Structural Classification of Proteins
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Fold: DNA/RNA-binding 3-helical bundle

core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

Lineage:

  1. Root: scop
  2. Class: All alpha proteins [46456]
  3. Fold: DNA/RNA-binding 3-helical bundle [46688]
    core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down

Superfamilies:

  1. Homeodomain-like [46689] (19)
    consists only of helices
    link to SUPERFAMILY database - Superfamily
    1. Homeodomain [46690] (42)
      Pfam 00046
      1. Engrailed Homeodomain [46691]
        1. Drosophila melanogaster [TaxId: 7227] [46692] (10) picpic
      2. Mating type protein A1 Homeodomain [46693]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46694] (6) picpic
      3. mat alpha2 Homeodomain [46695]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46696] (6) picpic
      4. Hepatocyte nuclear factor 1a (LFB1/HNF1) [46697]
        atypical Homeodomain with a large insertion into HTH motif
        1. Rat (Rattus rattus) [TaxId: 10117] [46698] (2) picpic
        2. Human (Homo sapiens) [TaxId: 9606] [81680] (1) picpic
      5. Oct-1 POU Homeodomain [46699]
        1. Human (Homo sapiens) [TaxId: 9606] [46700] (7) picpic
      6. Pit-1 POU homeodomain [46701]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [46702] (1) picpic
      7. Thyroid transcription factor 1 homeodomain [46703]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [46704] (1) picpic
      8. Oct-2 POU Homeodomain [46705]
        1. Human (Homo sapiens) [TaxId: 9606] [46706] (1) picpic
      9. Oct-3 POU Homeodomain [46707]
        1. Mouse (Mus musculus) [TaxId: 10090] [46708] (1) picpic
      10. Homeobox protein hox-b1 [46709]
        1. Human (Homo sapiens) [TaxId: 9606] [46710] (1) picpic
      11. Homeobox protein hox-a9 [100994]
        1. Mouse (Mus musculus) [TaxId: 10090] [100995] (1) picpic
      12. pbx1 [46711]
        1. Human (Homo sapiens) [TaxId: 9606] [46712] (2) picpic
        2. Mouse (Mus musculus) [TaxId: 10090] [46713] (2) picpic
      13. Insulin gene enhancer protein isl-1 [46714]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [46715] (1) picpic
      14. Msx-1 homeodomain [63463]
        1. Mouse (Mus musculus) [TaxId: 10090] [63464] (1) picpic
      15. Antennapedia Homeodomain [46716]
        1. Drosophila melanogaster [TaxId: 7227] [46717] (5) picpic
      16. Ultrabithorax (ubx) homeodomain [46718]
        1. Drosophila melanogaster [TaxId: 7227] [46719] (1) picpic
      17. Extradenticle (exd) homeodomain [46720]
        1. Drosophila melanogaster [TaxId: 7227] [46721] (3) picpic
      18. Even-skipped homeodomain [63465]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [63466] (1) picpic
      19. Fushi Tarazu protein [46722]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46723] (1) picpic
      20. VND/NK-2 protein [46724]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46725] (4) picpic
      21. Paired protein [46726]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46727] (1) picpic
      22. Homeo-prospero domain of Prospero protein [81681]
        single domain composed of a homeodomain-homology N-terminal region (1245-1295) and the prospero-specific C-terminal region (1296-1396) that forms a 4-helical bundle
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [81682] (2) picpic
      23. Homeodomain-only protein, Hop [109647]
        1. Mouse (Mus musculus) [TaxId: 10090] [109648] (2) picpic
          SQ Q8R1H0
      24. ZF-HD homeobox protein At5g65410 [116772]
        1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116773] (1) picpic
          SQ Q9FKP8 182-248
      25. ZF-HD homeobox protein At4g24660 [116774]
        1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [116775] (1) picpic
          SQ Q9SB61 148-215
      26. DNA-binding protein SATB2 [116776]
        1. Human (Homo sapiens) [TaxId: 9606] [116777] (1) picpic
          SQ Q9UPW6 615-672 # the structure of the 1st CUT domain (350-437) is also known: 1WIZ
      27. Homeobox-leucine zipper protein Homez [116778]
        1. Human (Homo sapiens) [TaxId: 9606] [116779] (1) picpic
          SQ Q8IX15 337-399
          Structural genomics target
      28. Hepatocyte nuclear factor 6 [116780]
        1. Mouse (Mus musculus) [TaxId: 10090] [116781] (1) picpic
          SQ O08755 291-437
      29. LAG1 longevity assurance homolog 5, LASS5 [140141]
        1. Mouse (Mus musculus) [TaxId: 10090] [140142] (1) picpic
          SQ Q9D6K9 77-135
      30. Paired box protein pax6 [140143]
        1. Human (Homo sapiens) [TaxId: 9606] [140144] (1) picpic
          SQ P26367 211-278
      31. Transcriptional adaptor 2-like, TADA2L, isoform b [140145]
        1. Human (Homo sapiens) [TaxId: 9606] [140146] (1) picpic
          SQ Q9BVJ0 72-118
      32. Lag1 longevity assurance homolog 6, LASS6 [140147]
        1. Mouse (Mus musculus) [TaxId: 10090] [140148] (1) picpic
          SQ Q8C172 76-127
      33. Homeobox protein prh [140149]
        1. Human (Homo sapiens) [TaxId: 9606] [140150] (1) picpic
          SQ Q03014 138-194
      34. Pituitary homeobox 2 [140151]
        1. Human (Homo sapiens) [TaxId: 9606] [140152] (1) picpic
          SQ Q99697 85-144
      35. Homeobox protein pknox1 [140153]
        1. Human (Homo sapiens) [TaxId: 9606] [140154] (1) picpic
          SQ P55347 257-318
      36. Homeotic bicoid protein [140155]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [140156] (1) picpic
          SQ P09081 97-163
      37. Hypothetical protein 4930532d21rik [140157]
        1. Mouse (Mus musculus) [TaxId: 10090] [140158] (1) picpic
          SQ Q8C0V1 712-760
      38. Homeobox-containing protein 1, HMBOX1 (Flj21616) [140159]
        1. Human (Homo sapiens) [TaxId: 9606] [140160] (1) picpic
          SQ Q6NT76 268-350
      39. Homeobox protein hox-b13 [140161]
        1. Human (Homo sapiens) [TaxId: 9606] [140162] (1) picpic
          SQ Q92826 216-273
      40. Zinc fingers and homeoboxes protein 1, ZHX1 [158242]
        1. Human (Homo sapiens) [TaxId: 9606] [158243] (1) picpic
          SQ Q9UKY1 565-640
    2. Recombinase DNA-binding domain [46728] (5)
      1. HIN recombinase (DNA-binding domain) [46729]
        1. Synthetic [46730] (8) picpic
      2. gamma,delta resolvase (C-terminal domain) [46731]
        1. Escherichia coli [TaxId: 562] [46732] (11) picpic
      3. Transposase tc3a1-65 [46733]
        1. Caenorhabditis elegans [TaxId: 6239] [46734] (2) picpic
          SQ P34257 2-104
      4. Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase [46735]
        contains additional helix at each terminus
        1. Bacteriophage mu [TaxId: 10677] [46736] (2) picpic
      5. Transposase [46737]
        1. Bacteriophage mu [TaxId: 10677] [46738] (2) picpic
    3. Myb/SANT domain [46739] (15)
      1. c-Myb, DNA-binding domain [46740]
        duplication
        1. Mouse (Mus musculus) [TaxId: 10090] [46742] (16) picpic
      2. b-Myb DNA binding domain [46743]
        1. Chicken (Gallus gallus) [TaxId: 9031] [46744] (1) picpic
      3. v-Myb [68960]
        1. Avian myeloblastosis virus [TaxId: 11866] [68961] (1) picpic
      4. Rap1 [63467]
        1. Human (Homo sapiens) [TaxId: 9606] [63468] (1) picpic
      5. SANT domain of the nucleosome remodeling ATPase ISWI [100996]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [100997] (1) picpic
      6. 2610100b20rik gene product [109649]
        1. Mouse (Mus musculus) [TaxId: 10090] [109650] (1) picpic
          SQ Q80TB4 1951-2032
      7. Hypothetical protein C14orf106 (KIAA1903) [116782]
        1. Human (Homo sapiens) [TaxId: 9606] [116783] (1) picpic
          SQ Q6P0N0 877-936
      8. Metastasis associated protein MTA3 [140163]
        1. Mouse (Mus musculus) [TaxId: 10090] [140164] (1) picpic
          SQ Q924K8 267-323
      9. REST corepressor 1, CoREST [140165]
        1. Human (Homo sapiens) [TaxId: 9606] [140166] (2) picpic
          SQ Q9UKL0 376-440
      10. Radialis [140167]
        stand-alone Myb/SANT domain
        1. Garden snapdragon (Antirrhinum majus) [TaxId: 4151] [140168] (1) picpic
          SQ Q58FS3 8-70
      11. DnaJ homolog subfamily C member 1 [140169]
        1. Human (Homo sapiens) [TaxId: 9606] [140170] (2) picpic
          SQ Q96KC8 327-385! SQ Q96KC8 484-543
      12. Nuclear receptor corepressor 2 [140171]
        1. Human (Homo sapiens) [TaxId: 9606] [140172] (1) picpic
          SQ Q9Y618 413-480
      13. MYSM1 (KIAA1915) [140173]
        1. Human (Homo sapiens) [TaxId: 9606] [140174] (1) picpic
          SQ Q5VVJ2 117-181
      14. Telomere binding protein TBP1 [158244]
        1. Tobacco (Nicotiana tabacum) [TaxId: 4097] [158245] (3) picpic
          SQ Q84ZU4 578-660
      15. Telomere repeat-binding protein [158246]
        1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [158247] (1) picpic
          SQ Q9LTI6 464-560
    4. SLIDE domain [100998] (1)
      myb-related probable DNA-binding motif
      1. SLIDE domain of the nucleosome remodeling ATPase ISWI [100999]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [101000] (1) picpic
    5. GARP response regulators [81683] (1)
      plant myb-related DNA-binding motif
      1. Arr10-B [81684]
        1. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [81685] (1) picpic
    6. DNA-binding domain of telomeric protein [46745] (2)
      part of Pfam 00249 (Myb/SANT domain)
      1. DNA-binding domain of human telomeric protein, hTRF1 [46746]
        1. Human (Homo sapiens) [TaxId: 9606] [46747] (4) picpic
          SQ P54274 379-430 # structure of dimerisation domain (62-265) is also known (scop_sp 63603)
      2. Telomeric repeat binding factor 2, TRF2 [116784]
        1. Human (Homo sapiens) [TaxId: 9606] [116785] (4) picpic
          SQ Q15554 446-500 # structure of dimerisation domain (43-245) is also known (scop_sp 63605)
    7. Paired domain [46748] (3)
      duplication: consists of two domains of this fold
      1. Pax-5 [68962]
        1. Human (Homo sapiens) [TaxId: 9606] [68963] (2) picpic
      2. Pax-6 [68936]
        1. Human (Homo sapiens) [TaxId: 9606] [46750] (1) picpic
      3. Paired protein (prd) [46751]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46752] (1) picpic
    8. DNA-binding domain of rap1 [46753] (1)
      duplication: consist of two domains of this fold
      1. DNA-binding domain of rap1 [46754]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [46755] (1) picpic
    9. Centromere-binding [46756] (2)
      duplication: tandem repeat of two similar domains
      1. DNA-binding domain of centromere binding protein B (CENP-B) [46757]
        1. Human (Homo sapiens) [TaxId: 9606] [46758] (2) picpic
      2. Ars-binding protein 1, ABP1 [74670]
        1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [74671] (1) picpic
    10. FIS-like [100918] (4)
      1. FIS protein [48285]
        includes N-terminal dimerisation subdomain
        1. Escherichia coli [TaxId: 562] [48286] (12) picpic
      2. DNA-binding domain of NTRC [48287]
        includes N-terminal dimerisation subdomain
        1. Salmonella typhimurium [TaxId: 90371] [48288] (1) picpic
      3. Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain [101001]
        1. Rhodobacter sphaeroides [TaxId: 1063] [101002] (1) picpic
      4. Transcriptional regulator TyrR, C-terminal domain [63470]
        1. Haemophilus influenzae [TaxId: 727] [63471] (1) picpic
    11. AraC type transcriptional activator [46759] (2)
      duplication: consists of two structural repeats bipartite HTH protein
      1. MarA [46760]
        1. Escherichia coli [TaxId: 562] [46761] (1) picpic
      2. Rob transcription factor, N-terminal domain [46762]
        1. Escherichia coli [TaxId: 562] [46763] (1) picpic
    12. Tetracyclin repressor-like, N-terminal domain [46764] (34)
      1. Tetracyclin repressor (Tet-repressor, TetR) [46765]
        1. Escherichia coli [TaxId: 562] [46766] (13) picpic
      2. Multidrug binding protein QacR [68964]
        1. Staphylococcus aureus [TaxId: 1280] [68965] (47) picpic
          SQ P23217
      3. Hypothetical transcriptional regulator YcdC [88973]
        1. Escherichia coli [TaxId: 562] [88974] (1) picpic
      4. Hypothetical transcriptional regulator YsiA [101003]
        1. Bacillus subtilis [TaxId: 1423] [101004] (1) picpic
      5. Hypothetical transcriptional regulator YfiR [101005]
        1. Bacillus subtilis [TaxId: 1423] [101006] (1) picpic
      6. Ethr repressor [109651]
        1. Mycobacterium tuberculosis [TaxId: 1773] [109652] (3) picpic
          SQ P96222 22-215
      7. A-factor receptor homolog CprB [109653]
        gamma-butyrolactone receptor
        1. Streptomyces coelicolor [TaxId: 1902] [109654] (2) picpic
          SQ O66122
      8. Putative transcriptional repressor YbiH [109655]
        1. Salmonella typhimurium [TaxId: 90371] [109656] (1) picpic
          SQ Q8ZQN9
      9. Putative transcriptional regulator YxaF [109657]
        1. Bacillus subtilis [TaxId: 1423] [109658] (1) picpic
          SQ P42105
      10. Transcriptional regulator BC3163 [140175]
        1. Bacillus cereus [TaxId: 1396] [140176] (1) picpic
          SQ Q81BJ4 9-77
      11. Putative transcriptional regulator [140177]
        1. Rhodococcus sp. rha1 [TaxId: 101510] [140178] (2) picpic
      12. Putative transcriptional regulator SCO5951 [140179]
        1. Streptomyces coelicolor [TaxId: 1902] [140180] (2) picpic
          SQ O54180 13-80
      13. Transcriptional regulator Cgl2612 [140181]
        1. Corynebacterium glutamicum [TaxId: 1718] [140182] (4) picpic
          SQ Q8NMG3 1-174
      14. Transcriptional regulator EF0787 [140183]
        1. Enterococcus faecalis [TaxId: 1351] [140184] (2) picpic
          SQ Q837P6 4-71
      15. Putative transcriptional regulator RHA1_ro09068 [140185]
        1. Rhodococcus sp. [TaxId: 1831] [140186] (2) picpic
          SQ Q0RX74 10-78
      16. Probable transcriptional regulator PA3133 [140187]
        1. Pseudomonas aeruginosa [TaxId: 287] [140188] (1) picpic
          SQ Q9HZ91 1-76
      17. Transcriptional regulator RHA1_ro04179 [140189]
        1. Rhodococcus sp. [TaxId: 1831] [140190] (4) picpic
          SQ Q0S914 9-77
      18. Transcriptional regulator BC5000 [140191]
        1. Bacillus cereus [TaxId: 1396] [140192] (2) picpic
          SQ Q815X4 6-77
      19. Probable transcriptional regulator RHA1_ro04631 [140193]
        1. Rhodococcus sp. rha1 [TaxId: 101510] [140194] (2) picpic
          SQ Q0S7R9 4-80
      20. Putative transcriptional regulator Rha04620 [140195]
        1. Rhodococcus sp. rha1 [TaxId: 101510] [140196] (1) picpic
      21. Hemolysin II regulatory protein, HlyIIR [140197]
        1. Bacillus cereus [TaxId: 1396] [140198] (1) picpic
          SQ Q7X506 4-76
      22. Putative transcriptional regulator SCO7704 [140199]
        1. Streptomyces coelicolor [TaxId: 1902] [140200] (1) picpic
          SQ Q93JG8 16-83
      23. Probable transcriptional regulator PA1836 [140201]
        1. Pseudomonas aeruginosa [TaxId: 287] [140202] (1) picpic
          SQ Q9I2Q9 6-75
      24. Putative regulator SCO4008 [140203]
        1. Streptomyces coelicolor [TaxId: 1902] [140204] (2) picpic
          SQ Q9ADP7 7-74
      25. Transcriptional regulator PsrA [140205]
        1. Pseudomonas aeruginosa [TaxId: 287] [140206] (1) picpic
          SQ Q9HZJ9 2-80
      26. Putative transcriptional regulator SCO0857 [140207]
        1. Streptomyces coelicolor [TaxId: 1902] [140208] (2) picpic
          SQ Q9RCV4 35-99
      27. Transcriptional regulator TM1030 [140209]
        1. Thermotoga maritima [TaxId: 2336] [140210] (5) picpic
          SQ Q9X0C0 1-75! SQ Q9X0C0 2-75
      28. Putative transcriptional regulator Atu0279 [140211]
        1. Agrobacterium tumefaciens [TaxId: 358] [140212] (1) picpic
          SQ Q8UIL4 3-76
      29. Transcriptional activator DhaS [158248]
        1. Lactococcus lactis [TaxId: 1358] [158249] (2) picpic
          SQ Q9CIV9 8-78
      30. Putative transcriptional regulator SCO4940 [158250]
        1. Streptomyces coelicolor [TaxId: 1902] [158251] (1) picpic
          SQ Q8CJS4 8-82
      31. Putative transcriptional regulator RHA1_ro03468 [158252]
        1. Rhodococcus sp. RHA1 [TaxId: 101510] [158253] (2) picpic
          SQ Q0SB15 18-87
      32. Putative regulatory protein Sco4313 [158254]
        1. Streptomyces coelicolor [TaxId: 1902] [158255] (1) picpic
          SQ Q9KXS8 8-86
      33. Transcriptional regulator Cgl1640/Cg1846 [158256]
        1. Corynebacterium glutamicum [TaxId: 1718] [158257] (1) picpic
          SQ Q8NQ14 1-78
      34. Putative transcriptional regulator SCO4850 [158258]
        1. Streptomyces coelicolor [TaxId: 1902] [158259] (1) picpic
          SQ Q9KZ96 15-89
    13. Middle operon regulator, Mor [109659] (1)
      contains extra N-terminal dimerisation subdomain: alpha-hairpin (27-72) dimer is a four-helical bundle with right-handed twist
      1. Middle operon regulator, Mor [109660]
        1. Bacteriophage Mu [TaxId: 10677] [109661] (1) picpic
          SQ P23848 27-120
    14. Psq domain [140213] (1)
      Pfam 05225
      1. Ligand-dependent corepressor (LCoR) [140214]
        1. Human (Homo sapiens) [TaxId: 9606] [140215] (1) picpic
          SQ Q96JN0 343-405
    15. Alr1493-like [140216] (1)
      Pfam 04255; DUF433; contains extra C-terminal helix and N-terminal dimerisation interlock subdomain (scop_cf 47405)
      1. Hypothetical protein Ava_0674 (Alr1493 orthologue) [140217]
        1. Anabaena variabilis [TaxId: 1172] [140218] (2) picpic
          SQ Q3MFD8 1-102
    16. Nanomeric phage protein-like [140219] (1)
      contains additional N and C-terminal helices and the C-terminal beta-strand forming an intersubunit beta-barrel with a channel
      1. Phage protein BC1890 [140220]
        1. Bacillus cereus [TaxId: 1396] [140221] (6) picpic
          SQ Q81ES4 13-132
          host bacterium
    17. SWIRM domain [140222] (3)
      Pfam 04433; contains extra N-terminal helix
      1. Transcription regulatory protein swi3 [140223]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [140224] (1) picpic
          SQ P32591 311-395
      2. Transcriptional adaptor 2-like, TADA2L [140225]
        1. Mouse (Mus musculus) [TaxId: 10090] [140226] (3) picpic
          SQ Q8CHV6 343-443! SQ Q8CHV6 355-443
      3. Lysine-specific histone demethylase 1, LSD1 [140227]
        1. Human (Homo sapiens) [TaxId: 9606] [140228] (9) picpic
          SQ O60341 169-279
    18. Cgl2762-like [158260] (1)
      Pfam 01527; Transposase 8
      1. Uncharacterized protein Cgl2762 [158261]
        1. Corynebacterium glutamicum [TaxId: 1718] [158262] (1) picpic
          SQ Q8NM20 1-89
    19. RpiR-like [158263] (1)
      Pfam 01418; contains two extra helices, one at each termini; overall arrangment of five helices is similar to the helical core of the lambda integrase-like catalytic domain (scop_fa 56350)
      1. Putative transcriptional regulator YbbH [158264]
        1. Bacillus subtilis [TaxId: 1423] [158265] (3) picpic
          SQ Q45581 1-83
  2. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46767] (1)
    link to SUPERFAMILY database - Superfamily
    1. Methylated DNA-protein cysteine methyltransferase, C-terminal domain [46768] (3)
      1. Ada DNA repair protein [46769]
        1. Escherichia coli [TaxId: 562] [46770] (1) picpic
      2. O6-alkylguanine-DNA alkyltransferase [46771]
        1. Human (Homo sapiens) [TaxId: 9606] [46772] (9) picpic
          SQ P16455 6-176
        2. Archaeon Pyrococcus kodakaraensis [TaxId: 311400] [46773] (1) picpic
  3. ARID-like [46774] (1)
    contains extra helices at both N- and C-termini
    link to SUPERFAMILY database - Superfamily
    1. ARID domain [46775] (4)
      1. DNA-binding domain from the dead ringer protein [46776]
        1. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [46777] (2) picpic
      2. MRF-2 DNA-binding domain [46779]
        1. Human (Homo sapiens) [TaxId: 9606] [46780] (2) picpic
      3. Transcription regulator Adr6 (Swi1) [74672]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74673] (2) picpic
      4. SWI-SNF complex protein p270, SMARCF1 [109662]
        1. Human (Homo sapiens) [TaxId: 9606] [109663] (1) picpic
          SQ O14497 617-736
  4. "Winged helix" DNA-binding domain [46785] (84)
    contains a small beta-sheet (wing)
    link to SUPERFAMILY database - Superfamily
    1. Biotin repressor-like [46786] (2)
      1. Biotin repressor, N-terminal domain [46787]
        the middle domain is an alpha+beta fold somewhat similar to the SH2 fold
        C-terminal domain has SH3-like common fold
        1. Escherichia coli [TaxId: 562] [46788] (5) picpic
      2. Putative transcriptional regulator TM1602, N-terminal domain [74674]
        1. Thermotoga maritima [TaxId: 2336] [74675] (1) picpic
    2. LexA repressor, N-terminal DNA-binding domain [46789] (1)
      1. LexA repressor, N-terminal DNA-binding domain [46790]
        1. Escherichia coli [TaxId: 562] [46791] (4) picpic
    3. Arginine repressor (ArgR), N-terminal DNA-binding domain [46792] (3)
      1. Arginine repressor (ArgR), N-terminal DNA-binding domain [46793]
        1. Escherichia coli [TaxId: 562] [46794] (1) picpic
        2. Bacillus stearothermophilus [TaxId: 1422] [46795] (1) picpic
        3. Bacillus subtilis [TaxId: 1423] [68966] (6) picpic
    4. Transcriptional repressor Rex, N-terminal domain [101007] (1)
      1. Transcriptional repressor Rex, N-terminal domain [101008]
        AT-rich DNA-binding protein p25
        1. Thermus aquaticus [TaxId: 271] [101009] (3) picpic
          SQ Q9X2V5; # CASP5
    5. CAP C-terminal domain-like [46796] (9)
      1. Catabolite gene activator protein (CAP), C-terminal domain [46797]
        N-terminal domain has double beta-helix fold
        1. Escherichia coli [TaxId: 562] [46798] (26) picpic
      2. CO-sensing protein CooA, C-terminal domain [46799]
        1. Rhodospirillum rubrum [TaxId: 1085] [46800] (1) picpic
      3. Listeriolysin regulatory protein PrfA, C-terminal domain [88975]
        1. Bacteria (Listeria monocytogenes) [TaxId: 1639] [88976] (11) picpic
      4. Transcriptional regulator PG0396, C-terminal domain [140229]
        1. Porphyromonas gingivalis [TaxId: 837] [140230] (1) picpic
          SQ Q7MAW7 152-232
      5. Probable transcription regulator BT4300, C-terminal domain [140231]
        1. Bacteroides thetaiotaomicron [TaxId: 818] [140232] (1) picpic
          SQ Q89ZS6 148-220
      6. Transcriptional regulator TTHA1359, C-terminal domain [140233]
        1. Thermus thermophilus [TaxId: 274] [140234] (1) picpic
          SQ Q5SIL0 118-199
      7. Cyclic AMP receptor-like protein Vfr [158266]
        1. Pseudomonas aeruginosa [TaxId: 287] [158267] (1) picpic
          SQ P55222 143-213
      8. Chlorophenol reduction protein CprK [158268]
        1. Desulfitobacterium dehalogenans [TaxId: 36854] [158269] (2) picpic
          SQ Q9LAS2 148-226
        2. Desulfitobacterium hafniense [TaxId: 49338] [158270] (7) picpic
          SQ Q18R04 148-227! SQ Q18R04 148-229
    6. Lrp/AsnC-like transcriptional regulator N-terminal domain [68967] (4)
      Swapped dimer with the "wing" C-terminal strands
      1. LprA [68968]
        1. Archaeon Pyrococcus furiosus [TaxId: 2261] [68969] (1) picpic
      2. Putative transcriptional regulator PH1519 [101010]
        archaeal feast/famine regulatory protein
        1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101011] (3) picpic
          identical sequence to Pyrococcus sp. ot3 protein
      3. Regulatory protein AsnC [140235]
        1. Escherichia coli [TaxId: 562] [140236] (2) picpic
          SQ P0ACI6 4-66
      4. Transcriptional regulator LrpC [140237]
        1. Bacillus subtilis [TaxId: 1423] [140238] (8) picpic
          SQ P96582 1-63
    7. ArsR-like transcriptional regulators [46801] (4)
      The N- and C-terminal helical extensions to the common fold form the dimer interface
      1. SmtB repressor [46802]
        1. Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129] [46803] (4) picpic
          SQ P30340
      2. Metal-sensing transcriptional repressor CzrA [109664]
        1. Staphylococcus aureus [TaxId: 1280] [109665] (2) picpic
          SQ O85142
      3. Putative arsenical resistance operon repressor AF0168 [116786]
        lacks the extra C-terminal helix
        1. Archaeoglobus fulgidus [TaxId: 2234] [116787] (1) picpic
          SQ O30069
      4. Cadmium efflux system accessory protein CadC [140239]
        1. Staphylococcus aureus [TaxId: 1280] [140240] (4) picpic
          SQ P20047 12-119
    8. Transcriptional regulator IclR, N-terminal domain [74676] (1)
      1. Transcriptional regulator IclR, N-terminal domain [74677]
        1. Thermotoga maritima [TaxId: 2336] [74678] (1) picpic
    9. MarR-like transcriptional regulators [63379] (20)
      The N- and C-terminal helical extensions to the common fold form the dimer interface
      1. Multiple antibiotic resistance repressor, MarR [68970]
        1. Escherichia coli [TaxId: 562] [68971] (1) picpic
      2. MexR repressor [81686]
        1. Pseudomonas aeruginosa [TaxId: 287] [81687] (1) picpic
      3. Transcriptional regulator SlyA [81688]
        1. Enterococcus faecalis [TaxId: 1351] [81689] (1) picpic
        2. Salmonella typhimurium [TaxId: 90371] [158271] (2) picpic
          SQ P40676 1-140
      4. Staphylococcal accessory regulator A homolog, SarR [63472]
        1. Staphylococcus aureus [TaxId: 1280] [63473] (1) picpic
      5. Staphylococcal accessory regulator A homolog, SarS [88977]
        duplication: tandem repeat of two SarR-like domains assembled together as in the SarR dimer
        1. Staphylococcus aureus [TaxId: 1280] [88978] (1) picpic
      6. Pleiotropic regulator of virulence genes, SarA [48292]
        closely related to SarR but adopts a different fold; possible experimental artifact?
        1. Staphylococcus aureus [TaxId: 1280] [48293] (5) picpic
      7. Putative transcriptional regulator YusO [101012]
        1. Bacillus subtilis [TaxId: 1423] [101013] (1) picpic
      8. Hypothetical protein PH1061 [101014]
        1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [101015] (1) picpic
      9. Putative transcriptional regulator TM0816 [140241]
        1. Thermotoga maritima [TaxId: 2336] [140242] (2) picpic
          SQ Q9WZS3 1-140
      10. Probable transcriptional regulator PA3067 [140243]
        1. Pseudomonas aeruginosa [TaxId: 287] [140244] (4) picpic
          SQ Q9HZE1 2-146
      11. Probable transcriptional regulator PA4135 [140245]
        1. Pseudomonas aeruginosa [TaxId: 287] [140246] (1) picpic
          SQ Q9HWP6 5-140
      12. Organic hydroperoxide resistance transcriptional regulator OhrR [140247]
        1. Bacillus subtilis [TaxId: 1423] [140248] (7) picpic
          SQ O34777 8-144
      13. Transcriptional regulator PA3341 [140249]
        1. Pseudomonas aeruginosa [TaxId: 287] [140250] (1) picpic
          SQ Q9HYQ4 8-144
      14. Protease production regulatory protein Hpr [140251]
        1. Bacillus subtilis [TaxId: 1423] [140252] (4) picpic
          SQ P11065 6-167
      15. Transcriptional regulator TM0710 [140253]
        1. Thermotoga maritima [TaxId: 2336] [140254] (4) picpic
          SQ Q9WZG9 5-143
      16. Transcriptional regulator DR1159 [140255]
        1. Deinococcus radiodurans [TaxId: 1299] [140256] (2) picpic
          SQ Q9RV71 8-179
      17. Transcriptional regulator MgrA [158272]
        1. Staphylococcus aureus [TaxId: 1280] [158273] (1) picpic
          SQ Q7A1J9 6-141
      18. Ta1064 (RFK), N-terminal domain [158274]
        1. Thermoplasma acidophilum [TaxId: 2303] [158275] (1) picpic
          SQ Q9HJA6 5-89
      19. Transcriptional regulator OEOE1854 [158276]
        1. Oenococcus oeni [TaxId: 1247] [158277] (4) picpic
          SQ Q04CY6 3-137
    10. DNA-binding protein Mj223 [81690] (1)
      homologous to the MarR-like family in the DNA-binding region but dimerizes differently through the N- and C-terminal helical extensions to the common fold
      1. DNA-binding protein Mj223 [81691]
        1. Archaeon Methanococcus jannaschii [TaxId: 2190] [81692] (1) picpic
    11. Penicillinase repressor [101016] (4)
      homologous to the MarR-like family in the DNA-binding region but has a different dimerisation subdomain
      1. Methicillin resistance regulatory protein MecI [101017]
        1. Staphylococcus aureus [TaxId: 1280] [101018] (8) picpic
      2. Penicillinase repressor BlaI [101019]
        1. Bacillus licheniformis [TaxId: 1402] [101020] (2) picpic
        2. Staphylococcus aureus [TaxId: 1280] [109666] (2) picpic
          SQ Q9K4N1
      3. Hypothetical protein Rv1846c [158278]
        MT1894
        1. Mycobacterium tuberculosis [TaxId: 1773] [158279] (2) picpic
          SQ P95163 3-124
    12. GntR-like transcriptional regulators [46804] (4)
      1. Fatty acid responsive transcription factor FadR, N-terminal domain [46805]
        1. Escherichia coli [TaxId: 562] [46806] (5) picpic
      2. Transcriptional repressor TraR, N-terminal domain [140257]
        1. Streptomyces sp. [TaxId: 1931] [140258] (1) picpic
          SQ Q54677 1-99
          78% identity to the UniProt entry species
      3. Transcriptional regulator YydK [158280]
        1. Bacillus subtilis [TaxId: 1423] [158281] (3) picpic
          SQ Q45591 5-82
      4. Putative transcriptional regulator RHA1_ro03477 [158282]
        1. Rhodococcus sp. RHA1 [TaxId: 101510] [158283] (1) picpic
          SQ Q0SB06 25-93
    13. N-terminal domain of Bacillus PurR [101021] (1)
      1. N-terminal domain of Bacillus PurR [101022]
        1. Bacillus subtilis [TaxId: 1423] [101023] (2) picpic
    14. Replication terminator protein (RTP) [46807] (1)
      1. Replication terminator protein (RTP) [46808]
        contains long helix in the C-terminal extension; forms dimer similar to the LysR-like dimer
        1. Bacillus subtilis [TaxId: 1423] [46809] (10) picpic
    15. LysR-like transcriptional regulators [88979] (2)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP dimer
      1. LysR-type regulatory protein CbnR [88980]
        1. Ralstonia eutropha [TaxId: 106590] [88981] (2) picpic
      2. Probable LysR-type transcriptional regulator PA0477 [140259]
        1. Pseudomonas aeruginosa [TaxId: 287] [140260] (4) picpic
          SQ Q9I641 3-91
    16. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46810] (1)
      contains beta-hairpin in the N-terminal extension and two helices in the C-terminal extension
      1. N-terminal domain of molybdate-dependent transcriptional regulator ModE [46811]
        1. Escherichia coli [TaxId: 562] [46812] (3) picpic
    17. Transcription factor MotA, activation domain [46813] (1)
      The N- and C-terminal helical extensions to the common fold form the dimer interface (distinct from that of ArsR-like family)
      1. Transcription factor MotA, activation domain [46814]
        1. Bacteriophage T4 [TaxId: 10665] [46815] (2) picpic
    18. Transcription factor E/IIe-alpha, N-terminal domain [101024] (1)
      contains extra N-terminal helix
      1. Transcription factor E/IIe-alpha, N-terminal domain [101025]
        1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [101026] (1) picpic
    19. FUR-like [101027] (1)
      contains extra N-terminal helix and an alpha+beta dimerisation subdomain
      1. Ferric uptake regulation protein, FUR [101028]
        1. Pseudomonas aeruginosa [TaxId: 287] [101029] (1) picpic
    20. Replication initiation protein [46816] (3)
      duplication: tandem repeat of two "winged helix" domains arranged with the pseudo twofold symmetry
      1. RepE54 [46817]
        1. Escherichia coli, mini-F plasmid [TaxId: 562] [46818] (5) picpic
      2. Replication protein A, repA [88982]
        1. Pseudomonas syringae pv. savastanoi [TaxId: 29438] [88983] (1) picpic
      3. Replication initiation protein PI [158284]
        1. Escherichia coli [TaxId: 562] [158285] (2) picpic
          SQ P03067 152-268! SQ P03067 9-151
    21. Helicase DNA-binding domain [46819] (5)
      follows the extended AAA-ATPase domain
      1. Holliday junction helicase RuvB [46820]
        1. Thermus thermophilus [TaxId: 274] [46821] (3) picpic
        2. Thermotoga maritima [TaxId: 2336] [63474] (6) picpic
      2. CDC6, C-terminal domain [46822]
        contains the N- and C-terminal helical extensions to the common fold
        1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [46823] (1) picpic
      3. CDC6-like protein APE0152, C-terminal domain [116788]
        1. Aeropyrum pernix [TaxId: 56636] [116789] (2) picpic
          SQ Q9YFU8
      4. Hypothetical protein SSO1545, C-terminal domain [140261]
        1. Sulfolobus solfataricus [TaxId: 2287] [140262] (2) picpic
          SQ Q97Y08 284-356
    22. RecQ helicase DNA-binding domain-like [101030] (3)
      follows the tandem AAA-ATPase domain
      1. DNA helicase RecQ DNA-binding domain [101031]
        1. Escherichia coli [TaxId: 562] [101032] (2) picpic
      2. Werner syndrome ATP-dependent helicase WRN [140263]
        1. Human (Homo sapiens) [TaxId: 9606] [140264] (1) picpic
          SQ Q14191 949-1092
      3. Hel308 helicase [158286]
        1. Archaeoglobus fulgidus [TaxId: 2234] [158287] (2) picpic
    23. SCF ubiquitin ligase complex WHB domain [74679] (4)
      1. Anaphase promoting complex (APC) [74680]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [74681] (1) picpic
        2. Human (Homo sapiens) [TaxId: 9606] [74682] (3) picpic
          SQ Q13616 17-776
      2. Cullin-3 homologue [101033]
        1. Mouse (Mus musculus) [TaxId: 10090] [101034] (1) picpic
      3. Cullin-4A [158288]
        1. Human (Homo sapiens) [TaxId: 9606] [158289] (1) picpic
          SQ Q13619 676-759
    24. C-terminal fragment of elongation factor SelB [74683] (1)
      1. C-terminal fragment of elongation factor SelB [74684]
        duplication: tandem repeat of four "winged helix" domains
        1. Moorella thermoacetica [TaxId: 1525] [74685] (21) picpic
    25. Restriction endonuclease FokI, N-terminal (recognition) domain [46824] (1)
      1. Restriction endonuclease FokI, N-terminal (recognition) domain [46825]
        duplication: consists of three elaborated "winged helix" domains
        1. Flavobacterium okeanokoites [TaxId: 244] [46826] (2) picpic
    26. TnsA endonuclease, C-terminal domain [46782] (1)
      1. TnsA endonuclease, C-terminal domain [46783]
        1. Escherichia coli [TaxId: 562] [46784] (2) picpic
          SQ P13988
    27. Plant O-methyltransferase, N-terminal domain [63475] (5)
      unknown function
      1. Chalcone O-methyltransferase [63476]
        1. Alfalfa (Medicago sativa) [TaxId: 3879] [63477] (2) picpic
      2. Isoflavone O-methyltransferase [63478]
        1. Alfalfa (Medicago sativa) [TaxId: 3879] [63479] (2) picpic
      3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [74686]
        1. Alfalfa (Medicago sativa) [TaxId: 3879] [74687] (2) picpic
      4. Aclacinomycin-10-hydroxylase RdmB [101035]
        evolved a different function; binds SAM and SAH
        1. Streptomyces purpurascens [TaxId: 1924] [101036] (4) picpic
          SQ Q54527
      5. Carminomycin 4-O-methyltransferase [109667]
        1. Streptomyces peucetius [TaxId: 1950] [109668] (2) picpic
          SQ Q06528
    28. Linker histone H1/H5 [46827] (3)
      1. Histone H5, globular domain [46828]
        1. Chicken (Gallus gallus) [TaxId: 9031] [46829] (1) picpic
      2. Histone H1, globular domain [46830]
        1. Chicken (Gallus gallus) [TaxId: 9031] [46831] (1) picpic
      3. Histone H1 homologue Hho1p [101037]
        duplication: contains two similar globular domains
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [101038] (4) picpic
    29. Forkhead DNA-binding domain [46832] (6)
      1. Afx (Foxo4) [46833]
        1. Human (Homo sapiens) [TaxId: 9606] [46834] (2) picpic
      2. Adipocyte-transcription factor FREAC-11 (s12, fkh-14) [46835]
        1. Human (Homo sapiens) [TaxId: 9606] [46836] (1) picpic
      3. Interleukin enhancer binding factor [88984]
        1. Human (Homo sapiens) [TaxId: 9606] [88985] (3) picpic
      4. Genesis [46837]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [46838] (2) picpic
      5. HFH-1 (HNF-3 forkhead homolog-1) [46839]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [46840] (1) picpic
      6. Forkhead box protein P2, FOXP2 [140265]
        1. Human (Homo sapiens) [TaxId: 9606] [140266] (8) picpic
          SQ O15409 503-584
    30. DNA-binding domain from rap30 [46841] (1)
      1. DNA-binding domain from rap30 [46842]
        1. Human (Homo sapiens) [TaxId: 9606] [46843] (2) picpic
    31. C-terminal domain of the rap74 subunit of TFIIF [63480] (1)
      1. C-terminal domain of the rap74 subunit of TFIIF [63481]
        peptide-recognition motif
        1. Human (Homo sapiens) [TaxId: 9606] [63482] (4) picpic
    32. C-terminal domain of RPA32 [46844] (1)
      1. C-terminal domain of RPA32 [46845]
        peptide-recognition motif
        1. Human (Homo sapiens) [TaxId: 9606] [46846] (2) picpic
    33. DEP domain [63483] (5)
      membrane-binding domain
      1. Segment polarity protein Dishevelled-1 [63484]
        1. Mouse (Mus musculus) [TaxId: 10090] [63485] (1) picpic
      2. Regulatory domain of epac2, domain 2 [81693]
        1. Mouse (Mus musculus) [TaxId: 10090] [81694] (1) picpic
      3. Pleckstrin [101039]
        1. Mouse (Mus musculus) [TaxId: 10090] [101040] (1) picpic
        2. Human (Homo sapiens) [TaxId: 9606] [116790] (2) picpic
          SQ P08567 125-219 # structure of the N-terminal PH domain (1-105) is also known (scop_sp 50741)
      4. Pleckstrin 2 [101041]
        1. Mouse (Mus musculus) [TaxId: 10090] [101042] (1) picpic
    34. Cell cycle transcription factor e2f-dp [46847] (2)
      heterodimer of two homologous chains
      1. Cell cycle transcription factor E2F-4 [88652]
        1. Human (Homo sapiens) [TaxId: 9606] [88653] (1) picpic
      2. Cell cycle transcription factor DP-2 [88654]
        1. Human (Homo sapiens) [TaxId: 9606] [88655] (1) picpic
    35. The central core domain of TFIIE beta [46850] (1)
      1. The central core domain of TFIIE beta [46851]
        1. Human (Homo sapiens) [TaxId: 9606] [46852] (2) picpic
    36. Z-DNA binding domain [46853] (4)
      Pfam 02295
      1. Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 [46854]
        1. Human (Homo sapiens) [TaxId: 9606] [46855] (9) picpic
      2. Dlm-1 [63486]
        1. Mouse (Mus musculus) [TaxId: 10090] [63487] (1) picpic
      3. dsRNA-binding protein E3 (E3L) [101043]
        1. Vaccinia virus [TaxId: 10245] [101044] (1) picpic
      4. 34L [109669]
        1. Yaba-like disease virus, YLDV [TaxId: 132475] [109670] (1) picpic
          SQ Q9DHS8 1-75
    37. P4 origin-binding domain-like [46856] (2)
      C-terminus passes through the first loop
      1. Class II MHC transcription factor RFX1 [46857]
        1. Human (Homo sapiens) [TaxId: 9606] [46858] (1) picpic
      2. P4 origin-binding domain [74688]
        1. Bacteriophage P4 [TaxId: 10680] [74689] (1) picpic
    38. ets domain [46859] (9)
      1. Fli-1 [46860]
        1. Human (Homo sapiens) [TaxId: 9606] [46861] (1) picpic
      2. ETS-1 transcription factor, residues 331-440 [46862]
        1. Mouse (Mus musculus) [TaxId: 10090] [46863] (6) picpic
          SQ P27577 301-440
        2. Human (Homo sapiens) [TaxId: 9606] [46864] (3) picpic
      3. Transcription factor PU.1, residues 171-259 [46865]
        1. Mouse (Mus musculus) [TaxId: 10090] [46866] (1) picpic
      4. GA binding protein (GABP) alpha [46867]
        1. Mouse (Mus musculus) [TaxId: 10090] [46868] (1) picpic
      5. Serum response factor accessory protein 1a, SAP-1 [46869]
        1. Human (Homo sapiens) [TaxId: 9606] [46870] (4) picpic
      6. Elk-1 [46871]
        1. Human (Homo sapiens) [TaxId: 9606] [46872] (1) picpic
      7. Sam pointed domain containing ets transcription SPDEF [140267]
        1. Human (Homo sapiens) [TaxId: 9606] [140268] (1) picpic
          SQ O95238 247-334
      8. E74-like factor 5 ese-2b [140269]
        1. Human (Homo sapiens) [TaxId: 9606] [140270] (1) picpic
          SQ Q9UKW6 173-265
    39. Heat-shock transcription factor [46873] (2)
      1. Heat-shock transcription factor [46874]
        1. Drosophila melanogaster [TaxId: 7227] [46875] (2) picpic
        2. Milk yeast (Kluyveromyces lactis) [TaxId: 28985] [46876] (9) picpic
    40. Interferon regulatory factor [46877] (3)
      Pfam 00605
      1. Interferon regulatory factor 1 (IRF-1) [46878]
        1. Mouse (Mus musculus) [TaxId: 10090] [46879] (1) picpic
      2. Interferon regulatory factor-2, IRF-2 [46880]
        1. Mouse (Mus musculus) [TaxId: 10090] [46881] (3) picpic
      3. Interferon regulatory factor 3, IRF-3 [116791]
        1. Human (Homo sapiens) [TaxId: 9606] [116792] (9) picpic
          SQ Q14653 3-112
    41. 39 kda initiator binding protein, IBP39, N-terminal domain [101045] (1)
      1. 39 kda initiator binding protein, IBP39, N-terminal domain [101046]
        1. Trichomonas vaginalis [TaxId: 5722] [101047] (2) picpic
    42. Iron-dependent repressor protein [46882] (3)
      1. Diphtheria toxin repressor (DtxR) [46883]
        1. Corynebacterium diphtheriae [TaxId: 1717] [46884] (17) picpic
          SQ P33120
      2. Iron-dependent regulator IdeR [46885]
        1. Mycobacterium tuberculosis [TaxId: 1773] [46886] (13) picpic
          SQ Q50495
      3. Manganese transport regulator MntR [88986]
        1. Bacillus subtilis [TaxId: 1423] [88987] (20) picpic
    43. Dissimilatory sulfite reductase DsvD [101048] (1)
      1. Dissimilatory sulfite reductase DsvD [101049]
        1. Desulfovibrio vulgaris [TaxId: 881] [101050] (3) picpic
    44. La domain [101051] (3)
      Pfam 05383; RNA-binding domain
      1. Lupus La autoantigen N-terminal domain [101052]
        1. Human (Homo sapiens) [TaxId: 9606] [101053] (12) picpic
        2. Trypanosoma brucei [TaxId: 5691] [101054] (1) picpic
      2. La-related protein 4 LARP4 [140271]
        C-mpl binding protein
        1. Human (Homo sapiens) [TaxId: 9606] [140272] (1) picpic
          SQ Q71RC2 112-199
    45. Methionine aminopeptidase, insert domain [46887] (2)
      circularly permuted version of the "winged helix" fold
      1. Methionine aminopeptidase, insert domain [46888]
        1. Archaeon Pyrococcus furiosus [TaxId: 2261] [46889] (4) picpic
        2. Human (Homo sapiens) [TaxId: 9606] [46890] (18) picpic
          SQ P50579 110-478
    46. PCI domain (PINT motif) [109671] (2)
      Pfam 01399
      1. COP9 signalosome complex subunit 4, GSN4 [109672]
        1. Mouse (Mus musculus) [TaxId: 10090] [109673] (1) picpic
          SQ O88544 296-366
      2. Hypothetical protein C20orf116 homolog [116793]
        1. Mouse (Mus musculus) [TaxId: 10090] [116794] (1) picpic
          SQ Q80WW9 216-274
    47. F93-like [109674] (3)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
      1. Hypothetical protein F93 [109675]
        1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [109676] (1) picpic
          SQ P20222
      2. Uncharacterized protein APE0880.1 [158290]
        1. Aeropyrum pernix [TaxId: 56636] [158291] (2) picpic
          SQ Q9YDN4 1-92
      3. STIV F93 [158292]
        different dimerization mode than SSV1 F93
        1. Sulfolobus turreted icosahedral virus [TaxId: 269145] [158293] (2) picpic
          SQ Q6Q0J9 5-93
    48. Archaeal DNA-binding protein [109677] (1)
      contains long helix in the C-terminal extension; forms dimer similar to the RTP and LysR dimers
      1. Sso10a (SSO10449) [109678]
        1. Archaeon Sulfolobus solfataricus [TaxId: 2287] [109679] (3) picpic
          SQ Q5W1E8
    49. TrmB-like [109680] (2)
      The N- and C-terminal helical extensions to the common fold form the dimer interface, distinct from other known families
      1. Hypothetical protein AF2008 [109681]
        1. Archaeoglobus fulgidus [TaxId: 2234] [109682] (1) picpic
          SQ O28271
      2. Hypothetical transcriptional regulator ST1889 [140273]
        1. Sulfolobus tokodaii [TaxId: 111955] [140274] (2) picpic
          SQ Q96ZE4 1-109
    50. Heat-inducible transcription repressor HrcA, N-terminal domain [109683] (1)
      similar domain organization to the transcriptional regulator IclR
      1. Heat-inducible transcription repressor HrcA, N-terminal domain [109684]
        1. Thermotoga maritima [TaxId: 2336] [109685] (1) picpic
          SQ Q9WZV5
    51. DNA replication factor Cdt1 [109686] (1)
      1. DNA replication factor Cdt1 [109687]
        1. Mouse (Mus musculus) [TaxId: 10090] [109688] (1) picpic
          SQ Q8R4E9 179-365
    52. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109689] (1)
      C-terminal part of Pfam 06272
      1. Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain [109690]
        1. Human (Homo sapiens) [TaxId: 9606] [109691] (1) picpic
          SQ Q9UBQ5
    53. Vacuolar sorting protein domain [109692] (3)
      duplication: tandem repeat of two "winged-helix" domains
      1. Vacuolar sorting protein SNF8 [109693]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109694] (2) picpic
          SQ Q12483 20-232
      2. Vacuolar protein sorting-associated protein VPS36 [109695]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109696] (2) picpic
          SQ Q06696 396-566
      3. Vacuolar protein sorting-associated protein VPS25 [109697]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [109698] (10) picpic
          SQ P47142
    54. Transcriptional regulator Rrf2 [109699] (2)
      Pfam 02082
      1. Hypothetical protein ywnA [109700]
        1. Bacillus subtilis [TaxId: 1423] [109701] (1) picpic
          SQ P71036 4-130
      2. Hypothetical protein BC1842 [140275]
        1. Bacillus cereus [TaxId: 1396] [140276] (3) picpic
          SQ Q81EX1 5-142
    55. Rio2 serine protein kinase N-terminal domain [109702] (1)
      1. Rio2 serine protein kinase N-terminal domain [109703]
        1. Archaeoglobus fulgidus [TaxId: 2234] [109704] (5) picpic
          SQ O30245 # AF2426
    56. Rad21/Rec8-like [116795] (1)
      Pfam 04824
      1. Sister chromatid cohesion protein 1 (SCC1), C-terminal domain [116796]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [116797] (1) picpic
          SQ Q12158 483-561
    57. Hypothetical protein PH1932 [116798] (1)
      contains new dimerisation all-alpha C-terminal subdomain
      1. Hypothetical protein PH1932 [116799]
        1. Pyrococcus horikoshii [TaxId: 53953] [116800] (2) picpic
          SQ O59595
    58. An Obfc1 domain [116801] (1)
      helix-loop insertion in the HTH motif
      1. OB fold-containing protein 1, Obfc1 [116802]
        1. Mouse (Mus musculus) [TaxId: 10090] [116803] (1) picpic
          SQ Q8K2X3 198-304
    59. ScpB/YpuH-like [116804] (1)
      Pfam 04079
      duplication: tandem repeat of two 'winged helix' domains; forms a dimer via the C-terminal domain
      1. Segregation and condensation protein B, ScpB [116805]
        1. Chlorobium tepidum [TaxId: 1097] [116806] (1) picpic
          SQ Q8KF54 1-162
    60. PadR-like [116807] (3)
      Pfam 03551; related to the MarR-like family (Pfam 01047)
      1. Predicted transcriptional regulator [116808]
        monomeric
        1. Clostridium thermocellum [TaxId: 1515] [116809] (1) picpic
          SQ Q4CEJ8 4-106
      2. Hypothetical protein AphA [116810]
        contains extra C-terminal dimerisation domain
        1. Vibrio cholerae [TaxId: 666] [116811] (1) picpic
          SQ Q9X399 # "winged helix" domain: 1-87, dimerisation domain: 91-179
      3. Hypothetical protein TM0937 [140277]
        1. Thermotoga maritima [TaxId: 2336] [140278] (1) picpic
          SQ Q9X035 4-117
    61. Hypothetical protein YhgG [116812] (1)
      1. Hypothetical protein YhgG [116813]
        1. Escherichia coli [TaxId: 562] [116814] (1) picpic
          SQ P64638
    62. ROK associated domain [140279] (3)
      found N-terminal to ROK domain in some proteins
      1. Mlc protein N-terminal domain [140280]
        1. Escherichia coli [TaxId: 562] [140281] (6) picpic
          SQ P50456 12-81
      2. N-acetylglucosamine kinase [140282]
        Transcriptional regulator, XylR-related
        1. Thermotoga maritima [TaxId: 2336] [140283] (1) picpic
          SQ Q9X0V1 10-71
      3. Transcriptional regulator VC2007 N-terminal domain [140284]
        1. Vibrio cholerae [TaxId: 666] [140285] (1) picpic
          SQ Q9KQJ1 10-80
    63. PF1790-like [140286] (1)
      sequence similarity to PH1932 in the N-terminal domain; the C-terminal domain provides new dimerisation interface made of a beta-hairpin and a coiled coil
      1. Transcriptional regulatory protein PF1790 [140287]
        1. Pyrococcus furiosus [TaxId: 2261] [140288] (2) picpic
          SQ Q8U030 1-194
    64. MukF N-terminal domain-like [140289] (1)
      N-terminal part of Pfam 03882
      1. Chromosome partition protein MukF (KicB), N-terminal domain [140290]
        1. Escherichia coli [TaxId: 562] [140291] (2) picpic
          SQ P60293 8-118
    65. CodY HTH domain [140292] (1)
      Pfam 08222
      1. GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain [140293]
        1. Bacillus subtilis [TaxId: 1423] [140294] (3) picpic
          SQ P39779 167-257
    66. FtsK C-terminal domain-like [140295] (2)
      PfamB 000224
      1. DNA translocase FtsK [140296]
        1. Escherichia coli [TaxId: 562] [140297] (1) picpic
          SQ P46889 1261-1329
        2. Pseudomonas aeruginosa [TaxId: 287] [140298] (15) picpic
          SQ Q9I0M3 742-811
    67. Nudix-associated domain [140299] (2)
      PfamB 002148; this domain is C-terminal to the Nudix domain in some bacterial proteins
      1. Hypothetical protein BT0354, C-terminal domain [140300]
        1. Bacteroides thetaiotaomicron [TaxId: 818] [140301] (4) picpic
          SQ Q8AAV8 150-225
      2. Hypothetical protein EF2700, C-terminal domain [140302]
        1. Enterococcus faecalis [TaxId: 1351] [140303] (2) picpic
          SQ Q830S2 205-268
    68. HxlR-like [140304] (5)
      Pfam 01638; DUF24; the N- and C-terminal helical extensions to the common fold form the dimer interface similar to that of the ArsR-like family (scop_fa 46801)
      1. Hypothetical protein PG0823 [140305]
        1. Porphyromonas gingivalis [TaxId: 837] [140306] (2) picpic
          SQ Q7M7B7 3-104
      2. Hypothetical protein PA1607 [140307]
        includes extra C-terminal SH3-like subdomain, which is segment-swapped in the dimer
        1. Pseudomonas aeruginosa [TaxId: 287] [140308] (2) picpic
          SQ Q9I3B4 5-146
      3. Hypothetical protein EF0647 [140309]
        1. Enterococcus faecalis [TaxId: 1351] [140310] (2) picpic
          SQ Q838C3 1-108
      4. Putative transcriptional regulator YtfH [140311]
        1. Salmonella typhimurium [TaxId: 90371] [140312] (2) picpic
          SQ Q7CP90 9-122
      5. Putative transcriptional regulator YtcD [158294]
        1. Bacillus subtilis [TaxId: 1423] [158295] (4) picpic
          SQ O34533 10-104
    69. Marine metagenome family WH1 [158296] (1)
      1. Hypothetical protein GOS_3836187 [158297]
        1. Environmental samples [158298] (1) picpic
          marine metagenome
    70. ReutB4095-like [158299] (1)
      probable biological unit is a homohexamer
      1. Putative DNA-binding protein ReutB4095 [158300]
        1. Ralstonia eutropha [TaxId: 106590] [158301] (2) picpic
          SQ Q46TT3 12-92
    71. PH0730 N-terminal domain-like [158302] (1)
      1. Hypothetical protein PH0730 [158303]
        1. Pyrococcus horikoshii [TaxId: 53953] [158304] (1) picpic
          SQ O58461 28-96
    72. FaeA-like [158305] (1)
      Pfam 04703
      1. P fimbrial regulatory protein PapI [158306]
        KS71A
        1. Escherichia coli [TaxId: 562] [158307] (1) picpic
          SQ P62584 5-77
    73. STY4665 C-terminal domain-like [158308] (1)
      Pfam 07515; DUF1528; the "wing" hairpin, linker between helices 1 and 2 and the C-terminal tail together form an open beta-sheet barrel
      1. Hypothetical protein STY4665 [158309]
        1. Salmonella typhi [TaxId: 90370] [158310] (1) picpic
          SQ Q8Z1C5 396-528
    74. PSPTO2686-like [158311] (1)
      Pfam 04337; DUF480; duplication: two "winged helix" domains are tightly packed "back-to-back" about pseudo twofold axis
      1. Hypothetical protein PSPTO2686 [158312]
        1. Pseudomonas syringae pv. tomato [TaxId: 323] [158313] (2) picpic
          SQ Q882E2 13-96! SQ Q882E2 97-180
    75. RHA1_ro06458-like [158314] (1)
      1. Hypothetical protein RHA1_ro06458 [158315]
        1. Rhodococcus sp. RHA1 [TaxId: 101510] [158316] (1) picpic
          SQ Q0S2K3 1-85
    76. YjcQ-like [158317] (1)
      Pfam 09639
      1. Uncharacterized protein YjcQ [158318]
        1. Bacillus subtilis [TaxId: 1423] [158319] (1) picpic
          SQ O31639 5-82
    77. F112-like [158320] (1)
      1. F-112 [158321]
        1. Sulfolobus virus-like particle SSV1 [TaxId: 244589] [158322] (1) picpic
          SQ P20220 4-73
    78. MerB N-terminal domain-like [158323] (1)
      1. Alkylmercury lyase MerB [158324]
        1. Escherichia coli [TaxId: 562] [158325] (1) picpic
          SQ P77072 21-80
    79. CED-4 C-terminal domain-like [158326] (1)
      similar domain architecture to AAA+ helicases
      1. Cell death protein 4, CED-4 [158327]
        1. Caenorhabditis elegans [TaxId: 6239] [158328] (1) picpic
          SQ P30429 386-543
    80. ELL N2 domain-like [158329] (1)
      PfamB 026212; includes recent PDB entry 2e5n
      1. RNA polymerase II elongation factor ELL [158330]
        1. Human (Homo sapiens) [TaxId: 9606] [158331] (1) picpic
          SQ P55199 197-297
    81. PF0610-like [158332] (1)
      PfamB 016993; insertion of a zinc-ribbon subdomain in the beta-hairpin "wing"
      1. Hypothetical protein PF0610 [158333]
        1. Pyrococcus furiosus [TaxId: 2261] [158334] (1) picpic
          SQ Q8U362 1-105
    82. Rv2827c N-terminal domain-like [158335] (1)
      ~80 N-terminal residues of Pfam 09407' DUF2005
      1. Hypothetical protein Rv2827c [158336]
        1. Mycobacterium tuberculosis [TaxId: 1773] [158337] (2) picpic
          SQ P71625 1-82
    83. Rps19E-like [158338] (1)
      Pfam 01090; local sequence similarity to members of the GntR-like family
      1. Ribosomal protein S19e [158339]
        1. Pyrococcus abyssi [TaxId: 29292] [158340] (1) picpic
          SQ Q9V0G8 2-150
    84. RPO3F domain-like [158341] (2)
      middle region of Pfam 05158
      1. DNA-directed RNA polymerase III subunit RPC6, RPO3F [158342]
        1. Mouse (Mus musculus) [TaxId: 10090] [158343] (1) picpic
          SQ Q921X6 11-79
        2. Human (Homo sapiens) [TaxId: 9606] [158344] (1) picpic
          SQ Q9H1D9 78-155
  5. C-terminal effector domain of the bipartite response regulators [46894] (3)
    binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
    link to SUPERFAMILY database - Superfamily
    1. PhoB-like [46895] (6)
      contains 4-stranded meander beta-sheet in the N-terminal extension
      1. OmpR [46896]
        1. Escherichia coli [TaxId: 562] [46897] (3) picpic
      2. PhoB [46898]
        1. Thermotoga maritima [TaxId: 2336] [68972] (1) picpic
        2. Escherichia coli [TaxId: 562] [46899] (4) picpic
      3. Response regulator DrrB [88988]
        1. Thermotoga maritima [TaxId: 2336] [88989] (1) picpic
      4. Probable regulatory protein EmbR [140313]
        N-terminal domain, unlike the other members
        1. Mycobacterium tuberculosis [TaxId: 1773] [140314] (3) picpic
