SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Lineage for Protein: automated matches

  1. Root: SCOPe 2.06
  2. 1976409Class a: All alpha proteins [46456] (289 folds)
  3. 1981147Fold a.4: DNA/RNA-binding 3-helical bundle [46688] (14 superfamilies)
    core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down
  4. 1981148Superfamily a.4.1: Homeodomain-like [46689] (20 families) (S)
    consists only of helices
  5. 1982024Family a.4.1.0: automated matches [191447] (1 protein)
    not a true family
  6. 1982025Protein automated matches [190674] (22 species)
    not a true protein

Species:

  1. 1982026African clawed frog (Xenopus laevis) [TaxId:8355] [225308] (1 PDB entry)
  2. 1982028Bacillus cereus [TaxId:1396] [231498] (1 PDB entry)
  3. 1982031Bacillus subtilis [TaxId:224308] [267907] (2 PDB entries)
    1. Domains for 3whb:
      1. 1982032Domain d3whba1: 3whb A:5-77 [265647]
        Other proteins in same PDB: d3whba2, d3whbb2
        automated match to d1vi0a1
        complexed with dcc
      2. 1982033Domain d3whbb1: 3whb B:6-77 [265649]
        Other proteins in same PDB: d3whba2, d3whbb2
        automated match to d1vi0a1
        complexed with dcc
    2. Domains for 3whc:
      1. 1982034Domain d3whca1: 3whc A:4-77 [265651]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
      2. 1982035Domain d3whcb1: 3whc B:6-77 [265653]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
      3. 1982036Domain d3whcc1: 3whc C:5-77 [265655]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
      4. 1982037Domain d3whcd1: 3whc D:6-77 [265657]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
      5. 1982038Domain d3whce1: 3whc E:4-77 [265659]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
      6. 1982039Domain d3whcf1: 3whc F:7-77 [265661]
        Other proteins in same PDB: d3whca2, d3whcb2, d3whcc2, d3whcd2, d3whce2, d3whcf2
        automated match to d1vi0a1
        complexed with st9
  4. 1982040Baker's yeast (Saccharomyces cerevisiae) [TaxId:559292] [233791] (1 PDB entry)
  5. 1982042Chicken (Gallus gallus) [TaxId:9031] [256162] (1 PDB entry)
  6. 1982044Escherichia coli [TaxId:562] [226228] (11 PDB entries)
    1. Domain for 2vkv:
    2. Domain for 2xrl:
    3. Domain for 4ac0:
    4. Domain for 4b1r:
    5. Domain for 4b3a:
    6. Domain for 4d7m:
    7. Domain for 4d7n:
    8. Domains for 5fkk:
      1. 2273360Domain d5fkka1: 5fkk A:3-67 [316661]
        Other proteins in same PDB: d5fkka2, d5fkka3, d5fkkb2, d5fkkb3
        automated match to d1a6ia1
        complexed with cl, mg, pg4, pge, so4, tdc; mutant
      2. 2273362Domain d5fkkb1: 5fkk B:3-67 [316663]
        Other proteins in same PDB: d5fkka2, d5fkka3, d5fkkb2, d5fkkb3
        automated match to d1a6ia1
        complexed with cl, mg, pg4, pge, so4, tdc; mutant
    9. Domain for 5fkl:
    10. Domain for 5fkm:
    11. Domain for 5fko:
  7. 1982052Fission yeast (Schizosaccharomyces pombe) [TaxId:4896] [255149] (1 PDB entry)
  8. 1982054Fruit fly (Drosophila melanogaster) [TaxId:7227] [271176] (1 PDB entry)
  9. 1982057Golden hamster (Mesocricetus auratus) [TaxId:10036] [187780] (1 PDB entry)
  10. 1982060Human (Homo sapiens) [TaxId:9606] [189258] (24 PDB entries)
    1. Domain for 1wqi:
    2. Domain for 1yz8:
    3. Domain for 2da1:
    4. Domain for 2da2:
    5. Domain for 2da3:
    6. Domain for 2da5:
    7. Domain for 2djn:
    8. Domain for 2dmq:
    9. Domain for 2dmt:
    10. Domain for 2dmu:
    11. Domain for 2dn0:
    12. Domain for 2k40:
    13. Domain for 2l7f:
    14. Domain for 2l7m:
    15. Domain for 2l7z:
    16. Domain for 2ltp:
    17. Domain for 2m0c:
    18. Domain for 2m34:
    19. Domain for 2me0:
    20. Domain for 2me6:
    21. Domain for 2n8g:
    22. Domain for 2yum:
    23. Domain for 3a03:
    24. Domains for 4rdu:
      1. 1982062Domain d4rdua_: 4rdu A: [261144]
        automated match to d1ftta_
        protein/DNA complex
      2. 1982063Domain d4rdud_: 4rdu D: [261145]
        automated match to d1ftta_
        protein/DNA complex
  11. 1982086Mouse (Mus musculus) [TaxId:10090] [188321] (5 PDB entries)
    1. Domain for 2d9a:
    2. Domain for 2dms:
    3. Domain for 2ld5:
    4. Domains for 2vi6:
      1. 1982088Domain d2vi6a_: 2vi6 A: [168625]
        automated match to d1ftta_
      2. 1982089Domain d2vi6b_: 2vi6 B: [168626]
        automated match to d1ftta_
      3. 1982090Domain d2vi6c_: 2vi6 C: [168627]
        automated match to d1ftta_
      4. 1982091Domain d2vi6d_: 2vi6 D: [168628]
        automated match to d1ftta_
      5. 1982092Domain d2vi6e_: 2vi6 E: [168629]
        automated match to d1ftta_
      6. 1982093Domain d2vi6f_: 2vi6 F: [168630]
        automated match to d1ftta_
      7. 1982094Domain d2vi6g_: 2vi6 G: [168631]
        automated match to d1ftta_
      8. 1982095Domain d2vi6h_: 2vi6 H: [168632]
        automated match to d1ftta_
    5. Domain for 2xsd:
  12. 1982099Mycobacterium tuberculosis [TaxId:1773] [232223] (13 PDB entries)
    1. Domain for 3g1l:
    2. Domain for 3g1m:
    3. Domain for 3g1o:
    4. Domain for 3o8g:
    5. Domain for 3o8h:
    6. Domain for 3q0u:
    7. Domains for 3q0v:
      1. 1982102Domain d3q0va1: 3q0v A:22-92 [248737]
        Other proteins in same PDB: d3q0va2, d3q0vb2
        automated match to d3sfia1
        complexed with ll4
      2. 1982103Domain d3q0vb1: 3q0v B:22-94 [248739]
        Other proteins in same PDB: d3q0va2, d3q0vb2
        automated match to d3g1ma1
        complexed with ll4
    8. Domain for 3q0w:
    9. Domain for 3q3s:
    10. Domain for 3sdg:
    11. Domain for 3sfi:
    12. Domain for 4dw6:
    13. Domain for 5eyr:
  13. 1982113Nematode (Caenorhabditis elegans) [TaxId:6239] [260682] (1 PDB entry)
  14. 1982115Norway rat (Rattus norvegicus) [TaxId:10116] [230637] (1 PDB entry)
  15. 1982118Pasteurella multocida [TaxId:747] [225420] (1 PDB entry)
  16. 1982120Streptomyces coelicolor [311233] (1 PDB entry)
  17. 1982123Trichomonas vaginalis [TaxId:5722] [233124] (4 PDB entries)
    1. Domains for 2k9n:
      1. 1982134Domain d2k9na1: 2k9n A:1-49 [242429]
        automated match to d3osgd1
      2. 1982135Domain d2k9na2: 2k9n A:50-107 [242430]
        automated match to d3osga2
    2. Domains for 2kdz:
      1. 1982132Domain d2kdza1: 2kdz A:1-49 [242473]
        automated match to d3osgd1
        protein/DNA complex
      2. 1982133Domain d2kdza2: 2kdz A:50-107 [242474]
        automated match to d3osga2
        protein/DNA complex
    3. Domains for 3osf:
      1. 1982128Domain d3osfa1: 3osf A:48-96 [233125]
        automated match to d1h88c1
        protein/DNA complex; complexed with ipa
      2. 1982129Domain d3osfa2: 3osf A:97-150 [233126]
        automated match to d1gv2a2
        protein/DNA complex; complexed with ipa
      3. 1982130Domain d3osfd1: 3osf D:48-96 [233127]
        automated match to d1h88c1
        protein/DNA complex; complexed with ipa
      4. 1982131Domain d3osfd2: 3osf D:97-150 [233128]
        automated match to d1gv2a2
        protein/DNA complex; complexed with ipa
    4. Domains for 3osg:
      1. 1982124Domain d3osga1: 3osg A:40-96 [233129]
        automated match to d1h88c1
        protein/DNA complex
      2. 1982125Domain d3osga2: 3osg A:97-150 [233130]
        automated match to d1gv2a2
        protein/DNA complex
      3. 1982126Domain d3osgd1: 3osg D:48-96 [233131]
        automated match to d1h88c1
        protein/DNA complex
      4. 1982127Domain d3osgd2: 3osg D:97-150 [233132]
        automated match to d1gv2a2
        protein/DNA complex
  18. 2268221Proteus mirabilis [TaxId:584] [311527] (1 PDB entry)
  19. 2268318Mannheimia haemolytica [TaxId:75985] [311624] (1 PDB entry)
  20. 2270517Mycobacterium tuberculosis [TaxId:83331] [313822] (9 PDB entries)
    1. Domain for 5ezg:
    2. Domain for 5ezh:
    3. Domain for 5f04:
    4. Domain for 5f08:
    5. Domain for 5f0c:
    6. Domain for 5f0f:
    7. Domain for 5f0h:
    8. Domain for 5f1j:
    9. Domain for 5f27:
  21. 2273365Escherichia coli [TaxId:83333] [316666] (1 PDB entry)
  22. 2287027Bacillus halodurans [TaxId:272558] [330328] (2 PDB entries)
    1. Domains for 5gp9:
      1. 2287055Domain d5gp9b1: 5gp9 B:8-78 [330356]
        Other proteins in same PDB: d5gp9a2, d5gp9b2
        automated match to d1vi0a1
        complexed with gol, mg, plm
      2. 2287082Domain d5gp9a1: 5gp9 A:3-78 [330383]
        Other proteins in same PDB: d5gp9a2, d5gp9b2
        automated match to d1vi0a1
        complexed with gol, mg, plm
    2. Domains for 5gpa:
      1. 2287028Domain d5gpaa1: 5gpa A:3-78 [330329]
        Other proteins in same PDB: d5gpaa2, d5gpab2
        automated match to d1vi0a1
        complexed with gol, mg
      2. 2287032Domain d5gpab1: 5gpa B:8-78 [330333]
        Other proteins in same PDB: d5gpaa2, d5gpab2
        automated match to d1vi0a1
        complexed with gol, mg

More info for Protein automated matches from a.4.1.0: automated matches

Timeline for Protein automated matches from a.4.1.0: automated matches: