] (3)
    there is an alpha-helical subdomain inserted in this domain
    1. NADPH-cytochrome p450 reductase [50439]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50440] (4)
    2. Sulfite reductase flavoprotein [50441]
      1. Escherichia coli [TaxId: 562] [50442] (2)
    3. Neuronal nitric-oxide synthase FAD/NADP+ domain [69274]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [69275] (2)
        SQ P29476 750-1413
2. Riboflavin kinase-like [82114] (2)
  uperfamily
  1. ATP-dependent riboflavin kinase-like [82115] (3)
    1. Riboflavin kinase [82116]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82117] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [89338] (4)
        encoded by FLJ11149
    2. Riboflavin kinase domain of bifunctional FAD synthetase [101786]
      1. Thermotoga maritima [TaxId: 2336] [101787] (7)
        SQ Q9WZW1
        TM0379
  2. CTP-dependent riboflavin kinase-like [159154] (2)
    Pfam 01982; newly characterized archaeal family (formerly DUF120)
    1. CTP-dependent riboflavin kinase, Rfk [159155]
      1. Thermoplasma acidophilum [TaxId: 2303] [159156] (1)
        SQ Q9HJA6 90-220
      2. Methanococcus jannaschii [TaxId: 2190] [159157] (7)
        SQ Q60365 1-136
3. FucI/AraA C-terminal domain-like [50443] (2)
  uperfamily
  1. L-fucose isomerase, C-terminal domain [50444] (1)
    1. L-fucose isomerase, C-terminal domain [50445]
      1. Escherichia coli [TaxId: 562] [50446] (1)
  2. AraA C-terminal domain-like [141331] (1)
    C-terminal part of Pfam 02610
    1. L-arabinose isomerase AraA [141332]
      1. Escherichia coli [TaxId: 562] [141333] (6)
        SQ P08202 329-498
4. Translation proteins [50447] (6)
  uperfamily
  1. Elongation factors [50448] (18)
    1. Elongation factor Tu (EF-Tu), domain 2 [50449]
      N-terminal domain is related to G proteins; C-terminal domain is (6,10) barrel of circularly permuted topology
      1. Escherichia coli [TaxId: 562] [50450] (8)
        SQ P02990
      2. Thermus aquaticus [TaxId: 271] [50451] (4)
      3. Thermus thermophilus [TaxId: 274] [50452] (9)
      4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [50453] (2)
        SQ P49410 56-452
    2. Elongation factor eEF-1alpha, domain 2 [50454]
      eukaryotic and archaeal homologue of EF-Tu
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50455] (6)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69276] (2)
        SQ P35021
    3. Elongation factor G (EF-G), domain II [50456]
      1. Thermus thermophilus [TaxId: 274] [50457] (9)
      2. Thermus thermophilus, EF-G-2 [TaxId: 274] [141334] (2)
        SQ Q5SI76 268-370
        TTHA1498
    4. Elongation factor 2 (eEF-2), domain II [82118]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82119] (22)
        SQ P32324
    5. Initiation factor eIF2 gamma subunit, domain II [74962]
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [74963] (5)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [101788] (1)
      3. Sulfolobus solfataricus [TaxId: 2287] [141335] (6)
        SQ Q980A5 207-320
    6. Initiation factor IF2/eIF5b, domains 2 and 4 [50458]
      the C-terminal domain 4 has the same fold as domain 2; it probably binds fMet-tRNAfmet
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [50459] (3)
      2. Bacillus stearothermophilus [TaxId: 1422] [50460] (1)
    7. Eukaryotic peptide chain release factor ERF2, post-G domain [110225]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110226] (3)
        SQ O74718
    8. Hypothetical protein PF0907 [110227]
      stand-alone protein related to this domain
      1. Pyrococcus furiosus [TaxId: 2261] [110228] (1)
        SQ Q8U2D2 18-108
    9. Elongation factor SelB, domains 2 and 4 [117218]
      EF-Tu homologue, contains extra C-terminal domain (domain 4) of the same fold as the postG domain 2
      1. Methanococcus maripaludis [TaxId: 39152] [117219] (3)
        SQ Q8J307
    10. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain [141336]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [141337] (1)
        SQ Q87WW1 238-329
  2. Ribosomal protein L3 [50461] (4)
    1. Ribosomal protein L3 [50462]
      superfamily fold is elaborated with additional structures
      1. Archaeon Haloarcula marismortui [TaxId: 2238] [50463] (58)
        SQ P20279
      2. Thermus thermophilus [TaxId: 274] [159158] (11)
        SQ Q72I04 1-205
      3. Escherichia coli [TaxId: 562] [159159] (29)
        SQ P60438 1-209
      4. Deinococcus radiodurans [TaxId: 1299] [159160] (9)
        SQ Q9RXK2 1-205
  3. Ribosomal protein L35ae [117220] (1)
    Pfam 01247
    1. Ribosomal protein L35ae [117221]
      1. Pyrococcus furiosus [TaxId: 2261] [117222] (1)
        SQ Q8TZV6
  4. RimM N-terminal domain-like [141338] (1)
    Pfam 01782
    1. 16S rRNA processing protein RimM, N-terminal domain [141339]
      1. Pseudomonas aeruginosa [TaxId: 287] [141340] (1)
        SQ Q9HXQ0 7-95
  5. Gar1-like SnoRNP [141341] (1)
    stand alone proteins, which are similar structurally but not sequentially to the elongation factor domains, unlike PF0907
    1. Gar1 homolog PF1791 [141342]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [141343] (4)
        SQ Q8U029 1-73
  6. AlaX-M N-terminal domain-like [159161] (1)
    Does NOT belong to Pfam 01411
    1. AlaX-M trans-editing enzyme, N-terminal domain [159162]
      1. Pyrococcus horikoshii [TaxId: 53953] [159163] (1)
        SQ O57848 1-87
Elongation factor/aminomethyltransferase common domain [50464] (2)
barrel, closed; n=6, S=10; greek-key
1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50465] (1)
  probably related to the second domain and its superfamiy by a circular permutation
  uperfamily
  1. EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain [50466] (12)
    1. Elongation factor Tu (EF-Tu) [50467]
      1. Escherichia coli [TaxId: 562] [50468] (8)
        SQ P02990
      2. Thermus aquaticus [TaxId: 271] [50469] (4)
      3. Thermus thermophilus [TaxId: 274] [50470] (9)
      4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [50471] (2)
        SQ P49410 56-452
    2. Elongation factor eEF-1alpha, C-terminal domain [50472]
      eukaryotic and archaeal homologue of EF-Tu
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50473] (6)
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69277] (2)
        SQ P35021
    3. Initiation factor eIF2 gamma subunit [74964]
      1. Archaeon Pyrococcus abyssi [TaxId: 29292] [74965] (5)
      2. Archaeon Methanococcus jannaschii [TaxId: 2190] [101789] (1)
      3. Sulfolobus solfataricus [TaxId: 2287] [141344] (6)
        SQ Q980A5 321-415
    4. Eukaryotic peptide chain release factor ERF2, C-terminal domain [110229]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110230] (3)
        SQ O74718
    5. Elongation factor SelB, domain 3 [117223]
      1. Methanococcus maripaludis [TaxId: 39152] [117224] (3)
        SQ Q8J307
    6. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 3-like domain [141345]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [141346] (1)
        SQ Q87WW1 330-434
2. Aminomethyltransferase beta-barrel domain [101790] (1)
  uperfamily
  1. Aminomethyltransferase beta-barrel domain [101791] (5)
    1. N,N-dimethylglycine oxidase, C-terminal domain [101792]
      1. Arthrobacter globiformis [TaxId: 1665] [101793] (3)
    2. Hypothetical protein YgfZ, C-terminal domain [101794]
      1. Escherichia coli [TaxId: 562] [101795] (2)
        SQ P39179
    3. Glycine cleavage system T protein, GcvT [110231]
      1. Thermotoga maritima [TaxId: 2336] [110232] (4)
        SQ Q9WY54
      2. Escherichia coli [TaxId: 562] [110233] (1)
        SQ P27248
      3. Pyrococcus horikoshii [TaxId: 53953] [117225] (1)
        SQ O58888
Split barrel-like [50474] (3)
barrel; n=6, S=10; greek-key
1. FMN-binding split barrel [50475] (4)
  related to the ferredoxin reductase-like FAD-binding domain
  uperfamily
  1. PNP-oxidase like [50476] (21)
    1. FMN-binding protein [50477]
      1. Desulfovibrio vulgaris, strain Miyazaki F [TaxId: 881] [50478] (10)
    2. Pyridoxine 5'-phoshate oxidase (PNP oxidase) [50479]
      elaborated with additional secondary structures; active as dimer
      1. Human (Homo sapiens) [TaxId: 9606] [82120] (1)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50480] (1)
      3. Escherichia coli [TaxId: 562] [50481] (7)
        SQ P28225
      4. Pseudomonas aeruginosa [TaxId: 287] [117226] (1)
        SQ Q820A5
      5. Pseudomonas fluorescens [TaxId: 294] [117227] (1)
        SQ Q51793
      6. Mycobacterium tuberculosis [TaxId: 1773] [141347] (2)
        SQ P65682 24-112
    3. Hypothetical protein Alr5027 [110234]
      1. Cyanobacterium (Nostoc sp. PCC 7120) [TaxId: 103690] [110235] (1)
        SQ Q8YMA7
    4. NimA-related protein DR0842 [117228]
      1. Deinococcus radiodurans [TaxId: 1299] [117229] (5)
        SQ Q9RW27
    5. Hypothetical protein Rv1155 [117230]
      1. Mycobacterium tuberculosis [TaxId: 1773] [117231] (6)
        SQ O06553
    6. Hypothetical protein Rv2991 [117232]
      1. Mycobacterium tuberculosis [TaxId: 1773] [117233] (1)
        SQ O53240
    7. Hypothetical protein BH0577 [141348]
      1. Bacillus halodurans [TaxId: 86665] [141349] (1)
        SQ Q9KFA8 10-165
    8. Hypothetical protein PA4388 [141350]
      1. Pseudomonas aeruginosa [TaxId: 287] [141351] (2)
        SQ Q9HW16 2-239
    9. General stress protein 26 [141352]
      1. Nostoc punctiforme pcc 73102 [TaxId: 63737] [141353] (2)
    10. Hypothetical protein Mll6688 [141354]
      binds FAD cofactor
      1. Mesorhizobium loti [TaxId: 381] [141355] (2)
        SQ Q988L5 1-148
    11. Cellular repressor of E1A-stimulated genes CREG1 [141356]
      1. Human (Homo sapiens) [TaxId: 9606] [141357] (4)
        SQ O75629 49-218
    12. Putative general stress protein BT1439 [141358]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [141359] (2)
        SQ Q8A7U5 3-137
    13. Hypotheical protein CAC3491 [141360]
      related to general stress protein 26(GS26) of B.subtilis
      1. Clostridium acetobutylicum [TaxId: 1488] [141361] (2)
        SQ Q97DI6 2-142
    14. Hypothetical protein Rv2074 [141362]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141363] (1)
        SQ Q10682 11-135
    15. 5-nitroimidazole resistance protein BT3078 [141364]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [141365] (1)
        SQ Q8A377 1-157
    16. Hypothetical protein Ta1372 [141366]
      1. Thermoplasma acidophilum [TaxId: 2303] [141367] (2)
        SQ Q9HIG7 16-208
  2. NADH:FMN oxidoreductase-like [50482] (5)
    different dimerization mode than in the PNP-oxidase like family
    1. FMN-binding protein MTH152 [50483]
      1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [50484] (1)
    2. Ferric reductase [63787]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [63788] (2)
    3. Putative styrene monooxygenase small component [101796]
      1. Thermus thermophilus [TaxId: 274] [101797] (2)
    4. Phenol 2-hydroxylase component B (PheA2) [101798]
      utilizes FAD rather than FMN
      1. Geobacillus thermoglucosidasius [TaxId: 1426] [101799] (2)
    5. Putative flavoprotein TTHA0420 [117234]
      1. Thermus thermophilus [TaxId: 274] [117235] (2)
        SQ Q5SL73
  3. UbiD middle domain-like [141368] (1)
    N terminal part of Pfam 01977; overall structural similarity to one subunit of the NADH:FMN oxidoreductase-like family (scop_fa 50482); not known to bind a flavin cofactor; also includes the N-terminal alpha+beta subdomain (~110 residues)
    1. 3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD [141369]
      1. Escherichia coli [TaxId: 562] [141370] (3)
        SQ P0AAB4 6-325
  4. MTH863-like [159164] (3)
    Pfam 04289; DUF447; a new dimerisation mode involving (included) all-alpha subdomain of the spectrin-like fold (scop_cf 46965)
    1. Hypothetical protein AF1834 [159165]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159166] (4)
        SQ O28442 1-189
    2. Hypothetical protein MM1853 [159167]
      1. Methanosarcina mazei [TaxId: 2209] [159168] (2)
        SQ Q8PVV4 19-210
    3. Uncharacterized protein MTH863 [159169]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [159170] (2)
        SQ O26951 15-220
2. PilZ domain-like [141371] (2)
  uperfamily
  1. PilZ domain [141372] (3)
    Pfam 07238
    1. Hypothetical protein VCA0042, C-terminal domain [141373]
      1. Vibrio cholerae [TaxId: 666] [141374] (1)
        SQ Q9KNC3 138-248
      2. Vibrio cholerae O395 [TaxId: 345073] [159171] (2)
    2. Hypothetical protein PA4608 [141375]
      1. Pseudomonas aeruginosa [TaxId: 287] [141376] (1)
        SQ Q9HVI1 1-125
  2. PilZ domain-associated domain [141377] (2)
    this domain preceeds PilZ domain in some proteins
    1. Hypothetical protein VCA0042, N-terminal domain [141378]
      1. Vibrio cholerae [TaxId: 666] [141379] (1)
        SQ Q9KNC3 23-137
      2. Vibrio cholerae O395 [TaxId: 345073] [159172] (2)
3. YkvR-like [159173] (1)
  provisional classification, pending better resolution structures
  1. YkvR-like [159174] (1)
    PfamB 102647
    1. Uncharacterized protein YkvR [159175]
      1. Bacillus subtilis [TaxId: 1423] [159176] (1)
        SQ O31683 1-96
Phage tail proteins [69278] (1)
core: barrel; n=6, S=10; greek-key; topologically similar to the FMN-binding split barrel
1. Phage tail proteins [69279] (3)
  uperfamily
  1. Baseplate protein-like [69280] (5)
    duplication: consists of two similar barrel domains that differ by the first strand directions; the barrels are differently decorated by alpha+beta insertions
    1. Baseplate structural protein gp27 [69281]
      1. Bacteriophage T4 [TaxId: 10665] [69282] (3)
    2. Hypothetical protein c3393 [159177]
      probable phage-related protein; similar to fusion of the T4 phage gp27 and (a part of) gp5
      1. Escherichia coli o6 [TaxId: 217992] [159178] (2)
        SQ Q8FED2 15-201! SQ Q8FED2 202-377
    3. Baseplate protein gpP [159179]
      43 kda tail protein; Pfam 06893
      1. Neisseria meningitidis [TaxId: 487] [159180] (4)
        SQ Q9JZC8 179-347! SQ Q9JZC8 6-178
        unidentified prophage?
      2. Bacteriophage mu [TaxId: 10677] [159181] (2)
        SQ P08558 177-346! SQ P08558 3-176
      3. Shewanella oneidensis [TaxId: 70863] [159182] (12)
        SQ Q8EDP4 181-348! SQ Q8EDP4 2-180
        Prophage MuSo2
  2. gpFII-like [74966] (2)
    similar to the N-terminal barrel of T4 gp27
    1. Tail attachment protein gpF3 [74967]
      1. Bacteriophage lambda [TaxId: 10710] [74968] (1)
    2. Gifsy-2 prophage protein STM1035 [159183]
      ATP-binding sugar transporter-like protein
      1. Salmonella typhimurium [TaxId: 90371] [159184] (1)
        SQ Q8ZQ92 1-93
  3. XkdM-like [159185] (1)
    Pfam 09393; DUF2001
    1. Phage-like element PBSX protein XkdM [159186]
      1. Bacillus subtilis [TaxId: 1423] [159187] (2)
        SQ P54332 5-143
Surface presentation of antigens (SPOA) [101800] (1)
segment-swapped dimer forming two identical conjoint barrels (n=6, S=10) topologically similar to the FMN-binding split barrel
1. Surface presentation of antigens (SPOA) [101801] (1)
  uperfamily
  1. Surface presentation of antigens (SPOA) [101802] (2)
    1. Putative flagelar motor switch protein FliN [101803]
      1. Thermotoga maritima [TaxId: 2336] [101804] (3)
        TM0680a
    2. Structural protein HrcQ2, C-terminal domain [101805]
      1. Pseudomonas syringae [TaxId: 317] [101806] (1)
FMT C-terminal domain-like [50485] (1)
barrel, open; n*=6, S*=10; greek-key
1. FMT C-terminal domain-like [50486] (2)
  uperfamily
  1. Post formyltransferase domain [50487] (5)
    1. Methionyl-tRNAfmet formyltransferase, C-terminal domain [50488]
      1. Escherichia coli [TaxId: 562] [50489] (2)
      2. Clostridium thermocellum [TaxId: 1515] [117236] (1)
        SQ Q4HJX2; 47% sequence identity; truncated C-terminal domain
        Structural genomics target; GI:67850689
    2. 10-formyltetrahydrofolate dehydrogenase domain 2 [101807]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [101808] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [141380] (2)
        SQ O75891 204-307
    3. Polymyxin resistance protein ArnA, domain 2 [141381]
      1. Escherichia coli [TaxId: 562] [141382] (9)
        SQ P77398 201-304! SQ P77398 204-304
  2. 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) [50490] (1)
    1. 3-methyladenine DNA glycosylase (AAG, ANPG, MPG) [50491]
      1. Human (Homo sapiens) [TaxId: 9606] [50492] (4)
Trypsin-like serine proteases [50493] (1)
barrel, closed; n=6, S=8; greek-key
duplication: consists of two domains of the same fold
1. Trypsin-like serine proteases [50494] (4)
  uperfamily
  1. Prokaryotic proteases [50495] (16)
    1. Achromobacter protease [50496]
      1. Achromobacter lyticus, strain m497-1 [TaxId: 224] [50497] (2)
    2. alpha-Lytic protease [50498]
      1. Lysobacter enzymogenes, 495 [TaxId: 69] [50499] (41)
    3. Protease A [50500]
      1. Streptomyces griseus, strain k1 [TaxId: 1911] [50501] (5)
    4. Glutamic acid-specific protease [50502]
      1. Streptomyces griseus [TaxId: 1911] [50503] (1)
    5. Trypsin [50504]
      1. Streptomyces griseus, strain k1 [TaxId: 1911] [50505] (3)
    6. Serine proteinase [50506]
      1. Streptomyces fradiae [TaxId: 1906] [50507] (1)
    7. Protease B [50508]
      1. Streptomyces griseus, strain k1 [TaxId: 1911] [50509] (29)
        Streptogrisin B
    8. Epidermolytic (exfoliative) toxin A [50510]
      probable glutamic acid-specific protease
      1. Staphylococcus aureus [TaxId: 1280] [50511] (4)
    9. Exfoliative toxin B [50512]
      1. Staphylococcus aureus [TaxId: 1280] [50513] (2)
    10. V8 protease [101809]
      glutamic acid-specific protease
      1. Staphylococcus aureus [TaxId: 1280] [101810] (3)
        SQ P04188 69-284
    11. Glutamyl endopeptidase [101811]
      1. Bacillus intermedius [TaxId: 1400] [101812] (2)
    12. Protease Do (DegP, HtrA), catalytic domain [74969]
      1. Escherichia coli [TaxId: 562] [74970] (14)
      2. Thermotoga maritima [TaxId: 2336] [89339] (1)
    13. Mitochondrial serine protease HtrA2, catalytic domain [74971]
      1. Human (Homo sapiens) [TaxId: 9606] [74972] (1)
    14. Stress sensor protease DegS, catalytic domain [110236]
      1. Escherichia coli [TaxId: 562] [110237] (31)
        SQ P31137 37-354 ! SQ P31137
    15. Protease PepD [141383]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141384] (6)
        SQ O53896 154-374
        Rv0983
  2. Eukaryotic proteases [50514] (68)
    1. Trypsin(ogen) [50515]
      1. Cow (Bos taurus) [TaxId: 9913] [50516] (282)
        SQ P00760
      2. Pig (Sus scrofa) [TaxId: 9823] [50517] (26)
        SQ P00761 9-231 ! SQ P00761
      3. Rat (Rattus norvegicus) [TaxId: 10116] [50518] (33)
      4. Human (Homo sapiens) [TaxId: 9606] [50519] (1)
      5. Human (Homo sapiens), trypsin IV (brain isoform) [TaxId: 9606] [69283] (1)
      6. North atlantic salmon (Salmo salar) [TaxId: 8030] [50520] (11)
      7. Pacific chum salmon (Oncorhynchus keta) [TaxId: 8018] [82121] (1)
      8. Mold (Fusarium oxysporum) [TaxId: 5507] [50521] (16)
      9. Narrow-clawed crayfish (Pontastacus leptodactylus) [TaxId: 6717] [141385] (1)
        SQ Q52V24 1-237
    2. (alpha,gamma)-chymotrypsin(ogen) [50522]
      1. Cow (Bos taurus) [TaxId: 9913] [50523] (62)
        SQ P00766
      2. Rat (Rattus norvegicus) [TaxId: 10116] [89340] (1)
      3. Red fire ant (Solenopsis invicta) [TaxId: 13686] [50524] (1)
    3. Neuropsin [50525]
      1. Mouse (Mus musculus) [TaxId: 10090] [50526] (1)
    4. Crab collagenase [50527]
      1. Atlantic sand fiddler crab (Uca pugilator) [TaxId: 6772] [50528] (1)
    5. HL collagenase [50529]
      1. Common cattle grub (Hypoderma lineatum) [TaxId: 7389] [50530] (2)
    6. Thrombin [50531]
      1. Human (Homo sapiens) [TaxId: 9606] [50532] (164)
        SQ P00734 331-361,364-421 ! SQ P00734 334-360 364-510 518-619 ! SQ P00734 328-620 ! SQ P00734 355-621 ! SQ P00734 328-620
      2. Cow (Bos taurus) [TaxId: 9913] [50533] (26)
        SQ P00734 333-622
    7. Procarboxypeptidase A-S6 subunit III (zymogen E) [50534]
      1. Cow (Bos taurus) [TaxId: 9913] [50535] (2)
    8. Elastase [50536]
      1. Human (Homo sapiens) [TaxId: 9606] [50537] (7)
      2. Pig (Sus scrofa) [TaxId: 9823] [50538] (94)
      3. Salmon (Salmo salar) [TaxId: 8030] [50539] (1)
      4. Worm (Eisenia fetida) [TaxId: 6396] [74973] (1)
        fibrinolytic enzyme component A
    9. Enteropeptidase (enterokinase light chain) [50540]
      1. Cow (Bos taurus) [TaxId: 9913] [50541] (1)
    10. Urokinase [50542]
      1. Human (Homo sapiens) [TaxId: 9606] [50543] (1)
    11. Heparin binding protein, HBP [50544]
      multifunctional protein (synonym: CAP37, azurocidin)
      1. Human (Homo sapiens) [TaxId: 9606] [50545] (4)
    12. Alpha tryptase I [89341]
      1. Human (Homo sapiens) [TaxId: 9606] [89342] (1)
    13. beta-Tryptase [50546]
      ring-like tetramer with active sites facing a central pore
      1. Human (Homo sapiens) [TaxId: 9606] [50547] (33)
    14. Cathepsin G [50548]
      1. Human (Homo sapiens) [TaxId: 9606] [50549] (4)
    15. Coagulation factor VIIa [50550]
      1. Human (Homo sapiens) [TaxId: 9606] [50551] (35)
        SQ P08709 213-466 ! SQ P08709 213-446
    16. Chymase (mast cell protease I) [89343]
      1. Human (Homo sapiens) [TaxId: 9606] [89344] (1)
    17. Chymase II (mast cell proteinase II) [50552]
      1. Rat (Rattus rattus) [TaxId: 10117] [50553] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [50554] (4)
    18. Kallikrein A [50555]
      1. Pig (Sus scrofa) [TaxId: 9823] [50556] (3)
    19. Kallikrein-13 [50572]
      1. Mouse (Mus musculus) [TaxId: 10090] [50573] (1)
    20. Kallikrein 6 [74974]
      1. Human (Homo sapiens) [TaxId: 9606] [74975] (3)
    21. Tonin [50557]
      1. Rat (Rattus rattus) [TaxId: 10117] [50558] (1)
    22. 7S NGF protease subunits [50559]
      two pairs of homologous but non-identical chains
      1. Mouse (Mus musculus) [TaxId: 10090] [50560] (1)
    23. Prostate specific antigen (PSA kallikrein) [82122]
      1. Horse (Equus caballus) [TaxId: 9796] [82123] (1)
    24. Factor B [50561]
      1. Human (Homo sapiens) [TaxId: 9606] [50562] (4)
        SQ P00751 268-764
    25. Factor D [50563]
      1. Human (Homo sapiens) [TaxId: 9606] [50564] (7)
    26. Two-chain tissue plasminogen activator (TC)-T-PA [50565]
      1. Human (Homo sapiens) [TaxId: 9606] [50566] (2)
    27. Single chain tissue plasminogen activator [50567]
      1. Human (Homo sapiens) [TaxId: 9606] [50568] (1)
      2. Vampire bat (Desmodus rotundus) [TaxId: 9430] [50569] (1)
    28. Venom serine protease [50570]
      1. Chinese green tree viper (Trimeresurus stejnegeri) [TaxId: 39682] [50571] (1)
      2. Hundred-pace snake (Agkistrodon acutus) [TaxId: 36307] [110238] (2)
        SQ Q9I8X1
    29. Coagulation factor IXa, protease domain [50583]
      1. Pig (Sus scrofa) [TaxId: 9823] [50584] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [50585] (1)
    30. Coagulation factor Xa, protease domain [50574]
      1. Human (Homo sapiens) [TaxId: 9606] [50575] (76)
        SQ P00742 235-467
      2. Cow (Bos taurus) [TaxId: 9913] [50576] (1)
    31. Coagulation factor Xa-trypsin chimera [50577]
      1. Synthetic, based on Homo sapiens sequence [50578] (1)
        Xa: residues 16-121; trypsin: residues 122-246
    32. Complement C1S protease, catalytic domain [63789]
      1. Human (Homo sapiens) [TaxId: 9606] [63790] (1)
    33. Complement C1R protease, catalytic domain [74976]
      1. Human (Homo sapiens) [TaxId: 9606] [74977] (5)
    34. Activated protein c (autoprothrombin IIa) [50579]
      1. Human (Homo sapiens) [TaxId: 9606] [50580] (1)
    35. Myeloblastin, PR3 [50581]
      1. Human (Homo sapiens) [TaxId: 9606] [50582] (1)
    36. Urokinase-type plasminogen activator (LMW U-PA), catalytic domain [50586]
      1. Human (Homo sapiens) [TaxId: 9606] [50587] (49)
        SQ P00749 156-178,179-424
    37. Plasmin(ogen), catalytic domain [50588]
      1. Human (Homo sapiens) [TaxId: 9606] [50589] (7)
    38. Granzyme A [89345]
      1. Human (Homo sapiens) [TaxId: 9606] [89346] (2)
    39. Granzyme B [50590]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50591] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [50592] (2)
    40. Granzyme K [82124]
      1. Human (Homo sapiens) [TaxId: 9606] [82125] (2)
    41. Duodenase [63791]
      new serine protease
      1. Cow (Bos taurus) [TaxId: 9913] [63792] (1)
    42. Beta-acrosin [50593]
      1. Sheep (Ovis aries) [TaxId: 9940] [50594] (1)
      2. Pig (Sus scrofa) [TaxId: 9823] [50595] (1)
    43. Matriptase MTSP1 [69284]
      1. Human (Homo sapiens) [TaxId: 9606] [69285] (4)
    44. Hepsin, catalytic domain [101813]
      1. Human (Homo sapiens) [TaxId: 9606] [101814] (4)
        SQ P05981 163-417
    45. Hepatocyte growth factor, HGF [110239]
      1. Human (Homo sapiens) [TaxId: 9606] [110240] (2)
        SQ P14210 495-728 ! SQ P14210 495-722
    46. Mannan-binding lectin serine protease 2 (MASP-2), catalytic domain [110241]
      1. Human (Homo sapiens) [TaxId: 9606] [110242] (2)
        SQ O00187 366-686
    47. Coagulation factor XI [117237]
      1. Human (Homo sapiens) [TaxId: 9606] [117238] (4)
        SQ P03951 388-624
  3. Viral proteases [50596] (9)
    beta sheet in the first domain is opened rather than forms a barrel
    1. Viral capsid protein [50597]
      1. Sindbis virus [TaxId: 11034] [50598] (14)
      2. Semliki forest virus [TaxId: 11033] [50599] (2)
      3. Venezuelan equine encephalitis virus [TaxId: 11036] [89347] (2)
    2. TEV protease (nucleat inclusion protein A, NIA) [82126]
      1. Tobacco etch virus, TEV [TaxId: 12227] [82127] (3)
        SQ P04517 2041-2279
    3. NS3 protease [50600]
      1. Human hepatitis C virus (HCV), different isolates [TaxId: 11103] [50601] (14)
        SQ P27958 1027-1206,1678-1669
        SQ P26662 1029-1202,1677-1689
        SQ O36579 1054-1207
      2. Dengue virus type 2 [TaxId: 11060] [50602] (3)
      3. West nile virus [TaxId: 11082] [141386] (2)
        SQ P06935 1520-1671
      4. Dengue virus [TaxId: 12637] [159188] (2)
    4. NSP4 proteinase [82128]
      minimal fold; contains C-terminal extension
      1. Equine arteritis virus, EAV [TaxId: 11047] [82129] (1)
  4. Viral cysteine protease of trypsin fold [50603] (8)
    1. 3C cysteine protease (picornain 3C) [50604]
      1. Human rhinovirus 2 [TaxId: 12130] [50605] (1)
      2. Human hepatitis A virus [TaxId: 208726] [50606] (7)
      3. Human poliovirus 1 Mahoney [TaxId: 12081] [74978] (3)
      4. Foot-and-mouth disease virus FMDV [TaxId: 12110] [159189] (4)
        SQ P49303 1657-1755! SQ P49303 1657-1857
    2. 2A cysteine proteinase [50607]
      1. Human rhinovirus 2 [TaxId: 12130] [50608] (1)
    3. Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2) [74979]
      contains an extra alpha-helical domain
      1. Transmissible gastroenteritis virus [TaxId: 11149] [74980] (4)
      2. Human coronavirus 229E [TaxId: 11137] [89348] (1)
      3. SARS coronavirus [TaxId: 227859] [89349] (26)
Replicase NSP9 [101815] (1)
barrel; n=6, S=8, greek-key; similar to one trypsin-like protease barrel
1. Replicase NSP9 [101816] (1)
  uperfamily
  1. Replicase NSP9 [101817] (1)
    1. Replicase NSP9 [101818]
      part of polyprotein 1AB; binds ssRNA
      1. SARS coronavirus [TaxId: 227859] [101819] (2)
mu transposase, C-terminal domain [50609] (1)
barrel; n=6, S=8, greek-key
1. mu transposase, C-terminal domain [50610] (1)
  uperfamily
  1. mu transposase, C-terminal domain [50611] (1)
    1. mu transposase, C-terminal domain [50612]
      1. Bacteriophage mu [TaxId: 10677] [50613] (2)
Domain of alpha and beta subunits of F1 ATP synthase-like [50614] (3)
barrel, closed; n=6, S=8; greek-key
1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50615] (1)
  uperfamily
  1. N-terminal domain of alpha and beta subunits of F1 ATP synthase [50616] (8)
    6 domains form a ring structure which contains a barrel, closed; n=24, S=24(?)
    1. F1 ATP synthase alpha subunit, domain 1 [88672]
      1. Cow (Bos taurus) [TaxId: 9913] [88673] (18)
        SQ P19483
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88674] (2)
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88675] (1)
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88676] (2)
    2. F1 ATP synthase beta subunit, domain 1 [88677]
      1. Cow (Bos taurus) [TaxId: 9913] [88678] (12)
        SQ P00829
      2. Rat (Rattus norvegicus) [TaxId: 10116] [88679] (8)
      3. Bacillus sp., strain ps3 [TaxId: 1409] [88680] (1)
      4. Spinach (Spinacia oleracea), chloroplast [TaxId: 3562] [88681] (2)
2. Alanine racemase C-terminal domain-like [50621] (2)
  the barrel is decorated with additional structures
  uperfamily
  1. Alanine racemase [88682] (3)
    1. Alanine racemase [50623]
      1. Bacillus stearothermophilus [TaxId: 1422] [50624] (8)
      2. Pseudomonas aeruginosa [TaxId: 287] [110243] (1)
        SQ Q9HTQ2
      3. Streptomyces lavendulae [TaxId: 1914] [110244] (3)
        SQ Q65YW7
  2. Eukaryotic ODC-like [88683] (6)
    barrel is open with strands 4 and 5 having swapped their positions, compared to the alanine racemase barrel
    1. Eukaryotic ornithine decarboxylase (ODC) [50625]
      1. Human (Homo sapiens) [TaxId: 9606] [50626] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [50627] (1)
      3. Trypanosoma brucei [TaxId: 5691] [50628] (5)
        SQ P07805
    2. Diaminopimelate decarboxylase LysA [89350]
      1. Mycobacterium tuberculosis [TaxId: 1773] [89351] (2)
      2. Escherichia coli [TaxId: 562] [101820] (2)
      3. Archaeon Methanococcus jannaschii [TaxId: 2190] [110245] (2)
        SQ Q58497
3. Aminopeptidase/glucanase lid domain [101821] (1)
  uperfamily
  1. Aminopeptidase/glucanase lid domain [101822] (7)
    1. Hypothetical protein YsdC [101823]
      1. Bacillus subtilis [TaxId: 1423] [101824] (1)
    2. Putative endoglucanase TM1048 [101825]
      1. Thermotoga maritima [TaxId: 2336] [101826] (1)
    3. Frv operon protein FrvX [117239]
      1. Pyrococcus horikoshii [TaxId: 53953] [117240] (3)
        SQ O59196 # PH1527
    4. Probable aminopeptidase ApeA [117241]
      1. Borrelia burgdorferi [TaxId: 139] [117242] (1)
        SQ Q45055; BB0366
    5. Deblocking aminopeptidase YhfE [141387]
      1. Bacillus cereus [TaxId: 1396] [141388] (16)
        SQ Q81HB5 74-186
        BC0901
    6. Aminopeptidase YpdE [141389]
      1. Shigella flexneri [TaxId: 623] [141390] (6)
        SQ Q83K87 67-147
        hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)
    7. Endoglucanase TM1049 [141391]
      1. Thermotoga maritima [TaxId: 2336] [141392] (1)
        SQ Q9X0D9 65-148
Small protein B (SmpB) [74981] (1)
barrel, closed; n=6, S=8, greek-key, partial similarity to the OB-fold
1. Small protein B (SmpB) [74982] (1)
  uperfamily
  1. Small protein B (SmpB) [74983] (2)
    1. Small protein B (SmpB) [74984]
      tmRNA-binding protein; SsrA-binding protein
      1. Aquifex aeolicus [TaxId: 63363] [74985] (5)
      2. Thermus thermophilus [TaxId: 274] [82130] (6)
        SQ Q8RR57 4-123
Acid proteases [50629] (1)
barrel, closed; n=6, S=10, complex topology
1. Acid proteases [50630] (3)
  uperfamily
  1. Retroviral protease (retropepsin) [50631] (8)
    dimer of identical mono-domain chains, each containing (6,10) barrel
    1. Human immunodeficiency virus type 1 protease [50632]
      1. Human immunodeficiency virus type 1 [TaxId: 11676] [50633] (317)
        SQ P35963 57-155 ! SQ P04587 69-167 ! SQ P03366 69-167 ! SQ P03367 69-167 ! SQ P03368 69-167
    2. Human immunodeficiency virus type 2 (HIV-2) protease [50634]
      1. Human immunodeficiency virus type 2 [TaxId: 11709] [50635] (21)
    3. Simian immunodeficiency virus (SIV) protease [50636]
      1. Simian immunodeficiency virus, different strains [TaxId: 11723] [50637] (18)
    4. Feline immunodeficiency virus (FIV) protease [50638]
      1. Feline immunodeficiency virus [TaxId: 11673] [50639] (7)
    5. Rous sarcoma virus protease [50640]
      1. Rous sarcoma virus, strain pr-C [TaxId: 11886] [50641] (2)
    6. Myeloblastosis-associated viral protease [50642]
      1. Avian myeloblastosis associated virus [TaxId: 11960] [50643] (1)
    7. EIAV protease [50644]
      1. Equine infectious anemia virus [TaxId: 11665] [50645] (2)
    8. Mason-Pfizer monkey virus protease [82131]
      1. Simian retrovirus 1, SRV-1 [TaxId: 11942] [82132] (1)
  2. Pepsin-like [50646] (26)
    duplication: consists of two similar barrel domains
    N-terminal: barrel, partly opened; n*=6, S*=10
    1. Endothiapepsin [50647]
      1. Chestnut blight fungus (Endothia parasitica) [TaxId: 5116] [50648] (36)
    2. Acid protease [50649]
      1. Fungus (Penicillium janthinellum), penicillopepsin [TaxId: 5079] [50650] (14)
      2. Fungus (Aspergillus phoenicis), aspergillopepsin [TaxId: 5063] [63794] (1)
      3. Fungus (Aspergillus oryzae) [TaxId: 5062] [89352] (2)
      4. Bread mold (Rhizopus chinensis) [TaxId: 4843] [50651] (8)
        SQ P06026 69-393
      5. Rhizomucor miehei [TaxId: 4839] [50652] (2)
      6. Yeast (Candida albicans) [TaxId: 5476] [50653] (2)
      7. Yeast (Candida tropicalis) [TaxId: 5482] [63795] (1)
      8. Baker's yeast (Saccharomyces cerevisiae), proteinase A [TaxId: 4932] [50654] (11)
        synonym: saccharopepsin
      9. Irpex lacteus (Polyporus tulipiferae), Polyporopepsin [TaxId: 5319] [110246] (1)
        SQ P17576 1-329
    3. Plant acid proteinase, phytepsin [50655]
      1. Cynara cardunculus [TaxId: 4265] [50656] (1)
      2. Barley (Hordeum vulgare) [TaxId: 4513] [50657] (1)
    4. Pepsin(ogen) [50658]
      1. Pig (Sus scrofa) [TaxId: 9823] [50659] (8)
      2. Human (Homo sapiens), isoform 3A [TaxId: 9606] [50660] (4)
      3. Human (Homo sapiens), progastricsin (pepsinogen C) [TaxId: 9606] [50661] (2)
      4. Atlantic cod (Gadus morhua) [TaxId: 8049] [50662] (1)
    5. Pepsin [50663]
      1. Mucor pusillus [TaxId: 4840] [50664] (1)
    6. Cathepsin D [50665]
      1. Human (Homo sapiens) [TaxId: 9606] [50666] (3)
    7. Chymosin (synonym: renin) [50667]
      1. Cow (Bos taurus) [TaxId: 9913] [50668] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [50669] (7)
      3. Mouse (Mus musculus) [TaxId: 10090] [50670] (4)
    8. beta-secretase (memapsin) [50671]
      1. Human (Homo sapiens) [TaxId: 9606] [50672] (90)
        SQ P56817 58-446 ! SQ P56817 60-447
    9. Plasmepsin (a hemoglobin-degrading enzyme) [50673]
      1. Plasmodium falciparum, plasmepsin II [TaxId: 5833] [50674] (24)
      2. Plasmodium falciparum, plasmepsin IV [TaxId: 5833] [74986] (1)
      3. Plasmodium vivax [TaxId: 5855] [50675] (2)
    10. Xylanase inhibitor TAXI-I [110247]
      pepsin-like protein that probably lost the protease activity
      1. Wheat (Triticum aestivum) [TaxId: 4565] [110248] (3)
        SQ Q8H0K8 22-402
  3. LPG0085-like [159190] (1)
    Pfam 05618; DUF785; single-domain protein similar to one pepsin domain with the conserved catalytic Asp motif (not in a few archaeal members of this Pfam family)
    1. Uncharacterized protein LPG0085 [159191]
      1. Legionella pneumophila [TaxId: 446] [159192] (2)
        SQ Q5ZZC6 26-166
ValRS/IleRS/LeuRS editing domain [50676] (1)
core: barrel, closed; n=6, S=8; topology is similar to that of the acid proteases barrel
1. ValRS/IleRS/LeuRS editing domain [50677] (1)
  uperfamily
  1. ValRS/IleRS/LeuRS editing domain [50678] (4)
    inserted into the catalytic domain
    1. Isoleucyl-tRNA synthetase (IleRS) [50679]
      1. Thermus thermophilus [TaxId: 274] [50680] (5)
      2. Staphylococcus aureus [TaxId: 1280] [50681] (3)
    2. Valyl-tRNA synthetase (ValRS) [50682]
      1. Thermus thermophilus [TaxId: 274] [50683] (5)
    3. Leucyl-tRNA synthetase (LeuRS) [82133]
      in the prokaryotic and mitochondrial LeuRS this domain is inserted into a different sequential position
      1. Thermus thermophilus [TaxId: 274] [82134] (3)
Urease metallochaperone UreE, N-terminal domain [69286] (1)
barrel, closed; n=6, S=8; a crossover loop topology
1. Urease metallochaperone UreE, N-terminal domain [69287] (1)
  uperfamily
  1. Urease metallochaperone UreE, N-terminal domain [69288] (2)
    1. Urease metallochaperone UreE, N-terminal domain [69289]
      1. Klebsiella aerogenes [TaxId: 28451] [69290] (3)
      2. Bacillus pasteurii [TaxId: 1474] [69291] (2)
Double psi beta-barrel [50684] (2)
barrel, closed; n=6, S=10; complex topology with crossover (psi) loops
1. Barwin-like endoglucanases [50685] (4)
  uperfamily
  1. Eng V-like [50686] (3)
    1. Endoglucanase V (Eng V) [50687]
      1. Humicola insolens [TaxId: 34413] [50688] (4)
      2. Fungus (Melanocarpus albomyces) [TaxId: 204285] [89353] (3)
    2. Endoglucanase (CMCase) [159193]
      1. Blue mussel (Mytilus edulis) [TaxId: 6550] [159194] (1)
        SQ P82186 1-180
  2. Pollen allergen PHL P 1 N-terminal domain [82135] (1)
    conserved Eng V active site residues and disulfides; better structural similarity to the ADC-like superfamily
    1. Pollen allergen PHL P 1 N-terminal domain [82136]
      1. Timothy grass (Phleum pratense) [TaxId: 15957] [82137] (1)
  3. Barwin [50689] (1)
    1. Barwin [50690]
      1. Barley (Hordeum vulgare) [TaxId: 4513] [50691] (2)
  4. MLTA-like [159195] (3)
    Pfam 03562 and Pfam 06725 cover the middle and C-terminal parts, respectively; contains large insert domain of the L25-like fold (scop_cf 50714)
    1. Membrane-bound lytic murein transglycosylase A, MLTA [159196]
      1. Agrobacterium tumefaciens [TaxId: 358] [159197] (1)
        SQ Q8UJB9 5-369
      2. Escherichia coli [TaxId: 562] [159198] (8)
        SQ P0A935 22-357! SQ P0A935 23-357! SQ P0A935 24-356
      3. Neisseria gonorrhoeae [TaxId: 485] [159199] (2)
        SQ Q9L6H1 40-441
2. ADC-like [50692] (3)
  uperfamily
  1. Pyruvoyl dependent aspartate decarboxylase, ADC [50693] (2)
    1. Pyruvoyl dependent aspartate decarboxylase, ADC [50694]
      autocatalytic enzyme
      1. Escherichia coli [TaxId: 562] [50695] (9)
      2. Helicobacter pylori [TaxId: 210] [110249] (2)
        SQ P56065
  2. Formate dehydrogenase/DMSO reductase, C-terminal domain [50696] (12)
    molybdopterine enzyme
    1. Dimethylsulfoxide reductase (DMSO reductase) [50697]
      1. Rhodobacter sphaeroides [TaxId: 1063] [50698] (1)
      2. Rhodobacter capsulatus [TaxId: 1061] [50699] (10)
    2. Formate dehydrogenase H [50700]
      1. Escherichia coli [TaxId: 562] [50701] (4)
    3. Formate dehydrogenase N, alpha subunit [74987]
      1. Escherichia coli [TaxId: 562] [74988] (2)
    4. Tungsten containing formate dehydrogenase, large subunit [82138]
      1. Desulfovibrio gigas [TaxId: 879] [82139] (1)
    5. Trimethylamine N-oxide reductase [50702]
      1. Shewanella massilia [TaxId: 76854] [50703] (1)
    6. Arsenite oxidase large subunit [50704]
      1. Alcaligenes faecalis [TaxId: 511] [50705] (2)
    7. Periplasmic nitrate reductase alpha chain, NapA [50706]
      1. Desulfovibrio desulfuricans [TaxId: 876] [50707] (8)
        dissimilatory nitrate reductase (NAP)
      2. Rhodobacter sphaeroides [TaxId: 1063] [101827] (1)
    8. Respiratory nitrate reductase 1 alpha chain [101828]
      1. Escherichia coli [TaxId: 562] [101829] (7)
        SQ P09152
    9. Transhydroxylase alpha subunit, AthL [110250]
      1. Pelobacter acidigallici [TaxId: 35816] [110251] (6)
        SQ P80563
    10. NADH-quinone oxidoreductase chain 3, Nqo3, C-terminal domain [141393]
      topoisomer of the common fold, lacking the second psi loop
      1. Thermus thermophilus [TaxId: 274] [141394] (4)
        SQ Q56223 686-767
  3. Cdc48 N-terminal domain-like [50708] (5)
    1. N-terminal domain of NSF-N, NSF-Nn [50709]
      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] [50710] (2)
      2. Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932] [50711] (1)
    2. N-terminal domain of VAT-N, VAT-Nn [50712]
      VAT-N is the N-terminal 'functional' domain of the VCP-like ATPase
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [50713] (2)
    3. Membrane fusion ATPase p97 N-terminal domain , P97-Nn [63796]
      1. Mouse (Mus musculus) [TaxId: 10090] [63797] (5)
    4. Peroxisome biogenesis factor 1 (PEX-1), N-terminal domain [110252]
      1. Mouse (Mus musculus) [TaxId: 10090] [110253] (1)
        SQ Q5BL07 13-179
Ribosomal protein L25-like [50714] (1)
barrel, closed; n=6, S=10; complex topology
1. Ribosomal protein L25-like [50715] (2)
  uperfamily
  1. Ribosomal protein L25-like [50716] (3)
    1. Ribosomal protein L25 [50717]
      1. Escherichia coli [TaxId: 562] [50718] (32)
    2. Ribosomal protein TL5 (general stress protein CTC) [63798]
      contains additional all-beta (sub)domain in the C-terminal extension
      1. Thermus thermophilus [TaxId: 274] [63799] (12)
      2. Deinococcus radiodurans [TaxId: 1299] [159200] (10)
        SQ Q9RX88 1-175
  2. Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [50719] (2)
    1. Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [50720]
      duplication, consists of two barrel domains with the swapping of N-terminal strands
      1. Escherichia coli [TaxId: 562] [50721] (14)
      2. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159201] (2)
Core binding factor beta, CBF [50722] (1)
barrel, closed; n=6, S=10; meander; capped at both ends by alpha-helices
1. Core binding factor beta, CBF [50723] (1)
  uperfamily
  1. Core binding factor beta, CBF [50724] (2)
    1. Core binding factor beta, CBF [50725]
      1. Human (Homo sapiens) [TaxId: 9606] [50726] (3)
      2. Mouse (Mus musculus) [TaxId: 10090] [50727] (3)
NifT/FixU barrel-like [159202] (1)
barrel, closed, n=6, S=10; meander
1. NifT/FixU-like [159203] (1)
  1. NifT/FixU [159204] (1)
    Pfam 06988
    1. Uncharacterized protein FixU (NifT) [159205]
      1. Rhodopseudomonas palustris [TaxId: 1076] [159206] (1)
        SQ Q6N0Y6 1-66
PH domain-like barrel [50728] (2)
barrel, partly opened; n*=6, S*=12; meander; capped by an alpha-helix
1. PH domain-like [50729] (13)
  uperfamily
  1. Pleckstrin-homology domain (PH domain) [50730] (51)
    Pfam 00169
    1. Phospholipase C delta-1 [50731]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50732] (1)
    2. beta-spectrin [50733]
      1. Mouse (Mus musculus), brain [TaxId: 10090] [50734] (2)
      2. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [50735] (1)
      3. Human (Homo sapiens), brain 2 isoform [TaxId: 9606] [117243] (1)
        SQ O15020 2219-2324
    3. Dynamin [50736]
      1. Human (Homo sapiens) [TaxId: 9606] [50737] (2)
    4. Bruton's tyrosine kinase [50738]
      contains Btk zinc-binding motif
      1. Human (Homo sapiens) [TaxId: 9606] [50739] (7)
    5. Pleckstrin [50740]
      1. Human (Homo sapiens) [TaxId: 9606] [50741] (9)
    6. Son of sevenless-1 (sos-1) [50742]
      1. Mouse (Mus musculus) [TaxId: 10090] [50743] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [50744] (4)
        SQ Q07889 189-1046
    7. GEF of TIAM1 (T-Lymphoma invasion and metastasis inducing protein 1) [50745]
      1. Mouse (Mus musculus) [TaxId: 10090] [50746] (1)
    8. Dbl's big sister, Dbs [74989]
      1. Mouse (Mus musculus) [TaxId: 10090] [74990] (4)
        SQ Q64096 624-958 # 98% sequence identity; the rat sequence Q63406 region 499-833 is 100% identical to the PDB sequence
    9. GEF of intersectin [74991]
      1. Human (Homo sapiens) [TaxId: 9606] [74992] (1)
    10. G-protein coupled receptor kinase 2 (beta-adrenergic receptor kinase 1) [50747]
      1. Human (Homo sapiens) [TaxId: 9606] [50748] (1)
      2. Cow (Bos taurus) [TaxId: 9913] [89354] (6)
    11. Dual adaptor of phosphotyrosine and 3-phosphoinositides DAPP1/PHISH [50749]
      1. Human (Homo sapiens) [TaxId: 9606] [50750] (2)
    12. Grp1 [50751]
      ARF1 Guanine nucleotide exchange factor and integrin binding protein homolog
      1. Mouse (Mus musculus) [TaxId: 10090] [50752] (8)
    13. UNC-89 [50753]
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [50754] (1)
    14. Tapp1 [74993]
      1. Human (Homo sapiens) [TaxId: 9606] [74994] (1)
    15. Rac-alpha serine/threonine kinase [89355]
      1. Human (Homo sapiens) [TaxId: 9606] [89356] (5)
        SQ P31749 1-117
    16. Rac-beta serine/threonine protein kinase (PKB/AKT) [110254]
      1. Human (Homo sapiens) [TaxId: 9606] [110255] (1)
        SQ P31751 1-111
    17. SH2 and PH domain-containing adapter protein APS [110256]
      1. Mouse (Mus musculus) [TaxId: 10090] [110257] (1)
        SQ Q9JID9 178-299
    18. Tapp2 [110258]
      1. Mouse (Mus musculus) [TaxId: 10090] [110259] (1)
        SQ Q9ERS5 1-113
    19. SET binding factor 1, Sbf1 [110260]
      1. Mouse (Mus musculus) [TaxId: 10090] [110261] (1)
        SQ Q8K2Z0 256-367
    20. Rac/CDC42 GEF 6, alpha-pix [110262]
      1. Mouse (Mus musculus) [TaxId: 10090] [110263] (1)
        SQ Q8K4I3 429-551
    21. Triple functional domain protein TRIO [110264]
      1. Human (Homo sapiens) [TaxId: 9606] [110265] (2)
        SQ O75962 1231-1535
    22. Oxysterol binding protein-related protein 8 (ORP-8, KIAA1451) [110266]
      1. Human (Homo sapiens) [TaxId: 9606] [110267] (1)
        SQ Q9BZF1 149-265
    23. Rho-GTPase-activating protein 25 (KIAA0053) [110268]
      1. Human (Homo sapiens) [TaxId: 9606] [110269] (1)
        SQ P42331 40-144
    24. Rho guanine nucleotide exchange factor 12 [110270]
      1. Human (Homo sapiens), gamma isoform [TaxId: 9606] [110271] (2)
        SQ Q9NZN5 766-1138
    25. Phosphoinositol 3-phosphate binding protein-1, PEPP1 [117244]
      1. Human (Homo sapiens) [TaxId: 9606] [117245] (2)
        SQ Q9H4M7 47-153
    26. 3-phosphoinositide dependent protein kinase-1 [117246]
      1. Human (Homo sapiens) [TaxId: 9606] [117247] (3)
        SQ O15530 409-550
    27. Dedicator of cytokinesis protein 9, DOCK9 [117248]
      1. Human (Homo sapiens) [TaxId: 9606] [117249] (1)
        SQ Q9BZ29 165-301
    28. FYVE, RhoGEF and PH domain containing protein 6, Fgd6 (KIAA1362) [117250]
      1. Mouse (Mus musculus) [TaxId: 10090] [117251] (1)
        SQ Q69ZL1 1303-1389
    29. Calcium-dependent activator protein for secretion, CAPS [117252]
      1. Human (Homo sapiens) [TaxId: 9606] [117253] (1)
        SQ Q8NFR0 522-634
    30. Rho guanine nucleotide exchange factor 11, PDZ-RhoGEF [117254]
      1. Human (Homo sapiens) [TaxId: 9606] [117255] (1)
        SQ O15085 714-1081
    31. Centaurin-delta 1 [141395]
      1. Human (Homo sapiens) [TaxId: 9606] [141396] (1)
        SQ Q8WZ64 483-584
    32. Cytohesin 3 [141397]
      1. Mouse (Mus musculus) [TaxId: 10090] [141398] (1)
        SQ O08967 261-387
    33. Exocyst complex protein EXO84 [141399]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141400] (4)
        SQ O54924 171-283
    34. Cytohesin 2 [141401]
      1. Mouse (Mus musculus) [TaxId: 10090] [141402] (2)
        SQ P63034 260-378
    35. Src kinase-associated phosphoprotein SKAP55 (SCAP1) [141403]
      1. Human (Homo sapiens) [TaxId: 9606] [141404] (4)
        SQ O15268 108-213
    36. Signal-transducing adaptor protein 1, STAP-1 [141405]
      1. Human (Homo sapiens) [TaxId: 9606] [141406] (1)
        SQ Q9ULZ2 16-151
    37. KIAA1914 [141407]
      1. Human (Homo sapiens) [TaxId: 9606] [141408] (1)
        SQ Q8N4X5 354-448
    38. Pleckstrin-2 [141409]
      1. Human (Homo sapiens) [TaxId: 9606] [141410] (1)
        SQ Q9NYT0 238-353
    39. Alpha-1-syntrophin [141411]
      1. Mouse (Mus musculus) [TaxId: 10090] [141412] (1)
        SQ Q61234 2-44,203-264
    40. Phosphoinositide phospholipase C, PLC-gamma-1 [141413]
      contains split PH domain
      1. Rat (Rattus norvegicus) [TaxId: 10116] [141414] (1)
        SQ P10686 489-525,870-933
    41. FYVE, RhoGEF and PH domain containing protein 3, FGD3 [141415]
      1. Human (Homo sapiens) [TaxId: 9606] [141416] (1)
        SQ Q5JSP0 605-703
    42. Src-associated adaptor protein Skap2 [141417]
      1. Mouse (Mus musculus) [TaxId: 10090] [141418] (9)
        SQ Q9Z2K4 105-212! SQ Q9Z2K4 109-219! SQ Q9Z2K4 14-222
    43. Protein kinase c, d2 type [141419]
      1. Human (Homo sapiens) [TaxId: 9606] [141420] (1)
        SQ Q9BZL6 398-509
    44. Phospholipase C-beta-2 [159207]
      1. Human (Homo sapiens) [TaxId: 9606] [159208] (2)
        SQ Q00722 11-141
    45. Rho guanine nucleotide exchange factor 9, Collybistin [159209]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [159210] (1)
        SQ Q9QX73 300-461
    46. DCC-interacting protein 13-alpha, APPL1 [159211]
      1. Human (Homo sapiens) [TaxId: 9606] [159212] (1)
        SQ Q9UKG1 274-374
    47. Rho GTPase-activating protein 21 [159213]
      1. Human (Homo sapiens) [TaxId: 9606] [159214] (6)
        SQ Q5T5U3 931-1063
  2. Phosphotyrosine-binding domain (PTB) [50755] (14)
    Pfam 00640
    1. X11 [50756]
      1. Human (Homo sapiens) [TaxId: 9606] [50757] (2)
    2. Insulin receptor substrate 1, IRS-1 [50758]
      duplication: contains two domains of this fold
      1. Human (Homo sapiens) [TaxId: 9606] [50759] (2)
    3. Shc adaptor protein [50760]
      1. Human (Homo sapiens) [TaxId: 9606] [50761] (3)
    4. Numb [50762]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [50763] (2)
      2. Mouse (Mus musculus) [TaxId: 10090] [117256] (1)
        SQ Q9QZS3 19-172
    5. Disabled homolog 1 (Dab1) [89357]
      1. Mouse (Mus musculus) [TaxId: 10090] [89358] (3)
    6. Disabled homolog 2 (Dab2) [101830]
      1. Mouse (Mus musculus) [TaxId: 10090] [101831] (2)
    7. Downstream of tyrosine kinase 5, Dok-5 [101832]
      1. Human (Homo sapiens) [TaxId: 9606] [101833] (1)
    8. Docking protein 1, Dok1 [101834]
      1. Mouse (Mus musculus) [TaxId: 10090] [101835] (2)
        SQ P97465 152-254
    9. FGFR substrate 2 (SNT-1) [117257]
      1. Human (Homo sapiens) [TaxId: 9606] [117258] (1)
        SQ Q7LDQ6 11-129
    10. Amyloid beta A4 precursor protein-binding family B member 2, Apbb2 [117259]
      1. Mouse (Mus musculus) [TaxId: 10090] [117260] (2)
        SQ Q9DBR4 582-704
    11. Tensin [141421]
      1. Human (Homo sapiens) [TaxId: 9606] [141422] (1)
        SQ Q9UPS7 1139-1285
        Tensin2
      2. Chicken (Gallus gallus) [TaxId: 9031] [141423] (1)
        SQ Q04205 1606-1738
    12. EPS8-like protein 1, EPS8L1 [141424]
      1. Mouse (Mus musculus) [TaxId: 10090] [141425] (2)
        SQ Q8R5F8 31-159
  3. Ran-binding domain [50764] (4)
    1. Nuclear pore complex protein Nup358 [50765]
      1. Human (Homo sapiens) [TaxId: 9606] [50766] (1)
    2. Ran-binding protein 1, Ranbp1 [69292]
      1. Human (Homo sapiens) [TaxId: 9606] [69293] (2)
    3. Ran binding protein 3 [141426]
      1. Human (Homo sapiens) [TaxId: 9606] [141427] (1)
        SQ Q9H6Z4 380-516
    4. Ran-binding protein 2 [141428]
      1. Human (Homo sapiens) [TaxId: 9606] [141429] (1)
        SQ P49792 2027-2154
  4. Enabled/VASP homology 1 domain (EVH1 domain) [50767] (8)
    1. Enabled [50768]
      1. Mouse (Mus musculus) [TaxId: 10090] [50769] (1)
      2. Homo sapiens [TaxId: 9606] [159215] (4)
    2. Ena/vasp-like protein [50770]
      1. Mouse (Mus musculus) [TaxId: 10090] [50771] (1)
    3. Vasodilator-stimulated phosphoprotein (VASP) [50772]
      1. Human (Homo sapiens) [TaxId: 9606] [50773] (1)
    4. Homer [50774]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50775] (3)
      2. Mouse (Mus musculus), 2b/vesl 2 [TaxId: 10090] [63800] (1)
    5. Actin regulatory protein WASP [82140]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [82141] (1)
    6. Sprouty-related, EVH1 domain-containing protein 1, Spred-1 [141430]
      1. Western clawed frog (Xenopus tropicalis) [TaxId: 8364] [141431] (4)
        SQ Q66JG9 10-123! SQ Q66JG9 9-123
  5. Dcp1 [101836] (1)
    close structural similarity to EVH1 domain
    1. Dcp1 [101837]
      decapping protein involved in mRNA degradation
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101838] (1)
  6. Third domain of FERM [50776] (9)
    1. Moesin [50777]
      1. Human (Homo sapiens) [TaxId: 9606] [50778] (3)
        SQ P26038 4-297
    2. Radixin [50779]
      1. Mouse (Mus musculus) [TaxId: 10090] [50780] (20)
    3. Ezrin [82142]
      complexed with the icam-2 cytoplasmic peptide, chain B
      1. Human (Homo sapiens) [TaxId: 9606] [82143] (1)
    4. Erythroid membrane protein 4.1R [50781]
      1. Human (Homo sapiens) [TaxId: 9606] [50782] (1)
    5. Merlin [69294]
      the neurofibromatosis 2 tumor suppressor protein
      1. Human (Homo sapiens) [TaxId: 9606] [69295] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [74995] (1)
    6. Talin [82144]
      1. Chicken (Gallus gallus) [TaxId: 9031] [82145] (6)
    7. Talin-1 [117261]
      1. Mouse (Mus musculus) [TaxId: 10090] [117262] (1)
        SQ P26039 209-410
    8. Focal adhesion kinase 1 [141432]
      1. Chicken (Gallus gallus) [TaxId: 9031] [141433] (5)
        SQ Q00944 254-363
  7. PreBEACH PH-like domain [82146] (2)
    1. PH-like domain of neurobeachin [82147]
      1. Human (Homo sapiens) [TaxId: 9606] [82148] (1)
    2. Lipopolysaccharide-responsive and beige-like anchor protein LRBA [117263]
      1. Human (Homo sapiens) [TaxId: 9606] [117264] (1)
        SQ P50851 2076-2489
  8. GRAM domain [101839] (1)
    1. Myotubularin-related protein 2, N-terminal domain [101840]
      1. Human (Homo sapiens) [TaxId: 9606] [101841] (4)
  9. TFIIH domain [110272] (2)
    1. TFIIH basal transcription factor complex p62 subunit (BTF2-p62), N-terminal domain [110273]
      1. Human (Homo sapiens) [TaxId: 9606] [110274] (2)
        SQ P32780 1-108
    2. RNA polymerase II transcription factor B 73 kDa, TFB1 [141434]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141435] (3)
        SQ P32776 2-115
  10. SSRP1-like [141436] (1)
    Pfam 03531; Structure-specific recognition protein family; duplication: comprises tandem repeat of two domains of this fold
    1. FACT complex subunit POB3, middle domain [141437]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141438] (6)
        SQ Q04636 237-474! SQ Q04636 238-474
  11. Necap1 N-terminal domain-like [141439] (1)
    Pfam 07933; DUF1681
    1. Necap1 [141440]
      1. Mouse (Mus musculus) [TaxId: 10090] [141441] (1)
        SQ Q9CR95 1-133
  12. VPS36 N-terminal domain-like [141442] (3)
    PfamB 030385
    1. Vacuolar protein sorting protein 36, VPS36 [141443]
      1. Human (Homo sapiens) [TaxId: 9606] [141444] (1)
        SQ Q86VN1 3-131
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141445] (2)
        SQ Q06696 1-99,252-282
      3. Mouse (Mus musculus) [TaxId: 10090] [141446] (1)
        SQ Q91XD6 10-130
  13. BPHL domain [159216] (2)
    Pfam 08000; DUF1696, bacterial proteins with PH-like domain
    1. Uncharacterized protein Exig2160 [159217]
      homododecameric ring assembly; olizomerization is mediated by the C-terminal alpha-hairpin extension
      1. Exiguobacterium sibiricum 255-15 [TaxId: 262543] [159218] (6)
        SQ B1YJX4 14-203
    2. Uncharacterized protein Shew0819 [159219]
      homopentameric ring assembly through the pairing of the beta-barrel edge strands
      1. Shewanella loihica [TaxId: 359303] [159220] (5)
        SQ A3QB43 9-124
2. PA2021-like [141447] (1)
  prokaryotiic proteins of PH domain-like fold lacking the N-terminal strand
  uperfamily
  1. PA2021-like [141448] (1)
    small family specific to Pseudomonas
    1. Hypothetical protein PA2021 [141449]
      1. Pseudomonas aeruginosa [TaxId: 287] [141450] (1)
        SQ Q9I293 1-74
Transcription factor IIA (TFIIA), beta-barrel domain [50783] (1)
barrel, closed; n=6, S=12; mixed beta-sheet
1. Transcription factor IIA (TFIIA), beta-barrel domain [50784] (1)
  dimer of non-identical beta-sheet domains
  uperfamily
  1. Transcription factor IIA (TFIIA), beta-barrel domain [50785] (4)
    heterodimer of two homologous chains
    1. Large chain TOA1, C-terminal domain [88684]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88685] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [101842] (1)
    2. Small chain TOA2, C-terminal domain [88686]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88687] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [101843] (1)
Hcp1-like [141451] (1)
barrel, closed; n=6, S=12; contains extra, non-barrel strand 7 at the C-terminus
1. Hcp1-like [141452] (1)
  probable biological unit is a ring-like hexamer containing a 24-stranded beta-barrel made of the subunit beta-sheets
  uperfamily
  1. Hcp1-like [141453] (1)
    Pfam 05638; DUF796
    1. Hemolysin-corregulated protein 1, Hcp1 [141454]
      1. Pseudomonas aeruginosa [TaxId: 287] [141455] (3)
        SQ Q9I747 2-162
        PA0085
YopT-like [159221] (1)
beta-sheet barrel, closed, n=6, S=12, capped at both ends by helices; intertwined dimer of beta-alpha-beta(2) subinits;
1. YopT-like [159222] (1)
  1. YopT-like [159223] (1)
    Pfam 09467
    1. Uncharacterized protein YopT [159224]
      probably of phage origin
      1. Bacillus subtilis [TaxId: 1423] [159225] (2)
        SQ O34498 2-71
Herpes virus serine proteinase, assemblin [50788] (1)
core: barrel, closed; n=7, S=8; complex topology
1. Herpes virus serine proteinase, assemblin [50789] (1)
  uperfamily
  1. Herpes virus serine proteinase, assemblin [50790] (5)
    1. Human cytomegalovirus protease [50791]
      1. Human cytomegalovirus [TaxId: 10359] [50792] (15)
    2. HSV-2 protease [50793]
      1. Herpes simplex virus type 2 [TaxId: 10310] [50794] (1)
    3. KSHV protease [50795]
      1. Kaposi's sarcoma-associated herpesvirus [TaxId: 37296] [50796] (3)
    4. Epstein-Barr virus protease [82149]
      1. Human herpesvirus 4 [TaxId: 10376] [82150] (1)
    5. VZV protease [50797]
      1. Varicella-Zoster virus [TaxId: 10335] [50798] (1)
PK beta-barrel domain-like [50799] (1)
barrel, closed; n=7, S=10; complex topology
1. PK beta-barrel domain-like [50800] (2)
  uperfamily
  1. Pyruvate kinase beta-barrel domain [50801] (6)
    this domain interrupts beta/alpha-barrel domain
    C-terminal domain is alpha/beta
    1. Pyruvate kinase (PK) [50802]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [50803] (14)
      2. Cat (Felis catus) [TaxId: 9685] [50804] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [82151] (4)
      4. Leishmania mexicana [TaxId: 5665] [50805] (8)
      5. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50806] (2)
      6. Escherichia coli [TaxId: 562] [50807] (3)
  2. MOSC (MOCO sulphurase C-terminal) domain [101844] (2)
    Pfam 03473
    1. Hypothetical protein YuaD [101845]
      1. Bacillus subtilis [TaxId: 1423] [101846] (1)
    2. Hypothetical protein YiiM [101847]
      1. Escherichia coli [TaxId: 562] [101848] (2)
XRCC4, N-terminal domain [50808] (1)
barrel, closed; n=7, S=10; order: 1234765; strands 1 and 5 are parallel to each other
1. XRCC4, N-terminal domain [50809] (1)
  an HTH motif connects strands 4 and 5
  uperfamily
  1. XRCC4, N-terminal domain [50810] (1)
    1. XRCC4, N-terminal domain [50811]
      1. Human (Homo sapiens) [TaxId: 9606] [50812] (2)
HesB-like domain [89359] (1)
barrel, closed; n=7, S=10; complex topology
1. HesB-like domain [89360] (1)
  uperfamily
  1. HesB-like domain [89361] (3)
    Pfam 01521; Iron-sulfur cluster scaffold domain
    1. Fe-S scaffold protein IscA (YfhF) [101849]
      1. Escherichia coli [TaxId: 562] [101850] (3)
        SQ P36539
    2. Hypothetical protein Aq_1857 [89362]
      1. Aquifex aeolicus [TaxId: 63363] [89363] (1)
    3. Putative Fe-S biosynthesis protein LSL1730 [159226]
      1. Lactobacillus salivarius [TaxId: 1624] [159227] (1)
        SQ Q1WRG6 1-118
Bacterial fluorinating enzyme, C-terminal domain [101851] (1)
barrel, closed; n=7, S=10; greek-key topology; one overside connection
1. Bacterial fluorinating enzyme, C-terminal domain [101852] (1)
  uperfamily
  1. Bacterial fluorinating enzyme, C-terminal domain [101853] (1)
    1. 5'-fluoro-5'-deoxyadenosine synthase [101854]
      1. Streptomyces cattleya [TaxId: 29303] [101855] (41)
SPOC domain-like [100938] (1)
barrel, closed; n=7, S=10; complex topology
1. SPOC domain-like [100939] (3)
  uperfamily
  1. SPOC domain [101856] (1)
    1. SMART/HDAC1 associated repressor protein, SHARP [101857]
      1. Human (Homo sapiens) [TaxId: 9606] [101858] (1)
  2. Ku70 subunit middle domain [100940] (1)
    includes C-terminal alpha-helical arm and DNA encircling insertion
    1. Ku70 subunit middle domain [100941]
      1. Human (Homo sapiens) [TaxId: 9606] [100942] (2)
  3. Ku80 subunit middle domain [100943] (1)
    includes C-terminal alpha-helical arm and DNA encircling insertion
    1. Ku80 subunit middle domain [100944]
      1. Human (Homo sapiens) [TaxId: 9606] [100945] (2)
BH3618-like [141456] (1)
barrel, closed; n=7, S=10; meander
1. BH3618-like [141457] (1)
  uperfamily
  1. BH3618-like [141458] (1)
    Pfam 02623; DUF180
    1. Hypothetical protein BH3618 [141459]
      B. subtilis YviF homolog
      1. Bacillus halodurans [TaxId: 86665] [141460] (2)
        SQ Q9K6V7 1-148
FAS1 domain [82152] (1)
core: barrel, closed; n=7, S=12; meander
1. FAS1 domain [82153] (1)
  uperfamily
  1. FAS1 domain [82154] (2)
    1. Immunogenic protein MPT70 [101859]
      1. Mycobacterium tuberculosis [TaxId: 1773] [101860] (1)
    2. Fasciclin I [82155]
      duplication: tandem repeat of four FAS1 domain
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [82156] (1)
Lipocalins [50813] (1)
barrel, closed or opened; n=8, S=12; meander
1. Lipocalins [50814] (9)
  bind hydrophobic ligands in their interior
  uperfamily
  1. Retinol binding protein-like [50815] (30)
    barrel, closed; n=8, S=12, meander
    1. Retinol binding protein [50816]
      1. Cow (Bos taurus) [TaxId: 9913] [50817] (13)
      2. Pig (Sus scrofa domestica) [TaxId: 9823] [50818] (1)
      3. Human (Homo sapiens) [TaxId: 9606] [50819] (4)
      4. Chicken (Gallus gallus) [TaxId: 9031] [50820] (1)
      5. Chicken (Gallus gallus), plasma isoform [TaxId: 9031] [69297] (1)
    2. Odorant-binding protein [50821]
      C-termini swapping dimer
      1. Cow (Bos taurus) [TaxId: 9913] [50822] (8)
      2. Pig (Sus scrofa) [TaxId: 9823] [50823] (9)
    3. Lipocalin allergen [50824]
      1. Cow (Bos taurus), bos d 2 [TaxId: 9913] [50825] (1)
      2. Horse (Equus caballus), equ c 1 [TaxId: 9796] [50826] (1)
    4. Salivary lipocalin [74996]
      1. Pig (Sus scrofa) [TaxId: 9823] [74997] (1)
    5. Aphrodisin, a sex pheromone [63805]
      1. Golden hamster (Mesocricetus auratus) [TaxId: 10036] [63806] (1)
    6. beta-Lactoglobulin [50827]
      1. Cow (Bos taurus) [TaxId: 9913] [50828] (26)
        SQ P02754
      2. Pig (Sus scrofa) [TaxId: 9823] [50829] (1)
      3. Reindeer (Rangifer tarandus) [TaxId: 9870] [141461] (6)
        SQ P02755 19-180
    7. Retinoic acid-binding protein [50830]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50831] (2)
    8. Major urinary protein/alpha-2u-globulin [50832]
      1. Mouse (Mus musculus) [TaxId: 10090] [50833] (19)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [50834] (2)
    9. Neutrophil gelatinase-associated lipocalin (NGAL) [50835]
      1. Human (Homo sapiens) [TaxId: 9606] [50836] (13)
    10. Lipocalin q83 [89364]
      activated expression by the myc oncogene
      1. Common quail (Coturnix coturnix) [TaxId: 9091] [89365] (1)
    11. Complement protein C8gamma [74998]
      1. Human (Homo sapiens) [TaxId: 9606] [74999] (2)
    12. Bilin-binding protein [50837]
      1. Cabbage butterfly (Pieris brassicae) [TaxId: 7116] [50838] (6)
    13. Alpha-crustacyanin [63807]
      1. European lobster (Homarus gammarus) [TaxId: 6707] [63808] (7)
    14. Outer membrane lipoprotein Blc [101861]
      bacterial lipocalin
      1. Escherichia coli [TaxId: 562] [101862] (1)
    15. Histamine binding protein [50839]
      1. Brown ear tick (Rhipicephalus appendiculatus) [TaxId: 34631] [50840] (2)
    16. Nitrophorin 1 [50841]
      1. Rhodnius prolixus [TaxId: 13249] [50842] (8)
    17. Nitrophorin 2 (prolixin-s) [50843]
      1. Rhodnius prolixus [TaxId: 13249] [50844] (14)
        SQ Q26241
    18. Nitrophorin 4 [50845]
      1. Rhodnius prolixus [TaxId: 13249] [50846] (34)
        SQ Q94734 22-205
    19. Von Ebner's gland protein (VEGP, tear lipocalin) [117265]
      1. Human (Homo sapiens) [TaxId: 9606] [117266] (1)
        SQ P31025 30-168
    20. Insecticyanin [141462]
      1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [141463] (1)
        SQ P00305 1-189
    21. Hypothetical protein YxeF [159228]
      1. Bacillus subtilis [TaxId: 1423] [159229] (1)
        SQ P54945 19-144
  2. Fatty acid binding protein-like [50847] (28)
    ten-stranded meander beta-sheet folded upon itself
    relates to the common fold by opening the barrel and insertion of beta-hairpin
    1. Muscle fatty acid binding protein (m-fabp) [50848]
      1. Human (Homo sapiens) [TaxId: 9606] [50849] (5)
      2. Cow (Bos taurus) [TaxId: 9913] [50850] (1)
    2. Intestinal fatty acid binding protein [50851]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50852] (11)
        SQ P02693
      2. Human (Homo sapiens) [TaxId: 9606] [50853] (3)
    3. Brain fatty acid binding protein [63809]
      1. Human (Homo sapiens) [TaxId: 9606] [63810] (3)
    4. Epidermal fatty acid binding protein [50854]
      1. Human (Homo sapiens) [TaxId: 9606] [50855] (2)
    5. Adipocyte lipid-binding protein, ALBP [50856]
      1. Mouse (Mus musculus) [TaxId: 10090] [50857] (17)
      2. Human (Homo sapiens) [TaxId: 9606] [110275] (4)
        SQ P15090
    6. Fatty acid-binding protein homolog 1 [89366]
      1. Flat worm (Echinococcus granulosus) [TaxId: 6210] [89367] (1)
    7. Fatty acid-binding protein [50858]
      1. Tobacco hornworm (Manduca sexta) [TaxId: 7130] [50859] (1)
      2. Desert locust (Schistocerca gregaria) [TaxId: 7010] [50860] (1)
    8. Cellular retinoic-acid-binding protein (CRABP) [50861]
      1. Human (Homo sapiens), CRABP-II [TaxId: 9606] [50862] (12)
      2. Cow and mouse (Bos taurus) and (Mus musculus), CRABP-I, identical sequences [TaxId: 9913] [50863] (3)
    9. Cellular retinol-binding protein II (CRBP) [50864]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50865] (9)
      2. Zebrafish (Danio rerio) [TaxId: 7955] [75000] (2)
    10. Cellular retinol-binding protein III [63811]
      1. Human (Homo sapiens) [TaxId: 9606] [63812] (1)
    11. Liver fatty acid binding protein [50866]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50867] (4)
      2. Human (Homo sapiens) [TaxId: 9606] [141464] (8)
        SQ P07148 1-127
    12. Liver basic fatty acid binding protein, LB_FABP [89368]
      1. Chicken (Gallus gallus) [TaxId: 9031] [89369] (5)
        SQ P80226
      2. Argentine common toad (Bufo arenarum) [TaxId: 38577] [89370] (1)
      3. Axolotl (Ambystoma mexicanum) [TaxId: 8296] [141465] (2)
        SQ P81400 1-125
    13. Cellular retinol-binding protein IV [82157]
      1. Human (Homo sapiens) [TaxId: 9606] [82158] (1)
    14. P2 myelin protein [50868]
      1. Cow (Bos taurus), caudal spinal root myelin [TaxId: 9913] [50869] (1)
      2. Horse (Equus caballus) [TaxId: 9796] [141466] (1)
        SQ P02690 1-131
    15. Ileal lipid-binding protein [50870]
      1. Human (Homo sapiens) [TaxId: 9606] [82159] (2)
      2. Pig (Sus scrofa) [TaxId: 9823] [50871] (2)
    16. Fatty acid-binding protein Sm14 [110276]
      1. Blood fluke (Schistosoma mansoni) [TaxId: 6183] [110277] (2)
        SQ P29498
    17. Der f 13 allergen [141467]
      1. House dust mite (Dermatophagoides farinae) [TaxId: 6954] [141468] (1)
        SQ Q1M2P5 1-131
  3. Thrombin inhibitor [50872] (1)
    topology permutation: strands 2 and 3 swapped their positions in the barrel
    1. Thrombin inhibitor [50873]
      1. Triatomine bug (Triatoma pallidipennis) [TaxId: 30077] [50874] (1)
  4. Hypothetical protein YodA [101863] (1)
    bacterial metal-binding, lipocalin-like protein
    1. Hypothetical protein YodA [101864]
      1. Escherichia coli [TaxId: 562] [101865] (5)
        SQ P76344
  5. Hypothetical protein YwiB [101866] (1)
    bacterial proteins with a fatty acid binding protein-like fold
    1. Hypothetical protein YwiB [101867]
      1. Bacillus subtilis [TaxId: 1423] [101868] (1)
  6. Phenolic acid decarboxylase (PAD) [141469] (1)
    Pfam 05870; dimeric enzyme made of lipocalin-like subunits
    1. P-coumaric acid decarboxylase, pdc [141470]
      1. Lactobacillus plantarum [TaxId: 1590] [141471] (1)
        SQ Q88RY7 1-178
  7. Dinoflagellate luciferase repeat [141472] (1)
    PfamB 017809; comprises a fatty acid binding protein-like fold, wrapped into the extra N- and C-terminal 'tails'
    1. Dinoflagellate luciferase [141473]
      1. Lingulodinium polyedrum [TaxId: 160621] [141474] (1)
        SQ O77206 868-1218
  8. Rv2717c-like [141475] (2)
    bacterial and plant proteins with a fatty acid binding protein-like fold
    1. Hypothetical protein Rv2717c [141476]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141477] (1)
        SQ O07216 4-164
    2. Hypothetical protein At1g79260 [141478]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141479] (3)
        SQ O64527 14-166
  9. All1756-like [159230] (1)
    cyanobacterial proteins with duplicated fatty acid binding protein-like domains; N-terminal and C-terminal domains correspond to PfamB 40396 and PfamB 60468, respectively
    1. Uncharacterized protein All1756 ortholog [159231]
      1. Nostoc punctiforme [TaxId: 272131] [159232] (4)
Streptavidin-like [50875] (8)
barrel, closed; n=8, S=10; meander
1. Avidin/streptavidin [50876] (1)
  uperfamily
  1. Avidin/streptavidin [50877] (2)
    1. Streptavidin [50878]
      1. Streptomyces avidinii [TaxId: 1895] [50879] (122)
    2. Avidin [50880]
      1. Chicken (Gallus gallus) [TaxId: 9031] [50881] (16)
2. beta-Barrel protease inhibitors [50882] (2)
  uperfamily
  1. Metalloprotease inhibitor [50883] (2)
    1. Metalloprotease inhibitor [50884]
      1. Erwinia chrysanthemi [TaxId: 556] [50885] (1)
      2. Pseudomonas aeruginosa, aprin [TaxId: 287] [63813] (1)
  2. Staphostatin [101869] (2)
    cysteine protease inhibitor; topology permutation: strand 3 is replaced with the N-terminal extra strand
    1. Staphostatin A (SAV1910, SA1726) [101870]
      1. Staphylococcus aureus [TaxId: 1280] [101871] (1)
    2. Staphostatin B (SspC) [101872]
      1. Staphylococcus aureus [TaxId: 1280] [101873] (5)
3. D-aminopeptidase, middle and C-terminal domains [50886] (1)
  uperfamily
  1. D-aminopeptidase, middle and C-terminal domains [50887] (1)
    1. D-aminopeptidase, middle and C-terminal domains [50888]
      duplication: both domains have this barrel fold
      1. Ochrobactrum anthropi [TaxId: 529] [50889] (1)
4. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69298] (1)
  uperfamily
  1. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69299] (2)
    1. Quinohemoprotein amine dehydrogenase A chain, domain 3 [69300]
      1. Paracoccus denitrificans [TaxId: 266] [69301] (2)
      2. Pseudomonas putida [TaxId: 303] [69302] (2)
5. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75001] (1)
  uperfamily
  1. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75002] (2)
    1. Dipeptidyl peptidase I (cathepsin C), exclusion domain [75003]
      1. Human (Homo sapiens) [TaxId: 9606] [75004] (3)
      2. Rat (Rattus norvegicus) [TaxId: 10116] [82160] (1)
6. YceI-like [101874] (1)
  uperfamily
  1. YceI-like [101875] (2)
    Pfam 04264
    1. Polyisoprenoid-binding protein TTHA0802 (TT1927B) [101876]
      1. Thermus thermophilus [TaxId: 274] [101877] (1)
        SQ P83815
        structural genomics
    2. Lipid binding protein YceI [117267]
      1. Escherichia coli [TaxId: 562] [117268] (1)
        SQ P0A8X2
7. Extracellular hemoglobin linker subunit, receptor domain [141480] (1)
  uperfamily
  1. Extracellular hemoglobin linker subunit, receptor domain [141481] (3)
    1. Hemoglobin linker chain l1 [141482]
      1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141483] (1)
        SQ Q9GV76 127-240
    2. Extracellular hemoglobin linker l3 subunit [141484]
      1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141485] (1)
        SQ Q2I742 119-240
    3. Extracellular hemoglobin linker l2 subunit [141486]
      1. Common earthworm (Lumbricus terrestris) [TaxId: 6398] [141487] (1)
        SQ Q2I743 139-299
8. YdhA-like [141488] (1)
  uperfamily
  1. YdhA-like [141489] (1)
    1. Hypothetical protein YdhA [141490]
      1. Escherichia coli [TaxId: 562] [141491] (1)
        SQ P28224 28-109
FomD barrel-like [159233] (1)
barrel, closed; n=8, S=12; meander; similar topology to the AOC barrel-like fold (reversed to the lipocalin barrel topology)
1. FomD-like [159234] (1)
  1. FomD-like [159235] (1)
    Pfam 04167; DUF402
    1. Hypothetical protein RHA1_ro00977 [159236]
      1. Rhodococcus sp. RHA1 [TaxId: 101510] [159237] (2)
        SQ Q0SI31 8-172
AOC barrel-like [141492] (2)
barrel, closed; n=8, S=10; meander; mirrored (reversed) topology to the Spreptavidin-like and Lipocalin-like folds
1. Allene oxide cyclase-like [141493] (1)
  uperfamily
  1. Allene oxide cyclase-like [141494] (2)
    Pfam 06351
    1. Allene oxide cyclase, AOC [141495]
      1. Thale cress (Arabidopsis thaliana), chloroplast AOC2 [TaxId: 3702] [141496] (18)
        SQ Q9LS02 80-253
      2. Thale cress (Arabidopsis thaliana), chloroplast AOC1 [TaxId: 3702] [141497] (1)
        SQ Q9LS03 81-254
2. SO1590-like [159238] (1)
  1. SO1590-like [159239] (2)
    1. Hypothetical protein SO1590 [159240]
      1. Shewanella oneidensis [TaxId: 70863] [159241] (2)
        SQ Q8EGL1 2-134
    2. Uncharacterized protein Sden_2034 [159242]
      1. Shewanella denitrificans [TaxId: 192073] [159243] (2)
        SQ Q12ML0 5-137
AttH-like [159244] (1)
duplication: two flattened beta-barrels of lipocalin-like topology are orthogonally packed with a pseudo twofold symmetry
1. AttH-like [159245] (1)
  1. AttH-like [159246] (1)
    Pfam 09410; DUF2006
    1. AttH-related protein NE1406 [159247]
      1. Nitrosomonas europaea [TaxId: 915] [159248] (2)
        SQ Q82US3 24-351
Cyclophilin-like [50890] (1)
barrel, closed; n=8, S=10; complex topology
1. Cyclophilin-like [50891] (4)
  uperfamily
  1. Cyclophilin (peptidylprolyl isomerase) [50892] (25)
    1. Cyclophilin (eukaryotic) [50893]
      1. Human (Homo sapiens), variant A [TaxId: 9606] [50894] (50)
        SQ P05092
      2. Human (Homo sapiens), variant B [TaxId: 9606] [50895] (1)
      3. Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606] [50896] (2)
      4. Mouse (Mus musculus), variant C [TaxId: 10090] [50897] (1)
      5. Nematode (Brugia malayi) [TaxId: 6279] [50898] (3)
      6. Caenorhabditis elegans, isoform 3 [TaxId: 6239] [50899] (5)
      7. Caenorhabditis elegans, isoform 5 [TaxId: 6239] [82161] (1)
      8. Plasmodium falciparum [TaxId: 5833] [50900] (2)
      9. Baker's yeast (Saccharomyces cerevisiae), variant A [TaxId: 4932] [101878] (2)
      10. Trypanosoma cruzi [TaxId: 5693] [117269] (2)
        SQ Q4DPB9 30-194
      11. Human (Homo sapiens), variant C [TaxId: 9606] [141498] (6)
        SQ P45877 32-212
      12. Aspergillus fumigatus [TaxId: 5085] [141499] (2)
        SQ Q9Y7F6 8-178
      13. Plasmodium yoelii [TaxId: 5861] [141500] (1)
        SQ Q7RSH5 25-210
    2. Cyclophilin 40 isomerase domain [63814]
      the other domain is formed by TPR repeats
      1. Cow (Bos taurus) [TaxId: 9913] [63815] (2)
    3. Peptidyl-prolyl cis-trans isomerase A, PpiA [50901]
      1. Escherichia coli [TaxId: 562] [50902] (6)
        SQ P20752
      2. Mycobacterium tuberculosis [TaxId: 1773] [117270] (1)
        SQ P65762
    4. Cyclophilin-like allergen Mal s 6 [141501]
      1. Malassezia sympodialis [TaxId: 76777] [141502] (1)
        SQ O93970 1-162
    5. Peptidyl-prolyl cis-trans isomerase E, PPIE, C-terminal domain [141503]
      N-terminal domain belongs to the RBD family (scop_fa 54929)
      1. Human (Homo sapiens) [TaxId: 9606] [141504] (1)
        SQ Q9UNP9 138-301
        structure of the N-terminal RBD is known, PDB 2cqb
    6. Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain [141505]
      1. Human (Homo sapiens) [TaxId: 9606] [141506] (2)
        SQ Q13356 280-457
    7. Cyclophilin-like protein PY00693 [141507]
      1. Plasmodium yoelii [TaxId: 5861] [141508] (1)
        SQ Q7RRM6 29-197
    8. Cyclophilin-like protein PPIL3B [141509]
      1. Human (Homo sapiens) [TaxId: 9606] [141510] (4)
        SQ Q9H2H8 1-160
    9. Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F [141511]
      1. Human (Homo sapiens) [TaxId: 9606] [141512] (5)
        SQ P30405 44-207
    10. Putative cyclophilin PFE0505w [141513]
      PPWD1 homologue
      1. Plasmodium falciparum [TaxId: 5833] [141514] (1)
        SQ Q8I402 592-746
    11. Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain [141515]
      1. Human (Homo sapiens) [TaxId: 9606] [141516] (3)
        SQ Q96BP3 483-646
    12. Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 [141517]
      1. Human (Homo sapiens) [TaxId: 9606] [141518] (1)
        SQ Q9Y3C6 1-166
  2. Outer surface protein, C-terminal domain [110278] (1)
    lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 05913
    1. Outer surface protein, C-terminal domain [110279]
      1. Bacillus cereus [TaxId: 1396] [110280] (1)
        SQ Q81HJ5
  3. TM1367-like [141519] (1)
    Pfam 04126; DUF369
    1. Hypothetical protein TM1367 [141520]
      1. Thermotoga maritima [TaxId: 2336] [141521] (3)
        SQ Q9X187 1-124
  4. PH0987 C-terminal domain-like [159249] (1)
    lacks the N-terminal strand of cyclophilin but the beta-barrel (7,10) remains closed; corresponds to the C-terminal part of Pfam 02682; Allophanate hydrolase subunit 1 (AHS1)
    1. Uncharacterized protein PH0987 [159250]
      1. Pyrococcus horikoshii [TaxId: 53953] [159251] (1)
        SQ O58715 86-217
Oncogene products [50903] (1)
barrel, closed; n=8, S=10; one overside connection
1. Oncogene products [50904] (1)
  duplication: N- and C-terminal halves are related by pseudo dyad
  uperfamily
  1. Oncogene products [50905] (3)
    1. p14-TCL1 [50906]
      an oncogene product involved in T-cell prolymphocytic leukemia
      1. Human (Homo sapiens) [TaxId: 9606] [50907] (1)
      2. Mouse (Mus musculus) [TaxId: 10090] [69303] (1)
    2. p13-MTCP1 [50908]
      involved in T cell malignancies
      1. Human (Homo sapiens) [TaxId: 9606] [50909] (3)
L,D-transpeptidase catalytic domain-like [141522] (1)
barrel, closed; n=8, S=10; one overside connection
1. L,D-transpeptidase catalytic domain-like [141523] (1)
  uperfamily
  1. L,D-transpeptidase catalytic domain-like [141524] (2)
    Pfam 03734; ErfK/YbiS/YcfS/YnhG
    1. L,D-transpeptidase, C-terminal, catalytic domain [141525]
      1. Enterococcus faecium [TaxId: 1352] [141526] (1)
        SQ Q3Y185 339-466
    2. Hypothetical protein YkuD, C-terminal domain [141527]
      1. Bacillus subtilis [TaxId: 1423] [141528] (2)
        SQ O34816 49-164
Sortase [63816] (1)
barrel, closed; n=8, S=10; mixed sheet; two overside connections
1. Sortase [63817] (1)
  uperfamily
  1. Sortase [63818] (3)
    1. Sortase A [63819]
      1. Staphylococcus aureus [TaxId: 1280] [63820] (4)
        SQ Q9S446 61-206
    2. Sortase B [101879]
      1. Staphylococcus aureus [TaxId: 1280] [101880] (4)
    3. Hypothetical protein BA4783 [110281]
      1. Bacillus anthracis [TaxId: 1392] [110282] (3)
        SQ Q81L49
PTSIIA/GutA-like [141529] (1)
barrel, closed; n=8, S=12; mixed sheet; two overside connections; duplication: consists of two intertwinned structural repeats
1. PTSIIA/GutA-like [141530] (1)
  uperfamily
  1. PTSIIA/GutA-like [141531] (1)
    Pfam 03829
    1. PTS system, IIa component (PTSIIA) [141532]
      1. Enterococcus faecalis [TaxId: 1351] [141533] (2)
        SQ Q831B0 3-123
        EF2603
Mannose 6-phosphate receptor domain [50910] (1)
barrel, partly open; n*=8, S*=10; one psi loop
1. Mannose 6-phosphate receptor domain [50911] (1)
  uperfamily
  1. Mannose 6-phosphate receptor domain [50912] (3)
    1. Cation-dependent mannose 6-phosphate receptor, extracytoplasmic domain [50913]
      1. Cow (Bos taurus) [TaxId: 9913] [50914] (15)
    2. Cation-independent mannose-6-phosphate receptor (MIR-receptor) [63821]
      1. Human (Homo sapiens) [TaxId: 9606] [63822] (5)
      2. Cow (Bos taurus) [TaxId: 9913] [110283] (3)
        SQ P08169 49-476
triple barrel [50915] (1)
dimer of two non-identical subunits; forms two similar barrels, n=8, S=10 each, that are fused together with the formation of third barrel, n=6, S=8
1. Rap30/74 interaction domains [50916] (1)
  uperfamily
  1. Rap30/74 interaction domains [50917] (2)
    1. TFIIF beta subunit, Rap30 [50918]
      1. Human (Homo sapiens) [TaxId: 9606] [50919] (1)
    2. TFIIF alpha subunit, Rap74 [50920]
      1. Human (Homo sapiens) [TaxId: 9606] [50921] (1)
4-bladed beta-propeller [50922] (1)
consists of four 4-stranded beta-sheet motifs; meander
1. Hemopexin-like domain [50923] (1)
  uperfamily
  1. Hemopexin-like domain [50924] (6)
    1. Hemopexin [50925]
      duplication: consists of two domains of this fold
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [50926] (3)
    2. Gelatinase A (MMP-2), C-terminal domain [50927]
      1. Human (Homo sapiens) [TaxId: 9606] [50928] (4)
    3. Gelatinase B (MMP-9) [82162]
      1. Human (Homo sapiens) [TaxId: 9606] [82163] (1)
    4. Collagenase (MMP1), C-terminal domain [50929]
      1. Pig (Sus scrofa) [TaxId: 9823] [50930] (3)
      2. Human (Homo sapiens) [TaxId: 9606] [117271] (1)
        SQ P03956 32-466
    5. Collagenase-3 (MMP-13), C-terminal domain [50931]
      1. Human (Homo sapiens) [TaxId: 9606] [50932] (1)
5-bladed beta-propeller [50933] (3)
consists of five 4-stranded beta-sheet motifs; meander
1. Tachylectin-2 [50934] (1)
  uperfamily
  1. Tachylectin-2 [50935] (1)
    1. Tachylectin-2 [50936]
      1. Japanese horseshoe crab (Tachypleus tridentatus) [TaxId: 6853] [50937] (1)
2. Arabinanase/levansucrase/invertase [75005] (5)
  uperfamily
  1. alpha-L-arabinanase-like [75006] (7)
    1. alpha-L-arabinanase [75007]
      1. Cellvibrio cellulosa [TaxId: 155077] [75008] (3)
    2. Arabinanase-TS [141534]
      1. Bacillus thermodenitrificans [TaxId: 33940] [141535] (1)
        SQ Q93HT9 1-312
    3. Endo-1,5-arabinanase [141536]
      1. Bacillus subtilis [TaxId: 1423] [141537] (1)
        SQ Q5MPF4 33-323
    4. Beta-D-xylosidase N-terminal domain [141538]
      1. Geobacillus stearothermophilus [TaxId: 1422] [141539] (16)
        SQ Q68HB3 3-324
      2. Bacillus subtilis [TaxId: 1423] [141540] (4)
        SQ P94489 2-324
      3. Bacillus halodurans [TaxId: 86665] [141541] (2)
        SQ Q9K6P5 4-320
      4. Clostridium acetobutylicum [TaxId: 1488] [141542] (8)
        SQ Q97DM1 2-322
  2. Levansucrase [101881] (1)
    1. Levansucrase [101882]
      1. Bacillus subtilis [TaxId: 1423] [101883] (4)
  3. Glycosyl hydrolases family 32 N-terminal domain [101884] (2)
    Pfam 00251; Glycosyl hydrolase family 32
    1. Beta-fructosidase (invertase), N-terminal domain [101885]
      1. Thermotoga maritima [TaxId: 2336] [101886] (7)
    2. Exo-inulinase [117272]
      1. Aspergillus awamori [TaxId: 105351] [117273] (3)
        SQ Q96TU3 20-536
  4. TM1225-like predicted glycosylases [110284] (1)
    Pfam 04041 DUF377
    1. Hypothetical protein TM1225 [110285]
      1. Thermotoga maritima [TaxId: 2336] [110286] (1)
        SQ Q9X0V2
  5. LmjF10.1260-like [141543] (1)
    1. Hypothetical protein LmjF10.1260 [141544]
      1. Leishmania major [TaxId: 5664] [141545] (1)
        SQ Q4QH86 2-311
3. Apyrase [101887] (1)
  distorted propeller with an alpha helix inserted between the second and third blades
  uperfamily
  1. Apyrase [101888] (1)
    Pfam 06079
    1. Soluble calcium-activated nucleotidase SCAN-1 [101889]
      1. Human (Homo sapiens) [TaxId: 9606] [101890] (4)
6-bladed beta-propeller [50938] (11)
consists of six 4-stranded beta-sheet motifs; meander
1. Sialidases [50939] (2)
  uperfamily
  1. Sialidases (neuraminidases) [50940] (11)
    1. Salmonella sialidase [50941]
      1. Salmonella typhimurium, strain lt2 [TaxId: 90371] [50942] (5)
    2. Influenza neuraminidase [50943]
      1. Influenza A virus, different strains [TaxId: 11320] [50944] (59)
        SQ P03472 84-470
      2. Influenza B virus, different strains [TaxId: 11520] [50945] (12)
    3. Paramyxovirus hemagglutinin-neuraminidase head domain [63823]
      1. Newcastle disease virus [TaxId: 11176] [63824] (5)
    4. Hemagglutinin-neuraminidase glycoprotein [101891]
      1. Human parainfluenza virus type 3 [TaxId: 11216] [101892] (5)
    5. Micromonospora sialidase, N-terminal domain [50946]
      1. Micromonospora viridifaciens [TaxId: 1881] [50947] (10)
        SQ Q02834 47-647
    6. Leech intramolecular trans-sialidase, C-terminal domain [50948]
      contains incomplete beta-barrel subdomain inserted in the second blade
      1. North american leech (Macrobdella decora) [TaxId: 6405] [50949] (5)
    7. Vibrio cholerae sialidase [50950]
      contains 2 additional domains of ConA-like fold
      1. Vibrio cholerae [TaxId: 666] [50951] (3)
        SQ P37060
    8. Trypanosoma sialidase [82164]
      1. Parasitic flagellate protozoan (Trypanosoma cruzi) [TaxId: 5693] [89371] (12)
        SQ Q26966
      2. Trypanosoma rangeli [TaxId: 5698] [82165] (10)
        SQ O44049 20-653
    9. Sialidase 2 (Neu2) [117274]
      1. Human (Homo sapiens) [TaxId: 9606] [117275] (8)
        SQ Q9Y3R4
  2. Endo-alpha-sialidase [117276] (1)
    possibly related by the other family by circular permutation; includes extra N-terminal domain [dN: alpha/beta ] and insert domain [dI: beta-barrel, similar to the Reductase/isomerase/elongation factor common domain (scop_cf 50412)]
    1. Endo-alpha-sialidase [117277]
      1. Bacteriophage K1F [TaxId: 344021] [117278] (2)
        SQ Q04830 245-909
2. Soluble quinoprotein glucose dehydrogenase [50952] (1)
  uperfamily
  1. Soluble quinoprotein glucose dehydrogenase [50953] (1)
    1. Soluble quinoprotein glucose dehydrogenase [50954]
      1. Acinetobacter calcoaceticus [TaxId: 471] [50955] (4)
3. Thermostable phytase (3-phytase) [50956] (1)
  uperfamily
  1. Thermostable phytase (3-phytase) [50957] (1)
    1. Thermostable phytase (3-phytase) [50958]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [50959] (5)
4. TolB, C-terminal domain [50960] (1)
  uperfamily
  1. TolB, C-terminal domain [50961] (1)
    1. TolB, C-terminal domain [50962]
      1. Escherichia coli [TaxId: 562] [50963] (10)
5. YWTD domain [63825] (1)
  uperfamily
  1. YWTD domain [63826] (2)
    1. Low density lipoprotein (LDL) receptor [63827]
      1. Human (Homo sapiens) [TaxId: 9606] [63828] (2)
    2. Nidogen [101893]
      1. Mouse (Mus musculus) [TaxId: 10090] [101894] (1)
6. Calcium-dependent phosphotriesterase [63829] (3)
  uperfamily
  1. SGL-like [63830] (3)
    1. Diisopropylfluorophosphatase (phosphotriesterase, DFP) [63831]
      1. Squid (Loligo vulgaris) [TaxId: 6622] [63832] (4)
        SQ Q7SIG4
    2. Lactonase Drp35 [141546]
      1. Staphylococcus aureus [TaxId: 1280] [141547] (24)
        SQ Q7A338 5-324! SQ Q99QV3 5-324
    3. Regucalcin [141548]
      Agr_c_1268p/Atu0702
      1. Agrobacterium tumefaciens [TaxId: 358] [141549] (1)
        SQ Q7D0W3 20-314
  2. Serum paraoxonase/arylesterase 1, PON1 [101895] (1)
    1. Serum paraoxonase/arylesterase 1, PON1 [101896]
      1. Rabit (Oryctolagus cuniculus) [TaxId: 9986] [101897] (1)
  3. All0351-like [159252] (1)
    N-terminal half is PfamB 89298 and C-terminal half is PfamB 80276; includes recent entry 2qe8 (Ava4197)
    1. Hypothetical protein All0351 homologue [159253]
      1. Nostoc punctiforme [TaxId: 272131] [159254] (1)
7. Tricorn protease N-terminal domain [69304] (1)
  possibly related to the second domain of tricorn protease (a distorted 7-bladed beta-propeller)
  uperfamily
  1. Tricorn protease N-terminal domain [69305] (1)
    1. Tricorn protease N-terminal domain [69306]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69307] (4)
8. Fucose-specific lectin [89372] (1)
  uperfamily
  1. Fucose-specific lectin [89373] (1)
    1. Fucose-specific lectin [89374]
      1. Orange peel mushroom (Aleuria aurantia) [TaxId: 5188] [89375] (3)
9. NHL repeat [101898] (1)
  uperfamily
  1. NHL repeat [101899] (2)
    Pfam 01436
    1. Brain tumor cg10719-pa [101900]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101901] (1)
    2. Serine/threonine-protein kinase PknD [101902]
      1. Mycobacterium tuberculosis [TaxId: 1773] [101903] (2)
10. GyrA/ParC C-terminal domain-like [101904] (1)
  beta-pinwheel, a variant of beta-propeller fold; unlike an canonical beta-propeller, strands 1 and 4 of each four-strand repeat unit are in one blade whereas strands 2 and 3 are in the next blade
  uperfamily
  1. GyrA/ParC C-terminal domain-like [101905] (2)
    Pfam 03989; functional conformational changes result in breaking the interface between the N- and C-terminal blades
    1. DNA gyrase A C-terminal domain [101906]
      1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [101907] (1)
    2. Topoisomerase IV subunit A, ParC, C-terminal domain [117279]
      1. Bacillus stearothermophilus [TaxId: 1422] [117280] (1)
        SQ Q45066 499-805 # 63% sequence identity; Bacillus subtilis TaxID: 1423
11. Kelch motif [117281] (1)
  uperfamily
  1. Kelch motif [117282] (2)
    Pfam 01344; sequence motif corresponding to one beta-sheet blade; similar sequences are found in the Galactose oxidase 7-bladed beta-propeller domain (scop_pr 50967)
    1. Kelch-like ECH-associated protein 1, KEAP1 [117283]
      1. Human (Homo sapiens) [TaxId: 9606] [117284] (3)
        SQ Q14145 322-609
      2. Mouse (Mus musculus) [TaxId: 10090] [141550] (4)
        SQ Q9Z2X8 324-613
7-bladed beta-propeller [50964] (14)
consists of seven 4-stranded beta-sheet motifs; meander
1. Galactose oxidase, central domain [50965] (1)
  uperfamily
  1. Galactose oxidase, central domain [50966] (3)
    1. Galactose oxidase, central domain [50967]
      N-terminal domain is a jelly-roll sandwich
      C-terminal domain is Immunoglobulin-like
      1. Dactylium dendroides [TaxId: 5132] [50968] (8)
        SQ Q01745 42-680
      2. Fungi (Fusarium sp.) [TaxId: 29916] [69308] (1)
        sequence identical to that of Dactylium dendroides
      3. Fusarium graminearum (Gibberella zeae) [TaxId: 5518] [159255] (3)
2. YVTN repeat-like/Quinoprotein amine dehydrogenase [50969] (3)
  uperfamily
  1. YVTN repeat [82166] (1)
    more regular propeller with clear sequence repeats
    1. Surface layer protein [82167]
      1. Archaeon Methanosarcina mazei [TaxId: 2209] [82168] (1)
  2. Quinohemoprotein amine dehydrogenase B chain [69309] (2)
    less regular propeller with imperfect sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
    1. Quinohemoprotein amine dehydrogenase B chain [69310]
      1. Paracoccus denitrificans [TaxId: 266] [69311] (2)
      2. Pseudomonas putida [TaxId: 303] [69312] (2)
  3. Methylamine dehydrogenase, H-chain [50970] (2)
    less regular propeller without notable sequence repeats; quinone cofactor is a tryptophan derivative in another subunit
    1. Methylamine dehydrogenase, H-chain [50971]
      1. Paracoccus denitrificans [TaxId: 266] [50972] (21)
      2. Gram negative methylotrophic bacteria (Thiobacillus versutus) [TaxId: 34007] [50973] (3)
3. Nitrous oxide reductase, N-terminal domain [50974] (1)
  uperfamily
  1. Nitrous oxide reductase, N-terminal domain [50975] (2)
    1. Nitrous oxide reductase, N-terminal domain [50976]
      1. Pseudomonas nautica [TaxId: 2743] [50977] (1)
      2. Paracoccus denitrificans [TaxId: 266] [63833] (1)
4. WD40 repeat-like [50978] (2)
  also contains 8-bladed propellers
  uperfamily
  1. WD40-repeat [50979] (12)
    1. beta1-subunit of the signal-transducing G protein heterotrimer [50980]
      1. Cow (Bos taurus) [TaxId: 9913] [50981] (11)
      2. Homo sapiens [TaxId: 9606] [159256] (1)
    2. Tup1, C-terminal domain [50983]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50984] (1)
    3. Groucho/tle1, C-terminal domain [75009]
      1. Human (Homo sapiens) [TaxId: 9606] [75010] (9)
    4. Arp2/3 complex 41 kDa subunit ARPC1 [69313]
      1. Cow (Bos taurus) [TaxId: 9913] [69314] (10)
        SQ Q58CQ2
    5. Cdc4 propeller domain [82169]
      8-bladed beta-propeller without perfect 8-fold symmetry
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82170] (1)
    6. F-box/WD-repeat protein 1 (beta-TRCP1) [89376]
      1. Human (Homo sapiens) [TaxId: 9606] [89377] (1)
    7. Actin interacting protein 1 [89378]
      14 repeats are arranged into two seven-bladed beta-propeller domains swapped with the N-terminal strands
      1. Nematode (Caenorhabditis elegans) [TaxId: 6239] [89379] (2)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [89380] (2)
    8. Antiviral protein Ski8 (Ski8p) [110287]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110288] (2)
        SQ Q02793
    9. Platelet-activating factor acetylhydrolase IB subunit alpha [159257]
      1. Mouse (Mus musculus) [TaxId: 10090] [159258] (10)
        SQ P43034 91-407
    10. F-box/WD repeat-containing protein 7, FBXW7 [159259]
      1. Human (Homo sapiens) [TaxId: 9606] [159260] (3)
        SQ Q969H0 365-706
  2. Cell cycle arrest protein BUB3 [110289] (1)
    possibly related to the WD-repeat family; both sequence similarity between the blades and the WD40 repeat signature are very weak
    1. Cell cycle arrest protein BUB3 [110290]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110291] (9)
        SQ P26449
5. RCC1/BLIP-II [50985] (2)
  two families are clearly related but differ by the number of strands per blade
  uperfamily
  1. Regulator of chromosome condensation RCC1 [50986] (1)
    1. Regulator of chromosome condensation RCC1 [50987]
      1. Human (Homo sapiens) [TaxId: 9606] [50988] (2)
  2. beta-lactamase inhibitor protein-II, BLIP-II [69315] (1)
    lacks the outer strands
    1. beta-lactamase inhibitor protein-II, BLIP-II [69316]
      1. Streptomyces exfoliatus [TaxId: 1905] [69317] (1)
6. Clathrin heavy-chain terminal domain [50989] (1)
  uperfamily
  1. Clathrin heavy-chain terminal domain [50990] (1)
    1. Clathrin heavy-chain terminal domain [50991]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [50992] (4)
7. Integrin alpha N-terminal domain [69318] (1)
  uperfamily
  1. Integrin alpha N-terminal domain [69319] (2)
    1. Integrin alpha N-terminal domain [69320]
      1. Human (Homo sapiens), isoform V [TaxId: 9606] [69321] (4)
        SQ P06756 31-986
      2. Human (Homo sapiens), isoform IIb [TaxId: 9606] [117285] (1)
        SQ P08514 32-483
8. Peptidase/esterase 'gauge' domain [50993] (2)
  uperfamily
  1. Prolyl oligopeptidase, N-terminal domain [50994] (1)
    1. Prolyl oligopeptidase, N-terminal domain [50995]
      1. Pig (Sus scrofa) [TaxId: 9823] [50996] (16)
        SQ P23687
  2. Acylamino-acid-releasing enzyme, N-terminal donain [117286] (1)
    1. Acylamino-acid-releasing enzyme, N-terminal donain [117287]
      1. Aeropyrum pernix [TaxId: 56636] [117288] (12)
        SQ Q9YBQ2
9. Tricorn protease domain 2 [69322] (1)
  distorted 7-bladed beta-propeller fold; possibly related to the N-terminal domain of tricorn protease (a 6-bladed beta-propeller)
  uperfamily
  1. Tricorn protease domain 2 [69323] (1)
    1. Tricorn protease domain 2 [69324]
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [69325] (4)
10. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75011] (1)
  uperfamily
  1. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75012] (1)
    1. 3-carboxy-cis,cis-mucoante lactonizing enzyme [75013]
      1. Neurospora crassa [TaxId: 5141] [75014] (1)
11. Putative isomerase YbhE [101908] (1)
  uperfamily
  1. Putative isomerase YbhE [101909] (1)
    1. Putative isomerase YbhE [101910]
      1. Escherichia coli [TaxId: 562] [101911] (1)
12. Sema domain [101912] (1)
  irregular 7-bladed beta-propeller with a large insertion in the fifth blade
  uperfamily
  1. Sema domain [101913] (3)
    Pfam 01403
    1. Semaphorin 4d [101914]
      1. Human (Homo sapiens) [TaxId: 9606] [101915] (1)
    2. Hepatocyte growth factor receptor [110292]
      1. Human (Homo sapiens) [TaxId: 9606] [110293] (1)
        SQ P08581 40-564
    3. Semaphorin 3a [110294]
      1. Mouse (Mus musculus) [TaxId: 10090] [110295] (1)
        SQ O08665 26-520
13. Oligoxyloglucan reducing end-specific cellobiohydrolase [110296] (1)
  duplication: # two beta-propeller domains are swapped with the N-terminal strands; similar domain arrangment to the Actin interacting protein 1 (scop_pr 89378)
  uperfamily
  1. Oligoxyloglucan reducing end-specific cellobiohydrolase [110297] (1)
    contains at least 9 BNR/Asp-box repeats (Pfam 02012) usually associated with the 6-bladed propeller Neuraminidases (scop_sf 50939)
    1. Oligoxyloglucan reducing end-specific cellobiohydrolase [110298]
      1. Yeast (Geotrichum sp. M128) [TaxId: 203496] [110299] (5)
        SQ Q8J0D2
14. Nucleoporin domain [117289] (1)
  uperfamily
  1. Nucleoporin domain [117290] (2)
    1. Nuclear pore complex protein Nup133 [117291]
      1. Human (Homo sapiens) [TaxId: 9606] [117292] (1)
        SQ Q8WUM0 75-477
    2. Nucleoporin NUP159 [117293]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117294] (1)
        SQ P40477 2-381
8-bladed beta-propeller [50997] (3)
consists of eight 4-stranded beta-sheet motifs; meander
also found in some members of the WD40-repeat superfamily
1. Quinoprotein alcohol dehydrogenase-like [50998] (1)
  uperfamily
  1. Quinoprotein alcohol dehydrogenase-like [50999] (6)
    1. Methanol dehydrogenase, heavy chain [51000]
      1. Methylophilus methylotrophus, w3a1 [TaxId: 17] [51001] (8)
      2. Methylobacterium extorquens [TaxId: 408] [63834] (3)
        SQ P16027
      3. Paracoccus denitrificans [TaxId: 266] [101916] (1)
    2. Ethanol dehydrogenase [51002]
      1. Pseudomonas aeruginosa [TaxId: 287] [51003] (1)
    3. Quinoprotein alcohol dehydrogenase, N-terminal domain [69326]
      fused with the C-terminal cytochrome c domain
      1. Comamonas testosteroni [TaxId: 285] [69327] (1)
      2. Pseudomonas putida, hk5 [TaxId: 303] [75015] (1)
2. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51004] (1)
  uperfamily
  1. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51005] (3)
    1. C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase [51006]
      the N-terminal domain is cytochrome c-like
      1. Paracoccus pantotrophus [TaxId: 82367] [51007] (12)
        formerly Thiosphaera pantotropha
      2. Pseudomonas aeruginosa [TaxId: 287] [51008] (9)
      3. Paracoccus denitrificans [TaxId: 266] [51009] (2)
3. DPP6 N-terminal domain-like [82171] (1)
  uperfamily
  1. DPP6 N-terminal domain-like [82172] (3)
    Pfam 00930
    1. Dipeptidyl peptidase IV/CD26, N-terminal domain [82173]
      1. Human (Homo sapiens) [TaxId: 9606] [82174] (58)
        SQ P27487 39-776 ! SQ P27487 ! SQ P27487
      2. Pig (Sus scrofa) [TaxId: 9823] [89381] (76)
    2. Dipeptidyl aminopeptidase-like protein 6, DPP6, N-terminal domain [117295]
      1. Human (Homo sapiens) [TaxId: 9606] [117296] (1)
        SQ P42658 127-849
Glycosyl hydrolase domain [51010] (1)
folded sheet; greek-key
1. Glycosyl hydrolase domain [51011] (5)
  this domain is C-terminal to the catalytic beta/alpha barrel domain
  uperfamily
  1. alpha-Amylases, C-terminal beta-sheet domain [51012] (46)
    this domain follows the catalytic beta/alpha barrel domain
    1. Bacterial alpha-Amylase [51013]
      1. Bacillus licheniformis [TaxId: 1402] [51014] (8)
      2. Pseudoalteromonas haloplanktis (Alteromonas haloplanktis) [TaxId: 228] [51015] (9)
      3. Bacillus subtilis [TaxId: 1423] [51016] (2)
        SQ P00691
      4. Bacillus stearothermophilus [TaxId: 1422] [51017] (1)
      5. Bacillus sp., ksm-k38 [TaxId: 1409] [89382] (6)
      6. Archaeon Pyrococcus woesei [TaxId: 2262] [89383] (3)
      7. Bacillus sp. 707 [TaxId: 1416] [117297] (4)
        SQ P19571 38-518
      8. Bacillus halmapalus [TaxId: 79882] [141551] (3)
        SQ P19571 432-518
      9. Halothermothrix orenii [TaxId: 31909] [141552] (1)
        SQ Q8GPL8 437-515
    2. Maltosyltransferase [63835]
      1. Thermotoga maritima [TaxId: 2336] [63836] (2)
    3. Cyclodextrin glycosyltransferase [51018]
      contains two more all-beta domains in C-terminal region, Immunoglobulin-like and trasthyretin-like
      1. Bacillus circulans, different strains [TaxId: 1397] [51019] (36)
      2. Bacillus stearothermophilus [TaxId: 1422] [51020] (1)
      3. Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId: 1422] [51021] (2)
      4. Bacillus sp., strain 1011 [TaxId: 1409] [51022] (8)
        SQ P05618
      5. Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId: 33950] [51023] (2)
      6. Thermoanaerobacterium [TaxId: 28895] [159261] (2)
    4. Animal alpha-amylase [51024]
      1. Pig (Sus scrofa) [TaxId: 9823] [51025] (14)
      2. Human (Homo sapiens) [TaxId: 9606] [51026] (43)
        SQ P04746 16-511 ! SQ 04746
      3. Yellow mealworm (Tenebrio molitor), larva [TaxId: 7067] [51027] (4)
    5. Fungal alpha-amylase [51028]
      1. Aspergillus niger, acid amylase [TaxId: 5061] [51029] (1)
      2. Aspergillus oryzae, Taka-amylase [TaxId: 5062] [51030] (8)
    6. Maltogenic amylase [51031]
      1. Thermus sp. [TaxId: 275] [51032] (2)
      2. Bacillus sp., cyclomaltodextrinase [TaxId: 1409] [75016] (1)
      3. Thermoactinomyces vulgaris, TVAI [TaxId: 2026] [75017] (9)
      4. Thermoactinomyces vulgaris, TVAII [TaxId: 2026] [51033] (25)
    7. Neopullulanase [82175]
      homologous to Maltogenic amylase
      1. Bacillus stearothermophilus [TaxId: 1422] [82176] (4)
    8. Cyclomaltodextrinase [101917]
      protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains
      1. Flavobacterium sp. 92 [TaxId: 197856] [101918] (1)
    9. Maltooligosyl trehalose synthase [82177]
      1. Archaeon Sulfolobus acidocaldarius [TaxId: 2285] [82178] (1)
    10. Glycosyltrehalose trehalohydrolase [51034]
      1. Archaeon Sulfolobus solfataricus, km1 [TaxId: 2287] [51035] (2)
      2. Deinococcus radiodurans [TaxId: 1299] [141553] (9)
        SQ Q9RX51 529-600
    11. 1,4-alpha-glucan branching enzyme [82179]
      1. Escherichia coli [TaxId: 562] [82180] (1)
    12. Isoamylase [51036]
      1. Pseudomonas amyloderamosa [TaxId: 32043] [51037] (1)
    13. G4-amylase (1,4-alpha-D-glucan maltotetrahydrolase) [51038]
      single beta-sheet; probable result of a decay of the common-fold
      1. Pseudomonas stutzeri [TaxId: 316] [51039] (9)
    14. Plant alpha-amylase [51040]
      single beta-sheet; probable result of a decay of the common-fold
      1. Barley (Hordeum vulgare), seeds, AMY2 isozyme [TaxId: 4513] [51041] (3)
      2. Barley (Hordeum vulgare), AMY1 isozyme [TaxId: 4513] [89384] (10)
    15. 4-alpha-glucanotransferase [75018]
      1. Thermotoga maritima [TaxId: 2336] [75019] (2)
    16. Oligo-1,6-glucosidase [51042]
      1. Bacillus cereus [TaxId: 1396] [51043] (1)
    17. Isomaltulose synthase PalI [89385]
      1. Klebsiella sp., lx3 [TaxId: 576] [89386] (1)
    18. Amylosucrase [69328]
      1. Neisseria polysaccharea [TaxId: 489] [69329] (10)
    19. Melibiase [75020]
      1. Chicken (Gallus gallus) [TaxId: 9031] [75021] (2)
        alpha-N-acetylgalactosaminidase
      2. Rice (Oryza sativa) [TaxId: 4530] [89387] (1)
        alpha-galactosidase
      3. Human (Homo sapiens) [TaxId: 9606] [101919] (2)
        alpha-galactosidase A
      4. Trichoderma reesei [TaxId: 51453] [110300] (2)
        SQ Q92456; Alpha-galactosidase agl1;
    20. A4 beta-galactosidase [82181]
      the catalytic domain of this protein is similar to that of the bacterial beta-amylase
      1. Thermus thermophilus [TaxId: 274] [82182] (2)
    21. Sucrose phosphorylase [101920]
      single beta-sheet; probable result of a decay of the common-fold
      1. Bifidobacterium adolescentis [TaxId: 1680] [101921] (5)
    22. Pullulanase PulA [159262]
      1. Klebsiella pneumoniae [TaxId: 573] [159263] (3)
        SQ P07206 973-1090
  2. Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 [89388] (6)
    interrupted by the catalytic domain; the C-terminal core is similar to the alpha-amylase domain
    1. Glucosylceramidase [89389]
      glycosyl hydrolase family 30; the N-terminal extension wraps around the C-terminal core
      1. Human (Homo sapiens) [TaxId: 9606] [89390] (27)
    2. Glycosyl hydrolase family 5 xylanase [101922]
      1. Erwinia chrysanthemi [TaxId: 556] [101923] (1)
    3. Alpha-l-arabinofuranosidase [101924]
      glycosyl hydrolase family 51
      1. Bacillus stearothermophilus [TaxId: 1422] [101925] (4)
      2. Clostridium thermocellum [TaxId: 1515] [141554] (12)
        SQ Q4CJG5 2-16,387-502
    4. Beta-D-xylosidase [101926]
      glycosyl hydrolase family 39
      1. Thermoanaerobacterium saccharolyticum [TaxId: 28896] [101927] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [141555] (24)
        SQ Q9ZFM2 5-14,362-503
  3. Putative alpha-L-fucosidase C-terminal domain [101928] (1)
    glycosyl hydrolase family 29; beta-sheet forms a closed beta-barrel (n=8, S=10)
    1. Putative alpha-L-fucosidase C-terminal domain [101929]
      1. Thermotoga maritima [TaxId: 2336] [101930] (3)
        TM0306
  4. Putative glucosidase YicI, domain 3 [117298] (1)
    1. Putative glucosidase YicI, domain 3 [117299]
      1. Escherichia coli [TaxId: 562] [117300] (15)
        SQ P31434
  5. Beta-galactosidase LacA, domain 2 [117301] (1)
    contains extra C-terminal beta-sandwich subdomain [greek-key; partial topological similarity to the immunoglobulin-like fold]
    1. Beta-galactosidase LacA, domain 2 [117302]
      1. Penicillium sp. [TaxId: 5081] [117303] (2)
        SQ Q700S9 41-1011
WW domain-like [51044] (3)
core: 3-stranded meander beta-sheet
1. WW domain [51045] (1)
  uperfamily
  1. WW domain [51046] (13)
    1. Mitotic rotamase PIN1 [51047]
      1. Human (Homo sapiens) [TaxId: 9606] [51048] (8)
    2. Formin binding protein FBP28 domain [51049]
      1. Domestic mouse (Mus musculus) [TaxId: 10090] [51050] (4)
    3. Dystrophin [51051]
      1. Human (Homo sapiens) [TaxId: 9606] [51052] (2)
    4. Ubiquitin ligase NEDD4 WWIII domain [63837]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [63838] (2)
      2. fruit fly (Drosophila melanogaster) [TaxId: 7227] [159264] (1)
    5. Hypothetical protein Yjq8 (Set2p) [51053]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51054] (1)
    6. Yap65 ww domain [69330]
      1. Human (Homo sapiens) [TaxId: 9606] [69331] (4)
    7. Splicing factor prp40 [82183]
      duplication: contains two WW domains connected by a helical linker
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82184] (1)
    8. Suppressor of deltex (Cg4244-pb) [110301]
      duplication: contains two WW domains connected by a helical linker
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110302] (1)
        SQ Q9Y0H4 474-554
    9. WW domain-binding protein 4, WBP4 [141556]
      1. Human (Homo sapiens) [TaxId: 9606] [141557] (1)
        SQ O75554 126-163
    10. Huntingtin-interacting protein HYPA/FBP11 [141558]
      1. Human (Homo sapiens) [TaxId: 9606] [141559] (4)
        SQ O75400 144-171! SQ O75400 146-173
    11. Amyloid beta A4 precursor protein-binding family B member 3, APBB3 [159265]
      1. Human (Homo sapiens) [TaxId: 9606] [159266] (1)
        SQ O95704 30-61
    12. Amyloid beta A4 precursor protein-binding family B member 1, APBB1 [159267]
      1. Human (Homo sapiens) [TaxId: 9606] [159268] (11)
        SQ O00213 241-290! SQ O00213 253-285
2. Carbohydrate binding domain [51055] (1)
  uperfamily
  1. Carbohydrate binding domain [51056] (3)
    1. Cellulose-binding domain of endoglucanase Z [51057]
      1. Erwinia chrysanthemi [TaxId: 556] [51058] (1)
    2. Chitin-binding domain of chitinase A1 [51059]
      1. Bacillus circulans [TaxId: 1397] [51060] (1)
    3. Chitinase B, C-terminal domain [51061]
      1. Serratia marcescens [TaxId: 615] [51062] (14)
3. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101931] (1)
  uperfamily
  1. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101932] (1)
    1. Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain [101933]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101934] (1)
Head domain of nucleotide exchange factor GrpE [51063] (1)
small mixed beta-sheet, 4 "generalized" strands
1. Head domain of nucleotide exchange factor GrpE [51064] (1)
  uperfamily
  1. Head domain of nucleotide exchange factor GrpE [51065] (1)
    1. Head domain of nucleotide exchange factor GrpE [51066]
      1. Escherichia coli [TaxId: 562] [51067] (1)
Coronavirus RNA-binding domain [110303] (1)
coiled antiparallel beta-sheet of 5 strands, order 51324; complex topology, crossing loops
1. Coronavirus RNA-binding domain [110304] (1)
  uperfamily
  1. Coronavirus RNA-binding domain [110305] (2)
    N-terminal part of Pfam 00937
    1. Nucleocapsid protein [110306]
      1. SARS coronavirus, (SARS-CoV) [TaxId: 227859] [110307] (1)
        SQ P59595 45-181
      2. Avian infectious bronchitis virus [TaxId: 11120] [141560] (8)
        SQ P32923 23-160! SQ P69596 29-160! SQ P69597 29-160
        different strains
Ribonuclease domain of colicin E3 [63839] (1)
twisted meander beta-sheet of 6 strands
1. Ribonuclease domain of colicin E3 [63840] (1)
  uperfamily
  1. Ribonuclease domain of colicin E3 [63841] (1)
    1. Ribonuclease domain of colicin E3 [63842]
      1. Escherichia coli [TaxId: 562] [63843] (4)
NAC domain [101940] (1)
core: twisted 7-stranded beta-sheet (half-barrel)
1. NAC domain [101941] (1)
  uperfamily
  1. NAC domain [101942] (1)
    Pfam 02365, NAM; transcription factor domain
    1. No apical meristem (NAM, ANAC) [101943]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [101944] (2)
At5g01610-like [141561] (1)
contains large meander beta-sheet bent into a scoop-like shape
1. At5g01610-like [141562] (1)
  uperfamily
  1. At5g01610-like [141563] (1)
    Pfam 04398; DUF538
    1. Hypothetical protein At5g01610 [141564]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141565] (1)
        SQ Q9M015 2-170
Carbonic anhydrase [51068] (1)
single sheet; 10 strands
1. Carbonic anhydrase [51069] (1)
  uperfamily
  1. Carbonic anhydrase [51070] (10)
    1. Carbonic anhydrase [51071]
      1. Human (Homo sapiens), erythrocytes, isozyme I [TaxId: 9606] [51072] (21)
      2. Human (Homo sapiens), erythrocytes, isozyme II [TaxId: 9606] [51073] (221)
        SQ P00918
      3. Cow (Bos taurus), isozyme II [TaxId: 9913] [51074] (3)
      4. Rat (Rattus norvegicus), isozyme III [TaxId: 10116] [51075] (1)
      5. Human (Homo sapiens), isozyme IV [TaxId: 9606] [51076] (1)
      6. Mouse (Mus musculus), isozyme IV [TaxId: 10090] [51077] (2)
      7. Mouse (Mus musculus), liver, isozyme V [TaxId: 10090] [51078] (4)
      8. Human (Homo sapiens), isozyme XII [TaxId: 9606] [63844] (2)
      9. Mouse (Mus musculus), isozyme XIV [TaxId: 10090] [101945] (2)
      10. Neisseria gonorrhoeae [TaxId: 485] [51079] (2)
LolA-like prokaryotic lipoproteins and lipoprotein localization factors [89391] (1)
11 stranded sheet partly folded in a corner-like structure filled with a few short helices
1. Prokaryotic lipoproteins and lipoprotein localization factors [89392] (3)
  uperfamily
  1. Outer-membrane lipoproteins carrier protein LolA [89393] (1)
    1. Outer-membrane lipoproteins carrier protein LolA [89394]
      1. Escherichia coli [TaxId: 562] [89395] (2)
  2. Outer membrane lipoprotein receptor LolB [89396] (1)
    1. Outer membrane lipoprotein receptor LolB [89397]
      1. Escherichia coli [TaxId: 562] [89398] (2)
  3. LppX-like [141566] (1)
    Pfam 07161; DUF1396; contains a large cavity between the 'flattened' beta-sheet and helix-containing loops
    1. Putative lipoprotein LppX [141567]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141568] (1)
        SQ P65306 46-233
YmcC-like [159269] (1)
12-stranded meander beta-sheet, folded into a deformed beta-barrel; topological similarity to the LolA-like fold (scop_cf 89391)
1. YmcC-like [159270] (1)
  1. YmcC-like [159271] (1)
    PfamB 007600
    1. Hypothetical lipoprotein YmcC [159272]
      1. Escherichia coli [TaxId: 562] [159273] (2)
        SQ P75884 17-214
Spiral beta-roll [159274] (1)
a large 15-stranded beta-sheet rolled about a single helix core; overlapping edges form a sandwich-like structure; topological similarity to the LolA-like fold (scop_cf 89391)
1. PA1994-like [159275] (1)
  1. PA1994-like [159276] (1)
    Pfam 06475; DUF1089
    1. Hypothetical protein PA1994 [159277]
      1. Pseudomonas aeruginosa [TaxId: 287] [159278] (2)
        SQ Q9I2B5 2-187
Bacteriochlorophyll A protein [51080] (1)
single sheet; 16 strands; meander
1. Bacteriochlorophyll A protein [51081] (1)
  uperfamily
  1. Bacteriochlorophyll A protein [51082] (2)
    1. Bacteriochlorophyll A protein [51083]
      1. Prosthecochloris aestuarii, strain 2k [TaxId: 1102] [51084] (1)
      2. Green sulfur bacterium (Chlorobium tepidum) [TaxId: 1097] [51085] (3)
open-sided beta-meander [51086] (2)
single sheet formed by beta-hairpin repeats; exposed on both sides in the middle
1. Outer surface protein [51087] (1)
  21 stranded sheet partly folded upon itself at the ends
  uperfamily
  1. Outer surface protein [51088] (2)
    1. Outer surface protein A [51089]
      1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [51090] (2)
    2. Outer surface protein B [101946]
      1. Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139] [101947] (2)
        SQ P17739 202-296
2. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82185] (1)
  11+ stranded sheet partly folded upon itself at the C-end
  uperfamily
  1. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82186] (1)
    1. Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain [82187]
      1. Human (Homo sapiens) [TaxId: 9606] [82188] (11)
        SQ Q8WTS6 52-366
beta-Prism I [51091] (3)
consists of 3 4-stranded sheets; strands are parallel to the 3-fold axis
duplication: has internal pseudo threefold symmetry
1. Vitelline membrane outer protein-I (VMO-I) [51092] (1)
  uperfamily
  1. Vitelline membrane outer protein-I (VMO-I) [51093] (1)
    1. Vitelline membrane outer protein-I (VMO-I) [51094]
      1. Hen (Gallus gallus) [TaxId: 9031] [51095] (1)
2. delta-Endotoxin (insectocide), middle domain [51096] (1)
  uperfamily
  1. delta-Endotoxin (insectocide), middle domain [51097] (4)
    1. delta-Endotoxin (insectocide), middle domain [51098]
      1. Bacillus thuringiensis tenebrionis, CRYIIIA (BT13) [TaxId: 1444] [51099] (1)
      2. Bacillus thuringiensis, CRY3bb1 [TaxId: 1428] [63845] (1)
      3. Bacillus thuringiensis, CRYIA (A) [TaxId: 1428] [51100] (1)
      4. Bacillus thuringiensis subsp. kurstaki, CRY2AA [TaxId: 29339] [63846] (1)
3. Mannose-binding lectins [51101] (1)
  uperfamily
  1. Mannose-binding lectins [51102] (8)
    1. Jacalin [51103]
      1. Jackfruit (Artocarpus heterophyllus) [TaxId: 3489] [51104] (10)
      2. Artocarpus hirsuta [TaxId: 291940] [110308] (2)
        SQ Q38723 64-217 95% sequence identity
    2. Artocarpin [75022]
      1. Jackfruit (Artocarpus heterophyllus) [TaxId: 3489] [75023] (5)
        SQ Q7M1T4
    3. Lectin MPA [51105]
      1. Osage orange (Maclura pomifera) [TaxId: 3496] [51106] (1)
    4. Heltuba lectin [51107]
      1. Jerusalem artishoke (Helianthus tuberosus) [TaxId: 4233] [51108] (3)
    5. Calystegia sepium agglutinin [101948]
      1. Hedge bindweed (Calystegia sepium) [TaxId: 47519] [101949] (1)
    6. Griffithsin [141569]
      single-chain subunits form a segment-swapped dimer
      1. Red alga (Griffithsia) [TaxId: 35158] [141570] (13)
        SQ P84801 1-121
      2. Griffithsia sp. Q66D336 [TaxId: 373036] [159279] (4)
beta-Prism II [51109] (1)
consists of 3 4-stranded sheets; strands are perpendicular to the 3-fold axis
duplication: consists of two domains of this fold
1. alpha-D-mannose-specific plant lectins [51110] (1)
  uperfamily
  1. alpha-D-mannose-specific plant lectins [51111] (6)
    1. Lectin (agglutinin) [51112]
      1. Snowdrop (Galanthus nivalis) [TaxId: 4670] [51113] (3)
      2. Garlic (Allium sativum) [TaxId: 4682] [51114] (2)
      3. Daffodil (Narcissus pseudonarcissus) [TaxId: 39639] [51115] (1)
      4. Bluebell (Scilla campanulata) [TaxId: 81759] [51116] (1)
    2. Fetuin-binding protein Scafet precursor [51117]
      duplication: consists of two beta-prism II domains
      1. Bluebell (Scilla campanulata) [TaxId: 81759] [51118] (1)
    3. Gastrodianin (antifungal protein) [117304]
      1. Gastrodia elata [TaxId: 91201] [117305] (2)
        SQ Q9AXZ2 29-140 # different isoforms
Single-stranded right-handed beta-helix [51125] (8)
superhelix turns are made of parallel beta-strands and (short) turns
1. beta-Roll [51120] (1)
  superhelix turns are made of two short strands each
  uperfamily
  1. Serralysin-like metalloprotease, C-terminal domain [51121] (4)
    duplication: halfturs of beta-helix are sequence and structural repeats; binds calcium ions between the turns
    1. Metalloprotease [51122]
      The catalytic N-terminal domain belong to the "zincin" superfamily
      1. Pseudomonas aeruginosa [TaxId: 287] [51123] (3)
        alkaline protease
      2. Serratia marcescens [TaxId: 615] [51124] (4)
        serralysin
      3. Erwinia chrysanthemi [TaxId: 556] [82189] (5)
        protease C
      4. Pseudomonas sp., tac ii 18 [TaxId: 306] [82190] (8)
        psychrophilic alkaline protease
2. Pectin lyase-like [51126] (11)
  superhelix turns are made of 3 strands each
  uperfamily
  1. Pectate lyase-like [51127] (6)
    1. Pectate lyase [51128]
      1. Erwinia chrysanthemi, type C [TaxId: 556] [51129] (14)
      2. Erwinia chrysanthemi, type A [TaxId: 556] [75024] (4)
      3. Erwinia chrysanthemi, type E [TaxId: 556] [51130] (1)
      4. Bacillus subtilis [TaxId: 1423] [51131] (2)
      5. Bacillus sp., strain ksmp15 [TaxId: 1409] [51132] (1)
        Low-molecular weight high-alkaline enzyme
    2. Major pollen allergen Jun a 1 [117306]
      1. Ozark white cedar (Juniperus ashei) [TaxId: 13101] [117307] (1)
        SQ P81294 22-367
  2. Pectin lyase [51133] (2)
    1. Pectin lyase [51134]
      1. Aspergillus niger, type A [TaxId: 5061] [51135] (2)
      2. Aspergillus niger, type B [TaxId: 5061] [51136] (1)
  3. Galacturonase [51137] (7)
    1. Rhamnogalacturonase A [51138]
      1. Aspergillus aculeatus [TaxId: 5053] [51139] (1)
    2. Polygalacturonase [51140]
      1. Erwinia carotovora, subsp. carotovora [TaxId: 554] [51141] (1)
      2. Fungus (Aspergillus aculeatus) [TaxId: 5053] [63847] (2)
      3. Fungus (Stereum purpureum), endo-polygalacturonase I [TaxId: 58369] [75025] (3)
      4. Fungus (Aspergillus niger), endo-polygalacturonase I [TaxId: 5061] [101950] (1)
      5. Fungus (Aspergillus niger), endo-polygalacturonase II [TaxId: 5061] [63382] (1)
      6. Fusarium moniliforme [TaxId: 117187] [69332] (1)
  4. Chondroitinase B [51144] (1)
    1. Chondroitinase B [51145]
      1. Pedobacter heparinus [TaxId: 984] [51146] (4)
        SQ Q46079 27-506
        synonym: Flavobacterium heparinum
  5. iota-carrageenase [69333] (1)
    1. iota-carrageenase [69334]
      1. Alteromonas sp., atcc 43554 [TaxId: 232] [69335] (2)
  6. Pectate transeliminase [101951] (1)
    1. Pectate transeliminase [101952]
      type L pectate lyase, pel9a
      1. Erwinia chrysanthemi [TaxId: 556] [101953] (1)
  7. Dextranase, catalytic domain [101954] (1)
    1. Dextranase, catalytic domain [101955]
      1. Penicillium minioluteum [TaxId: 28574] [101956] (2)
  8. Pectin methylesterase [51147] (2)
    1. Pectin methylesterase PemA [51148]
      1. Erwinia chrysanthemi [TaxId: 556] [51149] (1)
      2. Carrot (Daucus carota) [TaxId: 4039] [75026] (1)
  9. P22 tailspike protein [51150] (1)
    1. P22 tailspike protein [51151]
      1. Salmonella phage P22 [TaxId: 10754] [51152] (12)
  10. Virulence factor P.69 pertactin [51153] (1)
    1. Virulence factor P.69 pertactin [51154]
      1. Bordetella pertussis [TaxId: 520] [51155] (1)
  11. Filamentous hemagglutinin FhaB, secretion domain [101957] (1)
    1. Filamentous hemagglutinin FhaB, secretion domain [101958]
      1. Bordetella pertussis [TaxId: 520] [101959] (1)
3. Insect cysteine-rich antifreeze protein [51156] (1)
  superhelix turns are made of two short strands each
  uperfamily
  1. Insect cysteine-rich antifreeze protein [51157] (1)
    1. Insect cysteine-rich antifreeze protein [51158]
      1. Yellow mealworm (Tenebrio molitor) [TaxId: 7067] [51159] (2)
4. Cell-division inhibitor MinC, C-terminal domain [63848] (1)
  superhelix turns are made of three short strands each
  uperfamily
  1. Cell-division inhibitor MinC, C-terminal domain [63849] (1)
    1. Cell-division inhibitor MinC, C-terminal domain [63850]
      1. Thermotoga maritima [TaxId: 2336] [63851] (1)
5. Alpha subunit of glutamate synthase, C-terminal domain [69336] (1)
  uperfamily
  1. Alpha subunit of glutamate synthase, C-terminal domain [69337] (2)
    1. Alpha subunit of glutamate synthase, C-terminal domain [69338]
      Central domain (residues 423-780) may be a rudiment form of the FMN domain
      1. Azospirillum brasilense [TaxId: 192] [69339] (7)
      2. Synechocystis sp. [TaxId: 1143] [75027] (5)
6. C-terminal domain of adenylylcyclase associated protein [69340] (1)
  superhelix turns are made of two strands each
  uperfamily
  1. C-terminal domain of adenylylcyclase associated protein [69341] (2)
    1. C-terminal domain of adenylylcyclase associated protein [69342]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69343] (2)
      2. Human (Homo sapiens) [TaxId: 9606] [89399] (1)
7. Stabilizer of iron transporter SufD [101960] (1)
  superhelix turns are made of two very long strands each
  uperfamily
  1. Stabilizer of iron transporter SufD [101961] (1)
    1. Stabilizer of iron transporter SufD [101962]
      1. Escherichia coli [TaxId: 562] [101963] (1)
8. Pentapeptide repeat-like [141571] (1)
  superhelix turns are made of four short strands each; duplication: the sequence pentapeptide repeats correspond to individual strands
  uperfamily
  1. Pentapeptide repeats [141572] (3)
    Pfam 00805 (covers eight repeats or two full superhelical turns)
    1. Hypothetical protein Rv3361c (MT3469) [141573]
      1. Mycobacterium tuberculosis [TaxId: 1773] [141574] (8)
        SQ O50390 2-182
    2. NP275-NP276 [141575]
      Two consecuitive ORFs in the same frame that maintain the sequence periodicity; probable single ORF disrupted by the nonsense mutation
      1. Nostoc punctiforme [TaxId: 272131] [141576] (3)
    3. Lumenal RFR-domain protein [141577]
      1. Cyanothece sp. atcc 51142 [TaxId: 43989] [141578] (2)
Single-stranded left-handed beta-helix [51160] (4)
superhelix turns are made of parallel beta-strands and (short) turns
1. Trimeric LpxA-like enzymes [51161] (8)
  superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands
  uperfamily
  1. UDP N-acetylglucosamine acyltransferase [51162] (2)
    1. UDP N-acetylglucosamine acyltransferase [51163]
      1. Escherichia coli, gene lpxA [TaxId: 562] [51164] (6)
      2. Helicobacter pylori [TaxId: 210] [101964] (1)
  2. Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [51165] (1)
    contains extra N-terminal 3-helical domain
    1. Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [51166]
      1. Mycobacterium bovis [TaxId: 1765] [51167] (5)
  3. Galactoside acetyltransferase-like [51168] (4)
    1. Galactoside acetyltransferase [75028]
      1. Escherichia coli [TaxId: 562] [75029] (4)
    2. Maltose O-acetyltransferase [89400]
      1. Escherichia coli [TaxId: 562] [89401] (1)
    3. Xenobiotic acetyltransferase [51169]
      1. Pseudomonas aeruginosa [TaxId: 287] [51170] (2)
      2. Enterococcus faecium, VAT(D) [TaxId: 1352] [69344] (7)
        streptogramin A acetyltransferase
  4. GlmU C-terminal domain-like [51171] (4)
    1. N-acetylglucosamine 1-phosphate uridyltransferase GlmU, C-terminal domain [51172]
      1. Escherichia coli [TaxId: 562] [51173] (9)
      2. Streptococcus pneumoniae [TaxId: 1313] [63852] (5)
    2. Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain [141579]
      1. Potato (Solanum tuberosum) [TaxId: 4113] [141580] (12)
        SQ P23509 387-521
    3. UDP-glucose pyrophosphorylase 2 (UDPGP 2) [141581]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141582] (8)
        SQ Q9M9P3 384-469
  5. gamma-carbonic anhydrase-like [51174] (3)
    archaeal hexapeptide repeat proteins
    1. gamma-carbonic anhydrase [51175]
      1. Archaeon Methanosarcina thermophila [TaxId: 2210] [51176] (7)
    2. Ferripyochelin binding protein [101965]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101966] (3)
    3. Putative acetyltransferase/acyltransferase BC4754 [117308]
      1. Bacillus cereus [TaxId: 1396] [117309] (1)
        SQ Q816R4
  6. Serine acetyltransferase [110309] (2)
    1. Serine acetyltransferase [110310]
      extra N-terminal all-alpha subdomain belongs to Pfam 06426
      1. Haemophilus influenzae [TaxId: 727] [110311] (4)
        SQ P43886 1-241
      2. Escherichia coli [TaxId: 562] [110312] (1)
        SQ P05796
  7. YdcK-like [141583] (1)
    part of Pfam 00132
    1. Hypothetical protein YdcK [141584]
      1. Salmonella enterica [TaxId: 28901] [141585] (1)
        SQ Q5PHU6 3-322
  8. PglD-like [159280] (1)
    contains extra N-terminal alpha/beta subdomain
    1. Acetyltransferase PglD [159281]
      1. Campylobacter jejuni [TaxId: 197] [159282] (9)
        SQ Q0P9D1 3-197
2. An insect antifreeze protein [51177] (1)
  superhelical turns are made of three short strands
  uperfamily
  1. An insect antifreeze protein [51178] (2)
    1. Thermal hysteresis protein [51179]
      there are different numbers of superhelical turns (and sequence repeats) in different isoforms
      1. Spruce budworm (Choristoneura fumiferana), 5-turn isoforms [TaxId: 7141] [88689] (3)
      2. Spruce budworm (Choristoneura fumiferana), 7-turn isoforms [TaxId: 7141] [88690] (2)
3. Adhesin YadA, collagen-binding domain [101967] (1)
  superhelical turns are made of two short strands
  uperfamily
  1. Adhesin YadA, collagen-binding domain [101968] (1)
    1. Adhesin YadA, collagen-binding domain [101969]
      1. Yersinia enterocolitica [TaxId: 630] [101970] (1)
4. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159283] (1)
  probable rudiment form of the LpxA-like hexapeptide domain
  1. Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain [159284] (1)
    corresponds to the N-terminal part of Pfam 01050, but does not extend to the conserved functional motif; the predicted cupin fold may reside in the rest of the Pfam domain
    1. Putative mannose-1-phosphate guanylyl transferase (GDP)/mannose-6-phosphate isomerase TTHA1750 [159285]
      there is no the functional mannose-6-phosphate isomerase domain in this protein; this would-be the linker domain is the C-terminal one
      1. Thermus thermophilus [TaxId: 274] [159286] (1)
        SQ Q5SHI0 269-335
Double-stranded beta-helix [51181] (7)
one turn of helix is made by two pairs of antiparallel strands linked with short turns
has appearance of a sandwich of distinct architecture and jelly-roll topology
1. RmlC-like cupins [51182] (24)
  uperfamily
  1. dTDP-sugar isomerase [51183] (9)
    1. dTDP-4-dehydrorhamnose 3,5-epimerase RmlC [51184]
      synonym: dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
      1. Salmonella typhimurium [TaxId: 90371] [51185] (2)
      2. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [51186] (2)
      3. Streptococcus suis [TaxId: 1307] [89402] (7)
      4. Mycobacterium tuberculosis [TaxId: 1773] [101971] (6)
      5. Pseudomonas aeruginosa [TaxId: 287] [101972] (4)
      6. Archaeon Sulfolobus tokodaii [TaxId: 111955] [141586] (2)
        SQ Q96Z62 1-176
    2. dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD [101973]
      1. Amycolatopsis orientalis [TaxId: 31958] [101974] (2)
        SQ O52806
    3. Novobiocin biosynthesis protein NovW [141587]
      1. Streptomyces caeruleus [TaxId: 195949] [141588] (1)
        SQ Q9L9E5 1-190
    4. dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA [159287]
      1. Aneurinibacillus thermoaerophilus [TaxId: 143495] [159288] (8)
        SQ Q6T1W8 1-136! SQ Q6T1W8 2-136
  2. Glucose-6-phosphate isomerase, GPI [89403] (2)
    1. Glucose-6-phosphate isomerase, GPI [89404]
      Type II phosphoglucose isomerase
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89405] (6)
        SQ P83194
      2. Archaeon Thermococcus litoralis [TaxId: 2265] [101975] (11)
  3. Hypothetical protein TM1112 [89406] (1)
    1. Hypothetical protein TM1112 [89407]
      1. Thermotoga maritima [TaxId: 2336] [89408] (2)
  4. TM1287-like [89409] (4)
    1. Hypothetical protein TM1287 [89410]
      1. Thermotoga maritima [TaxId: 2336] [89411] (1)
    2. Hypothetical protein TTHA0104 [117310]
      1. Thermus thermophilus [TaxId: 274] [117311] (3)
        SQ Q5SM39
    3. Hypothetical protein TM1010 [141589]
      1. Thermotoga maritima [TaxId: 2336] [141590] (4)
        SQ Q9X0A3 2-135
    4. Hypothetical protein SPy1581 [141591]
      1. Streptococcus pyogenes [TaxId: 1314] [141592] (1)
        SQ Q99YR1 1-112
  5. TM1459-like [101976] (2)
    1. Hypothetical protein TM1459 [101977]
      1. Thermotoga maritima [TaxId: 2336] [101978] (1)
    2. Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain [141593]
      1. Streptomyces wedmorensis [TaxId: 43759] [141594] (20)
        SQ Q56185 77-198
  6. Germin/Seed storage 7S protein [51187] (9)
    1. Germin [63853]
      Metal (manganese)-binding protein with oxalate oxidase and superoxide dismutase activities; homohexamer
      1. Barley (Hordeum vulgare) [TaxId: 4513] [63854] (5)
    2. Auxin binding protein [75030]
      1. Maize (Zea mays) [TaxId: 4577] [75031] (2)
    3. Seed storage 7S protein [51188]
      duplication: consists of two germin-like domains spatially arranged as subunits in the RmlC dimer; trimer is similar to the germin hexamer
      1. French bean (Phaseolus vulgaris), phaseolin [TaxId: 3885] [51189] (2)
      2. Jack bean (Canavalia ensiformis), canavalin/vinculin [TaxId: 3823] [51190] (8)
      3. Soybean (Glycine max), proglycinin [TaxId: 3847] [69345] (3)
      4. Soybean (Glycine max), beta-conglycinin beta subunit [TaxId: 3847] [109608] (3)
        SQ P25974
      5. Soybean (Glycine max), glycinin A3B4 [TaxId: 3847] [89412] (1)
      6. Soybean (Glycine max), beta-conglycinin alpha prime subunit [TaxId: 3847] [110313] (1)
        SQ Q7XXT2 204-621
    4. Oxalate decarboxylase OxdC (YvrK) [75033]
      duplication: consists of two germin-like metal-ion binding domains
      1. Bacillus subtilis [TaxId: 1423] [75034] (3)
  7. YlbA-like [101979] (4)
    Pfam 05899; formerly pfam06038; duplication: consists of two germin-like domains
    1. Hypothetical protein YlbA [101980]
      1. Escherichia coli [TaxId: 562] [101981] (1)
    2. Glyoxylate-induced protein PA1140 [101982]
      1. Pseudomonas aeruginosa [TaxId: 287] [101983] (1)
    3. Hypothetical protein EF2996 [110314]
      1. Enterococcus faecalis [TaxId: 1351] [110315] (1)
        SQ Q82ZQ3
    4. Hypothetical protein DR1152 [110316]
      1. Deinococcus radiodurans [TaxId: 1299] [110317] (1)
        SQ Q9RV77
  8. Pirin-like [101984] (2)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Pirin [101985]
      Bcl-3 and nuclear factor I-interacting protein
      1. Human (Homo sapiens) [TaxId: 9606] [101986] (1)
    2. Hypothetical protein YhhW [141595]
      1. Escherichia coli [TaxId: 562] [141596] (1)
        SQ P46852 1-231
  9. Quercetin 2,3-dioxygenase-like [75035] (2)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Quercetin 2,3-dioxygenase [75036]
      1. Aspergillus japonicus [TaxId: 34381] [75037] (5)
    2. Hypothetical protein YxaG [141597]
      1. Bacillus subtilis [TaxId: 1423] [141598] (2)
        SQ P42106 5-334
  10. Type I phosphomannose isomerase [51191] (3)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin
    1. Phosphomannose isomerase [51192]
      1. Yeast (Candida albicans) [TaxId: 5476] [51193] (1)
        contains insert all-alpha subdomain; residues 152-266
    2. Mannose-6-phosphate isomerase ManA [101987]
      1. Bacillus subtilis [TaxId: 1423] [101988] (1)
    3. Putative mannosephosphate isomerase AF0035 [141599]
      1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [141600] (1)
        SQ O30200 1-299
  11. Homogentisate dioxygenase [51194] (1)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the C-terminal domain similar to the metal-binding site of germin
    1. Homogentisate dioxygenase [51195]
      1. Human (Homo sapiens) [TaxId: 9606] [51196] (2)
  12. Acireductone dioxygenase [82191] (2)
    1. Acireductone dioxygenase [82192]
      1. Klebsiella pneumoniae [TaxId: 573] [82193] (1)
        NMR-derived model
      2. Mouse (Mus musculus) [TaxId: 10090] [141601] (1)
        SQ Q99JT9 1-179
  13. KduI-like [110318] (2)
    Pfam 04962: duplication: consists of two germin-like domains
    1. 5-keto-4-deoxyuronate isomerase KduI [110319]
      1. Escherichia coli [TaxId: 562] [110320] (3)
        SQ Q46938 1-266
      2. Enterococcus faecalis [TaxId: 1351] [141602] (6)
        SQ Q838L9 1-260
  14. Ureidoglycolate hydrolase AllA [117312] (3)
    Pfam 04115; beta-hairpin-swapped dimeric protein of the germin-like fold
    1. Ureidoglycolate hydrolase AllA [117313]
      1. Shigella flexneri [TaxId: 623] [117314] (2)
        SQ P77731 ! SQ P63487
      2. Pseudomonas putida [TaxId: 303] [141603] (2)
        SQ P59285 1-166
      3. Escherichia coli [TaxId: 562] [141604] (2)
        SQ P63486 1-160
  15. Probable transcriptional regulator VC1968, C-terminal domain [117315] (1)
    1. Probable transcriptional regulator VC1968, C-terminal domain [117316]
      1. Vibrio cholerae [TaxId: 666] [117317] (1)
        SQ Q9KQN0
  16. YML079-like [117318] (3)
    Pfam 06172; DUF985
    1. Hypothetical protein YML079W [117319]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117320] (2)
        SQ Q03629
    2. Hypothetical protein Atu3615 [141605]
      1. Agrobacterium tumefaciens [TaxId: 358] [141606] (7)
        SQ Q8U9W0 4-143
    3. Hypothetical protein SO0799 [141607]
      1. Shewanella oneidensis [TaxId: 70863] [141608] (10)
        SQ Q8EIN8 1-158
  17. PA5104-like [141609] (1)
    Pfam 05962; DUF886; duplication: consists of two germin-like domains; overall structural similarity to the YlbA-like family (scop_fa 101979) except a deletion in the interdomain linker region
    1. Hypothetical protein PA5104 [141610]
      1. Pseudomonas aeruginosa [TaxId: 287] [141611] (4)
        SQ Q9HU79 2-196
  18. MJ0764-like [141612] (1)
    1. Hypothetical protein MJ0764 [141613]
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [141614] (1)
        SQ Q58174 1-108
  19. Cysteine dioxygenase type I [141615] (4)
    Pfam 05995, CDO_I
    1. Cysteine dioxygenase type I [141616]
      1. Mouse (Mus musculus) [TaxId: 10090] [141617] (4)
        SQ P60334 5-190
      2. Ralstonia eutropha [TaxId: 106590] [159289] (1)
        SQ Q46R41 11-202
      3. Human (Homo sapiens) [TaxId: 9606] [159290] (1)
        SQ Q16878 6-190
      4. Rattus norvegicus [TaxId: 10116] [159291] (1)
  20. 3-hydroxyanthranilic acid dioxygenase-like [141618] (2)
    Pfam 06052; 3-HAO
    1. 3-hydroxyanthranilate-3,4-dioxygenase [141619]
      1. Ralstonia metallidurans [TaxId: 119219] [141620] (4)
        SQ Q1LCS4 1-174
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [159292] (2)
        SQ P47096 1-175
  21. Acetylacetone-cleaving enzyme-like [159293] (1)
    PfamB 026844
    1. Putative acetyl/propionyl-CoA carboxylase subunit alpha Mpe_A3659 [159294]
      1. Rubrivivax gelatinosus [TaxId: 28068] [159295] (2)
        SQ A2SM23 1-144
  22. VPA0057-like [159296] (1)
    Pfam 06865; DUF1255; non-canonical dimerisation mode
    1. Uncharacterized protein VPA0057 [159297]
      1. Vibrio parahaemolyticus [TaxId: 670] [159298] (1)
        SQ Q87K41 2-94
  23. Gentisate 1,2-dioxygenase-like [159299] (3)
    Share a common two-domain fold with the 7S protein; there is a metal-binding site in the N-terminal domain similar to the metal-binding site of germin; homotetramer
    1. Gentisate 1,2-dioxygenase [159300]
      Salicylate 1,2-dioxygenase
      1. Escherichia coli [TaxId: 562] [159301] (4)
        SQ Q8X655 35-342
      2. Silicibacter pomeroyi [TaxId: 89184] [159302] (2)
        SQ Q5LLB1 19-373
      3. Pseudaminobacter salicylatoxidans [TaxId: 93369] [159303] (4)
        SQ Q67FT0 17-367
  24. EutQ-like [159304] (1)
    Pfam 06249
    1. Ethanolamine utilization protein EutQ [159305]
      1. Salmonella typhimurium [TaxId: 90371] [159306] (2)
        SQ Q9ZFV5 100-227
2. Clavaminate synthase-like [51197] (13)
  Iron and ketoglutarate-dependent enzymes; elaborated version of this common fold
  uperfamily
  1. Penicillin synthase-like [51198] (4)
    common fold is rather distorted
    1. Isopenicillin N synthase [51199]
      1. Emericella nidulans [TaxId: 162425] [51200] (29)
        SQ P05326
    2. Deacetoxycephalosporin C synthase [51201]
      1. Streptomyces clavuligerus [TaxId: 1901] [51202] (17)
        SQ P18548
    3. Anthocyanidin synthase [69346]
      1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [69347] (4)
    4. 1-aminocyclopropane-1-carboxylate oxidase 1 [141621]
      1. Petunia hybrida [TaxId: 4102] [141622] (2)
        SQ Q08506 2-308
  2. Clavaminate synthase [51203] (1)
    1. Clavaminate synthase [51204]
      1. Streptomyces clavuligerus [TaxId: 1901] [51205] (5)
  3. Gab protein (hypothetical protein YgaT) [63855] (1)
    1. Gab protein (hypothetical protein YgaT) [63856]
      unknown function
      1. Escherichia coli [TaxId: 562] [63857] (1)
  4. YhcH-like [89413] (1)
    1. Hypothetical protein HI0227 [89414]
      1. Haemophilus influenzae [TaxId: 727] [89415] (5)
  5. Type II Proline 3-hydroxylase (proline oxidase) [63858] (1)
    1. Type II Proline 3-hydroxylase (proline oxidase) [63859]
      1. Streptomyces sp. [TaxId: 1931] [63860] (2)
  6. TauD/TfdA-like [75038] (2)
    1. Taurine/alpha-ketoglutarate dioxygenase TauD [75039]
      1. Escherichia coli [TaxId: 562] [75040] (4)
    2. Putative alkylsulfatase AtsK [101989]
      1. Pseudomonas putida [TaxId: 303] [101990] (6)
        SQ Q9WWU5
  7. gamma-Butyrobetaine hydroxylase [89416] (2)
    Pfam 03322
    1. Carbapenem synthase, CarC [89417]
      1. Erwinia carotovora [TaxId: 554] [89418] (2)
    2. Clavaminate synthase-like protein At3g21360 [117321]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117322] (3)
        SQ Q9LIG0
  8. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82194] (1)
    1. Hypoxia-inducible factor HIF ihhibitor (FIH1) [82195]
      1. Human (Homo sapiens) [TaxId: 9606] [82196] (10)
  9. PhyH-like [141623] (2)
    Pfam 05721
    1. Syringomycin biosynthesis enzyme 2, SyrB2 [141624]
      1. Pseudomonas syringae pv. syringae [TaxId: 321] [141625] (6)
        SQ Q9RBY6 3-310
    2. Phytanoyl-CoA dioxygenase, PhyH [141626]
      1. Human (Homo sapiens) [TaxId: 9606] [141627] (1)
        SQ O14832 43-338
  10. AlkB-like [141628] (2)
    1. Alkylated DNA repair protein AlkB [141629]
      1. Escherichia coli [TaxId: 562] [141630] (7)
        SQ P05050 15-214
    2. AlkB homolog 3 [141631]
      Prostate cancer antigen 1, DEPC-1
      1. Human (Homo sapiens) [TaxId: 9606] [141632] (1)
        SQ Q96Q83 70-279
  11. Asparaginyl hydroxylase-like [141633] (1)
    Pfam 08007
    1. Putative asparaginyl hydroxylase YxbC [141634]
      1. Bacillus subtilis [TaxId: 1423] [141635] (4)
        SQ P46327 8-326
  12. YbiU-like [141636] (1)
    Pfam 07350; DUF1479
    1. Hypothetical protein YbiU [141637]
      1. Salmonella typhimurium [TaxId: 90371] [141638] (1)
        SQ Q8ZQM7 3-419
  13. TehB-like [159307] (2)
    Pfam 09313; DUF1971
    1. Uncharacterized protein YeaR [159308]
      1. Escherichia coli [TaxId: 562] [159309] (4)
        SQ P64488 1-109
    2. Tellurite resistance protein B, TehB [159310]
      1. Vibrio fischeri [TaxId: 668] [159311] (8)
        SQ Q5E3X2 5-100
3. cAMP-binding domain-like [51206] (3)
  uperfamily
  1. CO-sensing protein CooA, N-terminal domain [51207] (1)
    heme-binding domain
    1. CO-sensing protein CooA, N-terminal domain [51208]
      1. Rhodospirillum rubrum [TaxId: 1085] [51209] (1)
  2. Listeriolysin regulatory protein PrfA, N-terminal domain [89419] (1)
    1. Listeriolysin regulatory protein PrfA, N-terminal domain [89420]
      1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [89421] (11)
  3. cAMP-binding domain [51210] (14)
    Pfam 00027
    1. Catabolite gene activator protein, N-terminal domain [51211]
      1. Escherichia coli [TaxId: 562] [51212] (26)
    2. CRP-like transcriptional regulator TM1171, N-terminal domain [101991]
      1. Thermotoga maritima [TaxId: 2336] [101992] (1)
    3. Regulatory subunit of Protein kinase A [51213]
      duplication: consists of two similar domains
      1. Cow (Bos taurus) [TaxId: 9913] [51214] (4)
        SQ P00514 109-376
      2. Rat (Rattus norvegicus) [TaxId: 10116] [63861] (1)
    4. Regulatory domain of Epac2, domains 1 and 3 [82197]
      duplication: two homologous domains of this fold are separated in the sequence by a DEP domain
      1. Mouse (Mus musculus) [TaxId: 10090] [82198] (1)
    5. HCN pacemaker channel [101993]
      potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel
      1. Mouse (Mus musculus) [TaxId: 10090] [101994] (5)
    6. Putative ion channel CnbD [110321]
      1. Mesorhizobium loti [TaxId: 381] [110322] (4)
        SQ Q98GN8 218-350 # mll3241
    7. Probable cyclic nucleotide-gated ion channel 6 [117323]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117324] (1)
        SQ O82226 509-632
    8. Probable transcription regulator BT4300, N-terminal domain [141639]
      1. Bacteroides thetaiotaomicron [TaxId: 818] [141640] (1)
        SQ Q89ZS6 1-147
    9. Transcriptional regulator TTHA1359, N-terminal domain [141641]
      1. Thermus thermophilus [TaxId: 274] [141642] (1)
        SQ Q5SIL0 6-117
    10. Transcriptional regulator PG0396, N-terminal domain [141643]
      1. Porphyromonas gingivalis [TaxId: 837] [141644] (1)
        SQ Q7MAW7 10-151
    11. Cyclic AMP receptor-like protein Vfr [159312]
      1. Pseudomonas aeruginosa [TaxId: 287] [159313] (1)
        SQ P55222 9-142
    12. Chlorophenol reduction protein CprK [159314]
      1. Desulfitobacterium hafniense [TaxId: 49338] [159315] (7)
        SQ Q18R04 3-147! SQ Q18R04 9-147
      2. Desulfitobacterium dehalogenans [TaxId: 36854] [159316] (2)
        SQ Q9LAS2 19-147
4. Regulatory protein AraC [51215] (1)
  uperfamily
  1. Regulatory protein AraC [51216] (1)
    1. Regulatory protein AraC [51217]
      contains an alpha-hairpin in the C-terminal extension
      1. Escherichia coli [TaxId: 562] [51218] (4)
        SQ P03021
5. Thiamin pyrophosphokinase, substrate-binding domain [63862] (1)
  uperfamily
  1. Thiamin pyrophosphokinase, substrate-binding domain [63863] (2)
    1. Thiamin pyrophosphokinase, substrate-binding domain [63864]
      1. Mouse (Mus musculus) [TaxId: 10090] [63865] (2)
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63866] (1)
6. Calcium ATPase, transduction domain A [81653] (1)
  a distorted variant of double-helix
  uperfamily
  1. Calcium ATPase, transduction domain A [81652] (1)
    1. Calcium ATPase, transduction domain A [81651]
      1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [81650] (17)
        SQ P04191
7. TRAP-like [51219] (2)
  shorter variant of double-helix; assembles in large ring-like structures containing from 9 to 11 domains
  uperfamily
  1. Trp RNA-binding attenuation protein (TRAP) [51220] (2)
    oligomeric ring consists of 11 single-domain subunits
    1. Trp RNA-binding attenuation protein (TRAP) [51221]
      1. Bacillus subtilis [TaxId: 1423] [51222] (1)
      2. Bacillus stearothermophilus [TaxId: 1422] [51223] (19)
  2. PA3696/SPS0176-like [101995] (2)
    duplication: there are three structural repeats per subunit; nine domains per ring-like trimer
    1. Hypothetical protein SPyM3_0169 (SPyM18_0222, SPS0176) [101996]
      1. Streptococcus pyogenes [TaxId: 1314] [101997] (1)
    2. Hypothetical protein PA3696 [141645]
      1. Pseudomonas aeruginosa [TaxId: 287] [141646] (6)
        SQ Q9HXU4 5-244
Triple-stranded beta-helix [69348] (1)
(homo)trimer; each chain donates 3 beta-strands per turn of the helix
1. Phage fibre proteins [69349] (5)
  uperfamily
  1. Middle part of short tail fibre protein gp12 [69350] (1)
    1. Middle part of short tail fibre protein gp12 [88691]
      includes the N-terminal cap (sub)domain
      1. Bacteriophage T4 [TaxId: 10665] [88692] (1)
  2. Tail-associated lysozyme gp5, C-terminal domain [69353] (1)
    1. Tail-associated lysozyme gp5, C-terminal domain [69354]
      1. Bacteriophage T4 [TaxId: 10665] [69355] (1)
  3. Endo-alpha-sialidase [117325] (1)
    1. Endo-alpha-sialidase [117326]
      1. Bacteriophage K1F [TaxId: 344021] [117327] (2)
        SQ Q04830 245-909
  4. Lactophage receptor-binding protein domain [141647] (2)
    1. Baseplate protein (bpp), N-terminal domain [141648]
      includes extra N-terminal trimerization helix
      1. Lactococcus phage tp901-1 [TaxId: 35345] [141649] (3)
        SQ Q9G096 17-62
    2. Receptor binding protein, rbp, middle domain [141650]
      1. Lactococcus lactis phage p2 [TaxId: 100641] [141651] (6)
        SQ Q71AW2 141-161
  5. HylP-like [159317] (1)
    Pfam 07212
    1. Phage-associated hyaluronidase, HylP1 [159318]
      1. Streptococcus pyogenes [TaxId: 1314] [159319] (6)
        SQ Q9A0M7 7-336! SQ Q9A0M7 7-337
Triple beta-spiral [51224] (1)
trimer formed by the interlocking beta-hairpin repeat units
1. Fibre shaft of virus attachment proteins [51225] (2)
  uperfamily
  1. Adenovirus [51226] (1)
    1. Adenovirus [51227]
      1. Human adenovirus type 2 [TaxId: 10515] [51228] (3)
        SQ P10104
  2. Reovirus attachment protein sigma 1 [69356] (1)
    1. Reovirus attachment protein sigma 1 [69357]
      1. Reovirus [TaxId: 10891] [69358] (1)
Trimeric adhesin [101998] (1)
trimer; contains two different beta-prism-like domains connected by an linker subdomain of less regular structure
1. Trimeric adhesin [101999] (1)
  uperfamily
  1. Trimeric adhesin [102000] (1)
    1. Autotransporter Hia [102001]
      1. Haemophilus influenzae [TaxId: 727] [102002] (1)
beta-hairpin stack [69359] (1)
Trp-rich beta-hairpin repeat units form helical structures of 3 units per turn
1. Cell wall binding repeat [69360] (1)
  uperfamily
  1. Cell wall binding repeat [69361] (3)
    1. Choline binding domain of autolysin C-LytA [69362]
      1. Streptococcus pneumoniae [TaxId: 1313] [69363] (5)
    2. C-terminal domain of endolysin [89422]
      1. Bacteriophage cp-1 [TaxId: 10747] [89423] (6)
    3. Teichoic acid phosphorylcholine esterase Pce (LytD), C-terminal domain [141652]
      1. Streptococcus pneumoniae [TaxId: 1313] [141653] (1)
        SQ Q8DQ62 335-566
Barrel-sandwich hybrid [51229] (4)
sandwich of half-barrel shaped beta-sheets
1. Single hybrid motif [51230] (1)
  7 to 8 strands in 2 beta-sheets
  uperfamily
  1. Biotinyl/lipoyl-carrier proteins and domains [51231] (13)
    1. Biotinyl domain of acetyl-CoA carboxylase [51232]
      1. Escherichia coli [TaxId: 562] [51233] (4)
    2. Biotin carboxyl carrier domain of transcarboxylase (TC 1.3S) [51234]
      1. Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744] [51235] (3)
    3. Protein H of glycine cleavage system [51236]
      1. Pea (Pisum sativum) [TaxId: 3888] [51237] (3)
      2. Thermus thermophilus [TaxId: 274] [102003] (1)
    4. Lipoyl domain of dihydrolipoamide acetyltransferase [51238]
      component of the pyruvate dehydrogenase complex
      1. Bacillus stearothermophilus [TaxId: 1422] [51239] (2)
      2. Azotobacter vinelandii [TaxId: 354] [51240] (2)
      3. Escherichia coli [TaxId: 562] [51241] (1)
      4. Neisseria meningitidis [TaxId: 487] [69364] (1)
      5. Human (Homo sapiens) [TaxId: 9606] [51242] (4)
    5. Lipoyl domain of the 2-oxoglutarate dehydrogenase complex [51243]
      1. Azotobacter vinelandii [TaxId: 354] [51244] (2)
      2. Escherichia coli [TaxId: 562] [51245] (1)
      3. Homo sapiens [TaxId: 9606] [159320] (3)
    6. Lipoyl domain of the mitochondrial branched-chain alpha-ketoacid dehydrogenase [69365]
      1. Human (Homo sapiens) [TaxId: 9606] [69366] (2)
2. Rudiment single hybrid motif [51246] (2)
  uperfamily
  1. BC C-terminal domain-like [51247] (7)
    probable rudiment form of the biotinyl-carrier domain
    1. Biotin carboxylase (BC), C-domain [51248]
      subunit of acetyl-CoA and pyruvate carboxylases
      1. Escherichia coli [TaxId: 562] [51249] (13)
      2. Aquifex aeolicus [TaxId: 63363] [102004] (1)
    2. Glycinamide ribonucleotide synthetase (GAR-syn), C-domain [51250]
      1. Escherichia coli [TaxId: 562] [51251] (1)
      2. Thermotoga maritima [TaxId: 2336] [110323] (1)
        SQ Q9X0X7
    3. N5-carboxyaminoimidazole ribonucleotide synthetase PurK (AIRC), C-domain [51252]
      1. Escherichia coli [TaxId: 562] [51253] (6)
    4. Glycinamide ribonucleotide transformylase PurT, C-domain [51254]
      1. Escherichia coli [TaxId: 562] [51255] (7)
    5. Acetyl-CoA carboxylase, BC-C subdomain [117328]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [117329] (2)
        SQ Q00955 13-566
  2. Cytochrome f, small domain [51256] (5)
    1. Cytochrome f, small domain [51257]
      1. Turnip (Brassica rapa) [TaxId: 3711] [51258] (2)
      2. Chlamydomonas reinhardtii [TaxId: 3055] [51259] (6)
      3. Phormidium laminosum [TaxId: 32059] [51260] (1)
      4. Mastigocladus laminosus [TaxId: 83541] [102005] (1)
      5. Anabaena sp., strain PCC 7120 [TaxId: 1167] [159321] (1)
        SQ Q93SW9 214-279
3. Duplicated hybrid motif [51261] (2)
  half-barrel sheet of 8 strands sandwiched with two 3-stranded sheets
  uperfamily
  1. Glucose permease-like [51262] (3)
    1. Glucose permease IIa domain, IIa-glc [51263]
      1. Bacillus subtilis [TaxId: 1423] [51264] (2)
      2. Mycoplasma capricolum [TaxId: 2095] [51265] (1)
    2. Glucose-specific factor III (glsIII) [51266]
      synonym: enzyme IIa-glc
      1. Escherichia coli [TaxId: 562] [51267] (10)
  2. Peptidoglycan hydrolase LytM [102006] (1)
    Peptidase family M23; contains extra N-terminal, non-conserved beta-sheet subdomain
    1. Peptidoglycan hydrolase LytM [102007]
      1. Staphylococcus aureus [TaxId: 1280] [102008] (1)
4. Ribosomal L27 protein-like [110324] (2)
  rudiment single hybrid fold with a permuted topology
  uperfamily
  1. Ribosomal L27 protein [110325] (3)
    Pfam 01016
    1. Ribosomal protein L27 [110326]
      1. Thermus thermophilus [TaxId: 274] [110327] (2)
        SQ P84123
      2. Escherichia coli [TaxId: 562] [159322] (29)
        SQ P0A7L8 1-84
      3. Deinococcus radiodurans [TaxId: 1299] [159323] (11)
        SQ Q9RY65 2-85
  2. ECR1 N-terminal domain-like [159324] (5)
    ECR1 - Exosome complex RNA-binding protein 1
    1. Ribosomal RNA-processing protein 40, RRP40 [159325]
      1. Human (Homo sapiens) [TaxId: 9606] [159326] (1)
        SQ Q9NQT5 17-107
    2. Exosome component 1, EXOSC1 [159327]
      3'-5' exoribonuclease CSL4 homolog
      1. Human (Homo sapiens) [TaxId: 9606] [159328] (1)
        SQ Q9Y3B2 6-60
    3. Exosome complex RNA-binding protein 1, ECR1 [159329]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159330] (3)
        SQ O29758 2-52
      2. Sulfolobus solfataricus [TaxId: 2287] [159331] (2)
        SQ Q9UXC4 7-65
    4. Ribosomal RNA-processing protein 4, RRP4 [159332]
      1. Human (Homo sapiens) [TaxId: 9606] [159333] (1)
        SQ Q13868 25-72
beta-clip [51268] (7)
double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll
1. AFP III-like domain [51269] (1)
  duplication: consists of two structural repeats related by pseudo dyad
  uperfamily
  1. AFP III-like domain [51270] (5)
    Pfam 01354
    1. Type III antifreeze protein, AFP III [51271]
      1. Ocean pout (Macrozoarces americanus), different isoforms [TaxId: 8199] [51272] (31)
      2. Antarctic eel pout (Lycodichthys dearborni), RD1 isoform [TaxId: 8201] [89424] (1)
      3. Antarctic eel pout (Austrolycichthys brachycephalus) and (Lycodichthys dearborni), RD3 isoform [TaxId: 36221] [51273] (4)
        duplication: intramolecular dimer
    2. Spore coat polysaccharide biosynthesis protein SpsE, C-terminal domain [110328]
      1. Bacillus subtilis [TaxId: 1423] [110329] (1)
        SQ P39625
    3. Capsule biosynthesis protein SiaC, C-terminal domain [117330]
      1. Neisseria meningitidis [TaxId: 487] [117331] (4)
        SQ Q57265
2. SET domain [82199] (3)
  duplication: the core is composed of two structural repeats similar to (circularly permuted) repeats of AFPIII
  also contains a substrate-binding alpha+beta subdomain inserted in the core
  uperfamily
  1. Histone lysine methyltransferases [82200] (3)
    contains metal-binding preSET and postSET domains
    1. Dim-5 [82201]
      1. Fungus (Neurospora crassa) [TaxId: 5141] [82202] (2)
    2. SET domain of Clr4 [82203]
      ortholog of Dim-5
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82204] (2)
    3. Histone H3 K4-specific methyltransferase SET7/9 catalytic domain [82205]
      1. Human (Homo sapiens) [TaxId: 9606] [82206] (11)
        SQ Q8WTS6 52-336
  2. Viral histone H3 Lysine 27 Methyltransferase [82207] (1)
    consists of SET domain only; dimeric
    1. Viral histone H3 Lysine 27 Methyltransferase [82208]
      1. Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] [82209] (3)
  3. RuBisCo LSMT catalytic domain [82210] (1)
    1. RuBisCo LSMT catalytic domain [82211]
      1. Garden pea (Pisum sativum) [TaxId: 3888] [82212] (15)
3. Head decoration protein D (gpD, major capsid protein D) [51274] (1)
  uperfamily
  1. Head decoration protein D (gpD, major capsid protein D) [51275] (2)
    1. Head decoration protein D (gpD, major capsid protein D) [51276]
      1. Bacteriophage lambda [TaxId: 10710] [51277] (3)
        SQ P03712
      2. Bacteriophage P21 [TaxId: 10711] [117332] (3)
        SQ P36275
4. Urease, beta-subunit [51278] (1)
  uperfamily
  1. Urease, beta-subunit [51279] (3)
    1. Urease, beta-subunit [51280]
      1. Klebsiella aerogenes [TaxId: 28451] [51281] (27)
      2. Bacillus pasteurii [TaxId: 1474] [51282] (6)
      3. Helicobacter pylori [TaxId: 210] [69367] (2)
        fused with gamma subunit
5. MoeA C-terminal domain-like [63867] (1)
  uperfamily
  1. MoeA C-terminal domain-like [63868] (5)
    1. Molybdenum cofactor biosynthesis protein MoeA, C-terminal domain [63869]
      1. Escherichia coli [TaxId: 562] [63870] (27)
      2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102009] (1)
      3. Pyrococcus furiosus [TaxId: 2261] [117333] (1)
        SQ Q8U034
      4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117334] (1)
        SQ O59354; PH1647
    2. Gephyrin, C-terminal domain [110330]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110331] (4)
        SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
6. dUTPase-like [51283] (1)
  forms tight trimer through an additional beta-sheet in each subunit
  subunit beta-sheets are orthogonally packed around the three-fold axis
  uperfamily
  1. dUTPase-like [51284] (9)
    1. Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) [51285]
      1. Escherichia coli [TaxId: 562] [51286] (10)
        SQ P06968
      2. Mycobacterium tuberculosis, rv2697c [TaxId: 1773] [82213] (8)
      3. Human (Homo sapiens) [TaxId: 9606] [102010] (11)
      4. Feline immunodeficiency virus [TaxId: 11673] [51287] (8)
      5. Equine infectious anemia virus [TaxId: 11665] [51288] (2)
      6. Plasmodium falciparum [TaxId: 5833] [141654] (3)
        SQ Q8II92 1-159
    2. Bifunctional dCTP deaminase/dUTPase [89425]
      elaborated fold with additional structures
      1. Archaeon Methanococcus jannaschii [TaxId: 2190] [89426] (5)
        synonym: Methanocaldococcus jannaschii
    3. Deoxycytidine triphosphate deaminase (dCTP deaminase) [117335]
      1. Escherichia coli [TaxId: 562] [117336] (3)
        SQ P28248
    4. Monomeric viral dUTPase [141655]
      related to the trimeric dUTPase domain by domain duplication, fusion and partial deletion; retains only one of the three ancestral active sites
      1. Epstein-barr virus [TaxId: 10376] [141656] (4)
        SQ P03195 121-256! SQ P03195 4-116
        Human herpesvirus 4
7. Tlp20, baculovirus telokin-like protein [51289] (1)
  similar to dUTPase in fold and trimeric assembly
  uperfamily
  1. Tlp20, baculovirus telokin-like protein [51290] (1)
    1. Tlp20, baculovirus telokin-like protein [51291]
      1. AcMNPV (Autographa californica nuclear polyhedrosis virus) [TaxId: 46015] [51292] (1)
PheT/TilS domain [56036] (1)
core: 3 layers; contains beta-sandwich of unusual topology
1. PheT/TilS domain [56037] (2)
  contains putative tRNA-binding structural motif
  uperfamily
  1. tRNA-Ile-lysidine synthetase, TilS, C-terminal domain [116720] (1)
    PfamB 001050
    1. tRNA-Ile-lysidine synthetase, TilS, C-terminal domain [116721]
      formerly putative cell cycle protein MesJ
      1. Escherichia coli [TaxId: 562] [116722] (1)
  2. B3/B4 domain of PheRS, PheT [56038] (1)
    Pfam 03483; decorated with additional structures
    1. B3/B4 domain of PheRS, PheT [56039]
      1. Thermus thermophilus [TaxId: 274] [56040] (9)
        identical sequence to Thermus aquaticus, TaxId: 271
C-terminal autoproteolytic domain of nucleoporin nup98 [82214] (1)
multisheet protein with a mixture of beta-sandwich and beta-prism features
1. C-terminal autoproteolytic domain of nucleoporin nup98 [82215] (1)
  uperfamily
  1. C-terminal autoproteolytic domain of nucleoporin nup98 [82216] (1)
    1. C-terminal autoproteolytic domain of nucleoporin nup98 [82217]
      pore-targeting domain
      1. Human (Homo sapiens) [TaxId: 9606] [82218] (1)
Pseudo beta-prism [141657] (1)
beta-sandwich with one regular beta-sheet and the other beta-sheet bent in the middle with a set of aligned beta-bulges
1. Bacteriophage trimeric proteins domain [141658] (2)
  found in phage proteins that form trimers, but is not involved in the trimerisation
  uperfamily
  1. Mtd domain-like [141659] (1)
    1. Major tropism determinant (Mtd), N-terminal domain [141660]
      includes extra N-terminal trimerization domain; beta-alpha-beta(3)
      1. Bordetella phage bpp-1 [TaxId: 194699] [141661] (13)
        SQ Q775D6 5-170
        includes other related Bordetella phages
  2. Lactophage receptor-binding protein N-terminal domain [141662] (1)
    1. Receptor binding protein, rbp, N-terminal domain [141663]
      includes extra N-terminal trimerization helix
      1. Lactococcus lactis phage p2 [TaxId: 100641] [141664] (6)
        SQ Q71AW2 2-140
SARS ORF9b-like [141665] (1)
complex dimeric fold with three intersubunit beta-sheets packed around a single core
1. 'SARS ORF9b-like [141666] (1)
  uperfamily
  1. SARS ORF9b-like [141667] (1)
    PfamB 005852
    1. Hypothetical protein 5 (ORF-9b) [141668]
      1. SARS coronavirus [TaxId: 227859] [141669] (8)
        SQ P59636 9-98
Adsorption protein p2 [89427] (1)
multisheet protein containing partial beta-propeller and beta-sandwich regions
1. Adsorption protein p2 [89428] (1)
  uperfamily
  1. Adsorption protein p2 [89429] (1)
    1. Adsorption protein p2 [89430]
      synonym: receptor-binding protein p2
      1. Bacteriophage prd1 [TaxId: 10658] [89431] (2)
Baseplate structural protein gp8 [89432] (1)
multisheet protein with a mixture of beta-sandwich and beta-barrel features
1. Baseplate structural protein gp8 [89433] (1)
  uperfamily
  1. Baseplate structural protein gp8 [89434] (1)
    1. Baseplate structural protein gp8 [89435]
      1. Bacteriophage T4 [TaxId: 10665] [89436] (3)
Hedgehog/intein (Hint) domain [51293] (1)
complex fold made of five beta-hairpin units and a b-ribbon arc
1. Hedgehog/intein (Hint) domain [51294] (2)
  duplication: contains two intertwined structural repeats
  uperfamily
  1. Hedgehog C-terminal (Hog) autoprocessing domain [51295] (1)
    1. Hedgehog [51296]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [51297] (1)
  2. Intein (protein splicing domain) [51298] (4)
    1. VMA1-derived endonuclease (VDE) PI-Scei intein [51299]
      also contains a homing endonuclease and DNA-binding domains
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51300] (8)
        SQ P17255 284-737
    2. PI-Pfui intein [51301]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [51302] (1)
    3. GyrA intein [51303]
      miniintein lacking the homing endonuclease domain
      1. Mycobacterium xenopi [TaxId: 1789] [51304] (1)
    4. DnaB intein [102011]
      miniintein lacking the homing endonuclease domain
      1. Synechocystis sp. pcc 6803 [TaxId: 1148] [102012] (1)
LexA/Signal peptidase [51305] (1)
complex fold made of several coiled beta-sheets; contains an SH3-like barrel
1. LexA/Signal peptidase [51306] (2)
  uperfamily
  1. LexA-related [51307] (3)
    1. UmuD' [51308]
      self-processed fragment of UmuD SOS response protein
      1. Escherichia coli [TaxId: 562] [51309] (3)
    2. LexA C-terminal domain [63871]
      1. Escherichia coli [TaxId: 562] [63872] (6)
    3. lambda repressor C-terminal domain [51310]
      1. Bacteriophage lambda [TaxId: 10710] [51311] (2)
  2. Type 1 signal peptidase [51312] (1)
    contains additional all-beta subdomain inserted in the superfamily fold
    1. Type 1 signal peptidase [51313]
      1. Escherichia coli [TaxId: 562] [51314] (3)
        SQ P00803 81-324
Cloacin translocation domain [69368] (1)
complex fold made of several coiled beta-sheets
1. Cloacin translocation domain [69369] (1)
  uperfamily
  1. Cloacin translocation domain [69370] (2)
    Pfam 03515
    1. Colicin E3 N-terminal domain [69371]
      1. Escherichia coli [TaxId: 562] [69372] (3)
    2. Colicin B N-terminal domain [102013]
      1. Escherichia coli [TaxId: 562] [102014] (1)
Mss4-like [51315] (1)
complex fold made of several coiled beta-sheets
1. Mss4-like [51316] (4)
  duplication: tandem repeat of two similar structural motifs
  uperfamily
  1. RabGEF Mss4 [51317] (2)
    contains zinc-binding site
    1. RabGEF Mss4 [51318]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [51319] (1)
      2. Human (Homo sapiens) [TaxId: 9606] [51320] (3)
  2. Translationally controlled tumor protein TCTP (histamine-releasing factor) [63873] (3)
    contains an insertion of alpha helical hairpin; lacks zinc-binding site
    1. Translationally controlled tumor protein TCTP (histamine-releasing factor) [63874]
      1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [63875] (2)
      2. Plasmodium knowlesi [TaxId: 5850] [110332] (1)
        SQ P84152
      3. Human (Homo sapiens) [TaxId: 9606] [117337] (5)
        SQ P13693
  3. SelR domain [75041] (2)
    1. C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB [75042]
      1. Neisseria gonorrhoeae [TaxId: 485] [75043] (1)
    2. Peptide methionine sulfoxide reductase MsrB [141670]
      1. Bacillus subtilis [TaxId: 1423] [141671] (1)
        SQ P54155 1-143
  4. Glutathione-dependent formaldehyde-activating enzyme, Gfa [117338] (1)
    Pfam 04828; DUF636
    1. Glutathione-dependent formaldehyde-activating enzyme, Gfa [117339]
      1. Paracoccus denitrificans [TaxId: 266] [117340] (2)
        SQ Q51669
Cyanovirin-N [51321] (1)
complex fold
1. Cyanovirin-N [51322] (1)
  duplication: tandem repeat of two homologous motifs made three stranded beta-sheet and beta-hairpins
  uperfamily
  1. Cyanovirin-N [51323] (1)
    1. Cyanovirin-N [51324]
      1. Cyanobacterium (Nostoc ellipsosporum) [TaxId: 45916] [51325] (11)
Tp47 lipoprotein, N-terminal domain [82219] (1)
complex fold; consists of two intertwined subdomains
1. Tp47 lipoprotein, N-terminal domain [82220] (1)
  uperfamily
  1. Tp47 lipoprotein, N-terminal domain [82221] (1)
    1. Tp47 lipoprotein, N-terminal domain [82222]
      a penicillin-binding protein with carboxypeptidase activity
      1. Treponema pallidum [TaxId: 160] [82223] (1)
Methuselah ectodomain [63876] (1)
complex fold
1. Methuselah ectodomain [63877] (1)
  duplication: contains two similar sub domains connected by a structured linker
  uperfamily
  1. Methuselah ectodomain [63878] (1)
    1. Methuselah ectodomain [63879]
      1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63880] (5)
Head-binding domain of phage P22 tailspike protein [51326] (1)
complex fold made of bifurcated and partly folded beta-sheet
1. Head-binding domain of phage P22 tailspike protein [51327] (1)
  uperfamily
  1. Head-binding domain of phage P22 tailspike protein [51328] (1)
    1. Head-binding domain of phage P22 tailspike protein [51329]
      1. Salmonella bacteriophage P22 [TaxId: 10754] [51330] (1)
E2 regulatory, transactivation domain [51331] (1)
complex fold made of bifurcated and coiled beta-sheets
1. E2 regulatory, transactivation domain [51332] (1)
  uperfamily
  1. E2 regulatory, transactivation domain [51333] (3)
    1. E2 regulatory, transactivation domain [51334]
      1. Human papillomavirus type 18 [TaxId: 333761] [51335] (2)
        SQ Q80B71 1-193
      2. Human papillomavirus type 16 [TaxId: 333760] [51336] (2)
      3. Human papillomavirus type 11 [TaxId: 10580] [102015] (2)
MoeA N-terminal region -like [63881] (1)
complex fold made of bifurcated and coiled b-sheets
1. MoeA N-terminal region -like [63882] (1)
  uperfamily
  1. MoeA N-terminal region -like [63883] (5)
    1. Molybdenum cofactor biosynthesis protein MoeA, N-terminal and linker domains [63884]
      1. Escherichia coli [TaxId: 562] [63885] (27)
      2. Archaeon Pyrococcus horikoshii, PH0582 [TaxId: 53953] [102016] (1)
      3. Pyrococcus furiosus [TaxId: 2261] [117341] (1)
        SQ Q8U034
      4. Pyrococcus horikoshii, PH1647 [TaxId: 53953] [117342] (1)
        SQ O59354
    2. Gephyrin, domains 3 and 4 [110333]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [110334] (4)
        SQ Q03555 350-768 # structure on the N-terminal domain (1-201) is also known (1ihc; scop_sp 64101)
MOSC N-terminal domain-like [141672] (1)
complex fold; comprises a beta-hairpin and a meander 3-stranded sheet packed against beta-barrel: closed, n=5, S=8; contains three short helices
1. MOSC N-terminal domain-like [141673] (1)
  uperfamily
  1. MOSC N-terminal domain-like [141674] (1)
    Pfam 03476
    1. Hypothetical protein BB0938 [141675]
      1. Bordetella bronchiseptica [TaxId: 518] [141676] (1)
        SQ Q7WNU7 1-128
MAL13P1.257-like [141677] (1)
complex fold; duplication: consists of two intertwinned structural repeats related by pseudo dyad
1. MAL13P1.257-like [141678] (1)
  uperfamily
  1. MAL13P1.257-like [141679] (1)
    PANTHER 12857; DUF866_euk
    1. Hypothetical protein MAL13P1.257 [141680]
      1. Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141681] (2)
        SQ Q8IDI8 1-156
Composite domain of metallo-dependent hydrolases [51337] (1)
pseudobarrel; mixed sheet of 7 strand folded upon itself and "buckled" by two beta-turns
1. Composite domain of metallo-dependent hydrolases [51338] (11)
  this domain is interrupted by the catalytic beta/alpha barrel domain
  uperfamily
  1. Cytosine deaminase [69373] (1)
    1. Cytosine deaminase [69374]
      1. Escherichia coli [TaxId: 562] [69375] (8)
        SQ P25524
  2. alpha-Subunit of urease [51339] (3)
    1. alpha-Subunit of urease [51340]
      1. Klebsiella aerogenes [TaxId: 28451] [51341] (27)
      2. Bacillus pasteurii [TaxId: 1474] [51342] (6)
      3. Helicobacter pylori [TaxId: 210] [69376] (2)
  3. Hydantoinase (dihydropyrimidinase) [75044] (9)
    1. D-hydantoinase [75045]
      1. Thermus sp. [TaxId: 275] [75046] (2)
      2. Bacillus stearothermophilus [TaxId: 1422] [75047] (1)
      3. Burkholderia pickettii [TaxId: 329] [89437] (1)
      4. Bacillus sp. AR9 [TaxId: 301298] [141682] (2)
        SQ Q5DLU2 2-52,385-460
    2. L-hydantoinase [75048]
      1. Arthrobacter aurescens [TaxId: 43663] [75049] (1)
    3. Dihydropyrimidinase related protein-1 [102017]
      1. Mouse (Mus musculus) [TaxId: 10090] [102018] (1)
    4. Dihydropyrimidine amidohydrolase Pyd2 [141683]
      1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [141684] (12)
        SQ Q9P903 2-56,441-541
      2. Dictyostelium discoideum [TaxId: 44689] [141685] (1)
        SQ Q86LT2 7-59,394-490
    5. Two-domain dihydroorotase [141686]
      1. Aquifex aeolicus [TaxId: 63363] [141687] (3)
        SQ O66990 1-55,366-422
  4. SAH/MTA deaminase-like [82224] (5)
    1. Hypothetical protein TM0936 [82225]
      1. Thermotoga maritima [TaxId: 2336] [82226] (3)
    2. Hypothetical protein GOS_1943094 [159334]
      1. Environmental samples [159335] (1)
    3. Guanine deaminase [159336]
      1. Bradyrhizobium japonicum [TaxId: 375] [159337] (1)
        SQ Q89NG0 1-70,396-465
        Blr3880
      2. Human (Homo sapiens) [TaxId: 9606] [159338] (1)
        SQ Q9Y2T3 8-75,389-451
      3. Clostridium acetobutylicum [TaxId: 1488] [159339] (2)
        SQ Q97MB6 6-63,374-424
  5. Isoaspartyl dipeptidase [89438] (1)
    1. Isoaspartyl dipeptidase [89439]
      1. Escherichia coli [TaxId: 562] [89440] (5)
        SQ P39377
  6. N-acetylglucosamine-6-phosphate deacetylase, NagA [82227] (3)
    1. N-acetylglucosamine-6-phosphate deacetylase, NagA [82228]
      1. Bacillus subtilis [TaxId: 1423] [102019] (1)
      2. Thermotoga maritima [TaxId: 2336] [82229] (1)
        TM0814
      3. Escherichia coli [TaxId: 562] [141688] (10)
        SQ P0AF18 1-53,351-382
  7. D-aminoacylase [82230] (1)
    1. N-acyl-D-aminoacid amidohydrolase [82231]
      1. Alcaligenes faecalis [TaxId: 511] [82232] (8)
  8. Adenine deaminase [141689] (1)
    1. Putative adenine deaminase EF0837 [141690]
      1. Enterococcus faecalis [TaxId: 1351] [141691] (1)
        SQ Q837K0 2-52,320-369
  9. Zn-dependent arginine carboxypeptidase-like [159340] (3)
    1. Uncharacterized protein EAJ56179 [159341]
      1. Unidentified organism [TaxId: 32644] [159342] (8)
        94% identity to the Burkholderia phytofirmans ortholog Bphyt_2089 (SQ B2T4I1)
    2. Zn-dependent arginine carboxypeptidase [159343]
      1. Unidentified organism [TaxId: 32644] [159344] (16)
    3. Xaa-Pro dipeptidase [159345]
      1. Alteromonas macleodii [TaxId: 28108] [159346] (2)
  10. Imidazolonepropionase-like [159347] (4)
    1. Imidazolonepropionase [159348]
      1. Bacillus subtilis [TaxId: 1423] [159349] (4)
        SQ P42084 3-73,374-415
      2. Agrobacterium tumefaciens [TaxId: 358] [159350] (4)
        SQ Q8U8Z6 15-77,379-418
    2. Probable 4-imidazolone-5-propanoate amidohydrolase GOS_1928421 [159351]
      1. Environmental samples [159352] (2)
        marine metagenome
    3. Uncharacterized protein BL1453 [159353]
      1. Bifidobacterium longum [TaxId: 216816] [159354] (1)
        SQ Q8G4D5 7-68,393-448
  11. DR0824-like [159355] (1)
    1. Hypothetical protein DR0824 [159356]
      1. Deinococcus radiodurans [TaxId: 1299] [159357] (1)
        SQ Q9RW45 34-90,399-418
Epsilon subunit of F1F0-ATP synthase N-terminal domain [51343] (1)
pseudobarrel: sandwich of two sheets packed at a positive interstrand angle and interconnected with many short turns
1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51344] (1)
  uperfamily
  1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51345] (2)
    1. Epsilon subunit of F1F0-ATP synthase N-terminal domain [51346]
      delta subunit in mitochondria
      1. Escherichia coli [TaxId: 562] [51347] (4)
      2. Cow (Bos taurus) [TaxId: 9913] [51348] (5)
N-terminal domain of MutM-like DNA repair proteins [81625] (1)
pseudobarrel; capped on both ends by alpha-helices
1. N-terminal domain of MutM-like DNA repair proteins [81624] (1)
  uperfamily
  1. N-terminal domain of MutM-like DNA repair proteins [81623] (6)
    1. DNA repair protein MutM (Fpg) [81621]
      1. Thermus thermophilus [TaxId: 274] [81609] (1)
      2. Bacillus stearothermophilus [TaxId: 1422] [81612] (9)
      3. Escherichia coli [TaxId: 562] [81616] (1)
      4. Lactococcus lactis [TaxId: 1358] [81617] (7)
        SQ P42371
    2. Endonuclease VIII [82233]
      1. Escherichia coli [TaxId: 562] [82234] (9)
        SQ P50465
    3. Endonuclease VIII-like 1 (NEIL1) [110335]
      1. Human (Homo sapiens) [TaxId: 9606] [110336] (1)
        SQ Q96FI4 1-333
Hypothetical protein YojF [89441] (1)
pseudobarrel; capped at one end by an alpha-helix
1. Hypothetical protein YojF [89442] (1)
  uperfamily
  1. Hypothetical protein YojF [89443] (1)
    1. Hypothetical protein YojF [89444]
      1. Bacillus subtilis [TaxId: 1423] [89445] (1)
DNA-binding pseudobarrel domain [101935] (1)
core: barrel, open; n=7, S*=10; capped with helices at both ends; partial similarity to the AbrB/MazE/MraZ-like fold (scop_cf 89446)
1. DNA-binding pseudobarrel domain [101936] (2)
  uperfamily
  1. Type II restriction endonuclease effector domain [101937] (1)
    1. Restriction endonuclease EcoRII, N-terminal domain [101938]
      1. Escherichia coli [TaxId: 562] [101939] (1)
  2. B3 DNA binding domain [117343] (2)
    Pfam 02362
    1. DNA-binding protein RAV1 [117344]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117345] (1)
        SQ Q9ZWM9 182-298
    2. At1g16640 [141692]
      1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141693] (1)
        SQ Q9FX77 1-102
Double-split beta-barrel [89446] (2)
pseudobarrel; capped on both ends by alpha-helices
1. AbrB/MazE/MraZ-like [89447] (3)
  members of this superfamily are known or predicted to have DNA-binding function
  uperfamily
  1. Kis/PemI addiction antidote [89448] (1)
    forms intertwined homodimer
    1. MazE [89449]
      1. Escherichia coli [TaxId: 562] [89450] (2)
  2. AbrB N-terminal domain-like [54743] (2)
    dimeric fold similar to MazE; the DNA-binding site is similar to the conserved surface site of MraZ
    1. Transcription-state regulator AbrB, the N-terminal DNA recognition domain [54744]
      1. Bacillus subtilis [TaxId: 1423] [54745] (6)
    2. Putative transition state regulator ABH [159358]
      1. Bacillus subtilis [TaxId: 1423] [159359] (2)
        SQ P39758 1-54
  3. Hypothetical protein MraZ [102020] (1)
    duplication: contains two interlocking repeats of similar sequence arranged as subunits in the MazE homodimer
    1. Hypothetical protein MraZ [102021]
      1. Mycoplasma pneumoniae [TaxId: 2104] [102022] (3)
2. AF2212/PG0164-like [141694] (2)
  six-stranded barrel, topologically similar to the Reductase/isomerase/elongation factor domain fold (scop_cf 50412)
  uperfamily
  1. PG0164-like [141695] (1)
    duplication: comprises two intertwinned beta(2)-alpha-beta structural repeats
    1. Hypothetical protein PG0164 [141696]
      1. Porphyromonas gingivalis [TaxId: 837] [141697] (1)
        SQ Q7MXL1 20-104
  2. AF2212-like [159360] (1)
    Pfam 01954; DUF104; intertwinned homodimer of beta(2)-loop-beta subunits; the capping helices are replaced with extended loops
    1. Uncharacterized protein AF2212 [159361]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159362] (2)
        SQ O28071 1-61
PUA domain-like [88696] (1)
pseudobarrel; mixed folded sheet of 5 strands; order 13452; strand 1 and 3 are parallel to each other
1. PUA domain-like [88697] (13)
  uperfamily
  1. PUA domain [88698] (10)
    RNA-binding domain
    1. Pseudouridine synthase II TruB, C-terminal domain [88699]
      1. Escherichia coli [TaxId: 562] [88700] (3)
      2. Thermotoga maritima [TaxId: 2336] [102023] (8)
      3. Mycobacterium tuberculosis [TaxId: 1773] [102024] (1)
      4. Archaeon Methanococcus jannaschii [TaxId: 2190] [141698] (1)
        SQ Q57612 247-331
      5. Archaeon Pyrococcus furiosus [TaxId: 2261] [141699] (4)
        SQ Q7LWY0 250-333
    2. Archaeosine tRNA-guanine transglycosylase, C3 domain [88701]
      the last of the 3 additional C-terminal domains to the TGT-like domain
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [88702] (4)
    3. Hypothetical protein Ta1423, C-terminal domain [102025]
      this protein is related to the C-terminal part (domains C2 and C3) of Archaeosine tRNA-guanine transglycosylase
      1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [102026] (1)
    4. Nip7p homolog, C-terminal domain [110337]
      1. Human (Homo sapiens) [TaxId: 9606] [110338] (2)
        SQ Q9Y221
    5. Hypothetical protein APE0525, C-terminal domain [141700]
      1. Archaeon Aeropyrum pernix [TaxId: 56636] [141701] (3)
        SQ Q9YEQ6 91-186
    6. Uncharacterized protein AF0587 [159363]
      1. Archaeoglobus fulgidus [TaxId: 2234] [159364] (1)
        SQ O29668 460-527
  2. ATP sulfurylase N-terminal domain [63801] (5)
    contains extra structures; some similarity to the PK beta-barrel domain
    1. ATP sulfurylase N-terminal domain [63802]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63803] (8)
      2. Fungus (Penicillium chrysogenum) [TaxId: 5076] [63804] (2)
      3. Sulfur-oxidizing endosymbiont of Riftia pachyptila [TaxId: 35843] [69296] (1)
      4. Thermus thermophilus [TaxId: 274] [102027] (1)
      5. Human (Homo sapiens) [TaxId: 9606] [141702] (6)
        SQ O43252 229-389
  3. YggJ N-terminal domain-like [89451] (3)
    1. Hypothetical protein HI0303 [89452]
      1. Haemophilus influenzae [TaxId: 727] [89453] (2)
    2. Hypothetical protein YqeU [102028]
      1. Bacillus subtilis [TaxId: 1423] [102029] (1)
    3. Hypothetical protein TTHA0657 (TT1575) [117346]
      1. Thermus thermophilus [TaxId: 274] [117347] (3)
        SQ Q5SKI6
  4. Hypothetical protein EF3133 [110339] (1)
    Pfam 06171; DUF984
    1. Hypothetical protein EF3133 [110340]
      1. Enterococcus faecalis [TaxId: 1351] [110341] (1)
        SQ Q82ZD1
  5. Hypothetical protein TTHA0113 [117348] (1)
    Pfam 04266; DUF437
    1. Hypothetical protein TTHA0113 [117349]
      1. Thermus thermophilus [TaxId: 274] [117350] (2)
        SQ Q5SM30
  6. ProFAR isomerase associated domain [117351] (2)
    Pfam 07060; DUF1530
    1. Hypothetical protein PF0470 [117352]
      1. Pyrococcus furiosus [TaxId: 2261] [117353] (1)
        SQ Q8U3J6
    2. Hypothetical protein PF0455 [117354]
      1. Pyrococcus furiosus [TaxId: 2261] [117355] (1)
        SQ Q8U3L1
  7. yqfB-like [117356] (1)
    Pfam 06164; DUF978
    1. Hypothetical protein YqfB [117357]
      1. Escherichia coli [TaxId: 562] [117358] (1)
        SQ P67603
  8. Atu2648/PH1033-like [141703] (6)
    Pfam 01878; DUF55
    1. Hypothetical protein PP5205 [141704]
      1. Pseudomonas putida kt2440 [TaxId: 160488] [141705] (3)
        SQ Q88CH6 2-149
    2. Hypothetical protein PH1033 [141706]
      1. Pyrococcus horikoshii [TaxId: 53953] [141707] (3)
        SQ O58764 1-145
    3. Hypothetical protein PSPTO5229 [141708]
      PP5205 ortholog
      1. Pseudomonas syringae [TaxId: 317] [141709] (1)
        SQ Q87UR7 2-149
    4. Hypothetical protein RPA0253 [141710]
      1. Rhodopseudomonas palustris [TaxId: 1076] [141711] (1)
        SQ Q6ND56 2-137
    5. Hypothetical protein Atu2648 [141712]
      1. Agrobacterium tumefaciens [TaxId: 358] [141713] (1)
        SQ Q8UC50 2-147
    6. Hypothetical protein LmjF36.6870 [141714]
      1. Leishmania major [TaxId: 5664] [141715] (1)
        SQ Q4Q067 7-163
  9. Hypothetical RNA methyltransferase domain (HRMD) [141716] (3)
    N-terminal part of Pfam 03602, structurally similar to PUA domain family
    1. Hypothetical protein TTHA1280, N-terminal domain [141717]
      1. Thermus thermophilus [TaxId: 274] [141718] (10)
        SQ Q5SIT4 1-164
    2. Hypothetical protein SMu776, N-terminal domain [141719]
      1. Streptococcus mutans [TaxId: 1309] [141720] (1)
        SQ Q8DUW5 1-68
    3. Hypothetical protein PH1915, N-terminal domain [141721]
      1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [141722] (2)
        SQ O59578 1-72
  10. LON domain-like [141723] (2)
    Pfam 02190
    1. ATP-dependent protease La (Lon), N-terminal domain [141724]
      1. Escherichia coli [TaxId: 562] [141725] (8)
        SQ P0A9M0 8-117
    2. Hypothetical protein BPP1347 [141726]
      identical sequence to BP2131 and BB2413 from other Bordetella species
      1. Bordetella parapertussis [TaxId: 519] [141727] (2)
        SQ Q7WAM7 2-198
  11. PrgU-like [159365] (1)
    Pfam 09627
    1. Uncharacterized protein PrgU [159366]
      1. Enterococcus faecalis [TaxId: 1351] [159367] (2)
        SQ Q8KUD5 12-113
        EF0006
  12. SRA domain-like [159368] (2)
    Pfam 02182; recognizes the modified cytosine base (m5C) by flipping it out of DNA
    1. E3 ubiquitin-protein ligase UHRF1 [159369]
      1. Human (Homo sapiens) [TaxId: 9606] [159370] (7)
        SQ Q96T88 409-615! SQ Q96T88 414-617
      2. Mouse (Mus musculus) [TaxId: 10090] [159371] (7)
        SQ Q8VDF2 405-613! SQ Q8VDF2 418-625
  13. YtmB-like [159372] (1)
    PfamB 020780
    1. Hypothetical protein YtmB [159373]
      1. Bacillus subtilis [TaxId: 1423] [159374] (8)
        SQ O34365 1-80
AXH domain [102030] (1)
pseudobarrel; some similarity to OB-fold
1. AXH domain [102031] (1)
  uperfamily
  1. AXH domain [102032] (1)
    1. Ataxin-1 [102033]
      1. Human (Homo sapiens) [TaxId: 9606] [102034] (1)
FimD N-terminal domain-like [141728] (1)
pseudo barrel, capped by an alpha-helix; some topological similarity to the PRC-barrel domain (scop_sf 50346) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
1. FimD N-terminal domain-like [141729] (1)
  uperfamily
  1. Usher N-domain [141730] (1)
    N-terminal part of Pfam 00577
    1. Outer membrane usher protein FimD [141731]
      1. Escherichia coli [TaxId: 562] [141732] (4)
        SQ P30130 46-170! SQ P30130 70-170! SQ P30130 70-184
HisI-like [141733] (1)
pseudo barrel, capped by an alpha-helix; contains a beta-triangle structure on one side; some topological similarity to the Ribosomal protein L25-like fold (scop_cf 50714) and the N-terminal domain of Glutamine synthetase (scop_sf 54368)
1. HisI-like [141734] (1)
  uperfamily
  1. HisI-like [141735] (1)
    Pfam 01502; PRA-CH; metalloenzyme, probable biological unit is dimeric
    1. Phosphoribosyl-AMP cyclohydrolase HisI [141736]
      1. Methanobacterium thermoautotrophicum [TaxId: 145262] [141737] (2)
        SQ O26347 8-131
MFPT repeat-like [141738] (1)
consists of two similar pseudo barrel subdomains with structural similarity to a circularly permuted SAND domain (scop_fa 63764)
1. MFPT repeat-like [141739] (1)
  uperfamily
  1. MFPT repeat [141740] (2)
    PfamB 008194
    1. Sperm motility protein MFP2 [141741]
      1. Pig roundworm (Ascaris suum), isoform B [TaxId: 6253] [141742] (4)
        SQ Q7YXJ9 185-368! SQ Q7YXJ9 6-184
        MFPTb
      2. Pig roundworm (Ascaris suum), isoform A [TaxId: 6253] [141743] (2)
        SQ Q7YXK2 175-344! SQ Q7YXK2 5-174
        MFPTa
P-domain of calnexin/calreticulin [63886] (1)
non-globular proline-rich hairpin
1. P-domain of calnexin/calreticulin [63887] (1)
  uperfamily
  1. P-domain of calnexin/calreticulin [63888] (2)
    1. Calreticulin [63889]
      1. Rat (Rattus norvegicus) [TaxId: 10116] [63890] (3)
    2. Calnexin [69377]
      1. Dog (Canis familiaris) [TaxId: 9615] [69378] (1)