          SQ P66799 10-104
      5. Transcriptional regulatory protein PrrA [140315]
        1. Mycobacterium tuberculosis [TaxId: 1773] [140316] (4) picpic
          SQ P0A5Z6 128-233
    2. GerE-like (LuxR/UhpA family of transcriptional regulators) [46900] (5)
      contains additional, fourth helix in the C-terminal extension
      1. Germination protein GerE [63488]
        single-domain protein homologous to the C-terminal domain of NarL
        1. Bacillus subtilis [TaxId: 1423] [63489] (1) picpic
      2. Quorum-sensing transcription factor TraR, C-terminal domain [74690]
        1. Agrobacterium tumefaciens [TaxId: 358] [74691] (2) picpic
      3. Nitrate/nitrite response regulator (NarL) [46901]
        1. Escherichia coli [TaxId: 562] [46902] (11) picpic
      4. Transcriptional regulator RcsB [88990]
        1. Erwinia amylovora [TaxId: 552] [88991] (1) picpic
      5. Response regulatory protein StyR, C-terminal domain [140317]
        1. Pseudomonas fluorescens [TaxId: 294] [140318] (2) picpic
          SQ O30989 131-200
    3. Spo0A [46903] (2)
      elaborated with additional helices
      1. Spo0A [46904]
        1. Bacillus stearothermophilus [TaxId: 1422] [46905] (1) picpic
        2. Bacillus subtilis [TaxId: 1423] [74692] (1) picpic
  6. TrpR-like [48295] (3)
    contains an extra shared helix after the HTH motif
    link to SUPERFAMILY database - Superfamily
    1. Trp repressor, TrpR [48296] (1)
      intertwined dimer of identical 6-helical subunits
      1. Trp repressor, TrpR [48297]
        1. Escherichia coli [TaxId: 562] [48298] (16) picpic
    2. Chromosomal replication initiation factor DnaA C-terminal domain IV [81695] (2)
      monomeric; contains additional N-terminal helices
      1. Chromosomal replication initiation factor DnaA C-terminal domain IV [81696]
        1. Aquifex aeolicus [TaxId: 63363] [81697] (5) picpic
        2. Escherichia coli [TaxId: 562] [88992] (1) picpic
    3. SPO1678-like [158345] (1)
      Pfam 06627; DUF1153
      1. Uncharacterized protein SPO1678 [158346]
        1. Silicibacter pomeroyi [TaxId: 89184] [158347] (1) picpic
          SQ Q5LST8 1-93
  7. Ribosomal protein L11, C-terminal domain [46906] (1)
    link to SUPERFAMILY database - Superfamily
    1. Ribosomal protein L11, C-terminal domain [46907] (6)
      1. Ribosomal protein L11, C-terminal domain [46908]
        1. Bacillus stearothermophilus [TaxId: 1422] [46909] (9) picpic
        2. Thermotoga maritima [TaxId: 2336] [46910] (6) picpic
        3. Archaeon Haloarcula marismortui [TaxId: 2238] [109705] (39) picpic
          SQ P14122 67-136
        4. Deinococcus radiodurans [TaxId: 1299] [158348] (4) picpic
          SQ Q9RSS7 72-144
        5. Escherichia coli [TaxId: 562] [158349] (29) picpic
          SQ P0A7J7 73-141
        6. Thermus thermophilus [TaxId: 274] [158350] (16) picpic
          SQ P36238 70-139! SQ P36238 71-137
  8. Ribosomal protein S18 [46911] (1)
    link to SUPERFAMILY database - Superfamily
    1. Ribosomal protein S18 [46912] (2)
      1. Ribosomal protein S18 [46913]
        1. Thermus thermophilus [TaxId: 274] [46914] (47) picpic
          SQ P80382
        2. Escherichia coli [TaxId: 562] [158351] (24) picpic
          SQ P0A7T7 19-73
  9. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46915] (1)
    link to SUPERFAMILY database - Superfamily
    1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46916] (2)
      1. Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 [46917]
        links two duplicated two-domain units formed by domains 1-2 and 4-5
        1. Streptomyces antibioticus [TaxId: 1890] [46918] (2) picpic
        2. Mouse (Mus musculus) [TaxId: 10090] [116815] (1) picpic
          SQ Q8K1R3 273-363
  10. N-terminal Zn binding domain of HIV integrase [46919] (1)
    link to SUPERFAMILY database - Superfamily
    1. N-terminal Zn binding domain of HIV integrase [46920] (2)
      Zn-binding site is near the C-terminus
      1. N-terminal Zn binding domain of HIV integrase [46921]
        1. Human immunodeficiency virus type 1 [TaxId: 11676] [46922] (7) picpic
        2. Human immunodeficiency virus type 2 [TaxId: 11709] [46923] (1) picpic
  11. RNA polymerase subunit RPB10 [46924] (1)
    link to SUPERFAMILY database - Superfamily
    1. RNA polymerase subunit RPB10 [46925] (2)
      Zn-binding site is near the N-terminus
      1. RNA polymerase subunit RPB10 [46926]
        1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [46927] (1) picpic
        2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [63490] (30) picpic
          SQ P22139; part of multichain biological unit
  12. Sigma3 and sigma4 domains of RNA polymerase sigma factors [88659] (3)
    link to SUPERFAMILY database - Superfamily
    1. Sigma3 domain [88660] (3)
      1. Sigma70 [88661]
        1. Thermus thermophilus [TaxId: 274] [88662] (16) picpic
          SQ Q9WX78
      2. Sigma factor SigA [88663]
        1. Thermus aquaticus [TaxId: 271] [88664] (1) picpic
      3. Sigma factor sigma-28 (FliA) [101055]
        1. Aquifex aeolicus [TaxId: 63363] [101056] (2) picpic
    2. Sigma4 domain [88665] (7)
      1. Sigma70 (SigA, RpoD) [88666]
        1. Thermus thermophilus [TaxId: 274] [88667] (16) picpic
          SQ Q9WX78
        2. Escherichia coli [TaxId: 562] [116816] (2) picpic
          SQ P00579 546-613
        3. Thermotoga maritima [TaxId: 2336] [116817] (1) picpic
          SQ P77994 313-399
        4. Thermus aquaticus [TaxId: 271] [88669] (3) picpic
      2. SigmaE factor (RpoE) [88993]
        1. Escherichia coli [TaxId: 562] [88994] (3) picpic
      3. SigmaF [74769]
        1. Bacillus stearothermophilus [TaxId: 1422] [74770] (1) picpic
      4. Sigma factor sigma-28 (FliA) [101057]
        1. Aquifex aeolicus [TaxId: 63363] [101058] (2) picpic
    3. YlxM/p13-like [109706] (2)
      Pfam 04297; UPF0122
      structural and detectable sequence similarity to Sigma4 domain; contains extra C-terminal all-alpha oligomerization subdomain; forms different, helix-swapped dimers
      1. Hypothetical protein SPy1201 [109707]
        1. Streptococcus pyogenes [TaxId: 1314] [109708] (1) picpic
          SQ P67253
      2. Hypothetical protein SAV1236 [116818]
        1. Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280] [116819] (1) picpic
          SQ P67248
  13. KorB DNA-binding domain-like [109709] (1)
    contains HTH motif in the common core; also contains extra N-terminal helix and C-terminal subdomain of 4 helices (left-handed superhelix)
    link to SUPERFAMILY database - Superfamily
    1. KorB DNA-binding domain-like [109710] (2)
      [N-terminal half of Pfam 06613]
      1. Transcriptional repressor protein KorB DNA-binding domain [109711]
        1. Escherichia coli [TaxId: 562] [109712] (1) picpic
          SQ P07674 137-252 # structure of the C-terminal domain (297-358) is determined separately; scop_sp 69244
      2. Putative partitioning protein ParB/Spo0J [109713]
        1. Thermus thermophilus [TaxId: 274] [109714] (1) picpic
          SQ Q9LCY0 # Fragment
  14. Rps17e-like [116820] (1)
    link to SUPERFAMILY database - Superfamily
    1. Rps17e-like [116821] (1)
      Pfam 00833
      1. ribosomal protein S17e [116822]
        1. Methanobacterium thermoautotrophicum [TaxId: 145262] [116823] (1) picpic
          SQ O26894; MTH803
Enter search key:
MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk