SCOPe 2.06: Protein: automated matches

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

Root: SCOPe 2.06
Class a: All alpha proteins [46456] (289 folds)
Fold 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
Superfamily a.4.6: C-terminal effector domain of the bipartite response regulators [46894] (4 families)
binds to DNA and RNA polymerase; the N-terminal, receiver domain belongs to the CheY family
Family a.4.6.0: automated matches [191513] (1 protein)
not a true family
Protein automated matches [190858] (17 species)
not a true protein

Species:

Bacillus subtilis [TaxId:1423] [225130] (3 PDB entries)
1. Domain for 2d1v:
  - Domain d2d1va_: 2d1v A: [203860]
    automated match to d1gxqa_
2. Domains for 2krf:
  1. Domain d2krfa_: 2krf A: [264359]
    automated match to d2rnja_
  2. Domain d2krfb_: 2krf B: [264360]
    automated match to d2rnja_
3. Domain for 3ulq:
  - Domain d3ulqb_: 3ulq B: [265526]
    automated match to d2rnja_
    protein/DNA complex; complexed with mn
Deinococcus radiodurans [TaxId:1299] [226279] (2 PDB entries)
1. Domain for 3q9s:
  - Domain d3q9sa2: 3q9s A:123-212 [215134]
    Other proteins in same PDB: d3q9sa1
    automated match to d1kgsa1
2. Domains for 3q9v:
  1. Domain d3q9va_: 3q9v A: [248810]
    automated match to d2pmub_
  2. Domain d3q9vb_: 3q9v B: [248811]
    automated match to d2pmub_
Enterococcus faecalis [TaxId:226185] [230777] (1 PDB entry)
- Domain for 2hwv:
  - Domain d2hwva1: 2hwv A:134-232 [230778]
    Other proteins in same PDB: d2hwva2
    automated match to d2pmub_
    complexed with so4
Escherichia coli K-12 [TaxId:83333] [226337] (1 PDB entry)
- Domain for 3zq7:
  - Domain d3zq7a_: 3zq7 A: [218399]
    automated match to d1gxqa_
Helicobacter pylori [TaxId:85963] [255221] (3 PDB entries)
1. Domain for 2hqn:
  - Domain d2hqna1: 2hqn A:119-223 [242053]
    Other proteins in same PDB: d2hqna2
    automated match to d2d1va_
2. Domains for 2hqr:
  1. Domain d2hqra2: 2hqr A:118-223 [242057]
    Other proteins in same PDB: d2hqra1, d2hqrb1
    automated match to d1kgsa1
  2. Domain d2hqrb2: 2hqr B:118-223 [242059]
    Other proteins in same PDB: d2hqra1, d2hqrb1
    automated match to d1kgsa1
3. Domain for 2k4j:
  - Domain d2k4ja1: 2k4j A:13-115 [242376]
    Other proteins in same PDB: d2k4ja2
    automated match to d1odda_
Klebsiella pneumoniae [TaxId:1185418] [255488] (1 PDB entry)
- Domain for 2m87:
  - Domain d2m87a_: 2m87 A: [243136]
    automated match to d1gxpb_
Klebsiella pneumoniae [TaxId:573] [255310] (3 PDB entries)
1. Domain for 2jzy:
  - Domain d2jzya_: 2jzy A: [242326]
    automated match to d1gxpa_
2. Domain for 2mlk:
  - Domain d2mlka1: 2mlk A:131-239 [257942]
    Other proteins in same PDB: d2mlka2
    automated match to d3zq7a_
3. Domains for 4nhj:
  1. Domain d4nhja_: 4nhj A: [257989]
    automated match to d3zq7a_
    protein/DNA complex
  2. Domain d4nhjb_: 4nhj B: [257990]
    automated match to d3zq7a_
    protein/DNA complex
Mycobacterium tuberculosis [TaxId:1773] [188191] (3 PDB entries)
1. Domains for 1zlj:
  1. Domain d1zlja_: 1zlj A: [162519]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  2. Domain d1zljb1: 1zlj B:144-209 [162520]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  3. Domain d1zljc_: 1zlj C: [162521]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  4. Domain d1zljd_: 1zlj D: [162522]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  5. Domain d1zlje_: 1zlj E: [162523]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  6. Domain d1zljf1: 1zlj F:144-209 [162524]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  7. Domain d1zljg_: 1zlj G: [162525]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
  8. Domain d1zljh_: 1zlj H: [162526]
    Other proteins in same PDB: d1zljb2, d1zljf2
    automated match to d1fsea_
2. Domains for 1zlk:
  1. Domain d1zlka_: 1zlk A: [241141]
    automated match to d1zljb_
    protein/DNA complex
  2. Domain d1zlkb_: 1zlk B: [241142]
    automated match to d1zljb_
    protein/DNA complex
3. Domains for 3c57:
  1. Domain d3c57a_: 3c57 A: [199160]
    automated match to d3c57b_
  2. Domain d3c57b_: 3c57 B: [195256]
    automated match to d1zljb_
Mycobacterium tuberculosis [TaxId:83332] [225356] (2 PDB entries)
1. Domain for 2oqr:
  - Domain d2oqra2: 2oqr A:129-226 [205352]
    Other proteins in same PDB: d2oqra1, d2oqra3
    automated match to d1p2fa1
    complexed with act, bme, la
2. Domains for 2pmu:
  1. Domain d2pmua_: 2pmu A: [205543]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
  2. Domain d2pmub_: 2pmu B: [205544]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
  3. Domain d2pmuc_: 2pmu C: [205545]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
  4. Domain d2pmud_: 2pmu D: [205546]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
  5. Domain d2pmue_: 2pmu E: [205547]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
  6. Domain d2pmuf_: 2pmu F: [205548]
    automated match to d1gxpb_
    complexed with cl, gly, k, po4, unx
Salmonella typhimurium [TaxId:602] [267786] (1 PDB entry)
- Domain for 2jpc:
  - Domain d2jpca_: 2jpc A: [264340]
    automated match to d2rnja_
Staphylococcus aureus [TaxId:1280] [225593] (4 PDB entries)
1. Domain for 2rnj:
  - Domain d2rnja_: 2rnj A: [243728]
    automated match to d1zlja_
2. Domains for 2z9m:
  1. Domain d2z9ma_: 2z9m A: [304800]
    automated match to d2d1va_
  2. Domain d2z9mb_: 2z9m B: [304801]
    automated match to d2d1va_
3. Domains for 2zxj:
  1. Domain d2zxja_: 2zxj A: [207996]
    automated match to d1gxqa_
  2. Domain d2zxjb_: 2zxj B: [207997]
    automated match to d1gxqa_
4. Domains for 4qwq:
  1. Domain d4qwqa_: 4qwq A: [276149]
    automated match to d4ixaa_
  2. Domain d4qwqb_: 4qwq B: [276251]
    automated match to d4ixaa_
Staphylococcus aureus [TaxId:1458279] [275992] (1 PDB entry)
- Domains for 4u88:
  1. Domain d4u88a_: 4u88 A: [275993]
    automated match to d4ixaa_
  2. Domain d4u88b_: 4u88 B: [275994]
    automated match to d4ixaa_
Staphylococcus epidermidis [TaxId:176280] [236417] (1 PDB entry)
- Domains for 4ixa:
  1. Domain d4ixaa_: 4ixa A: [240272]
    automated match to d4ixab_
  2. Domain d4ixab_: 4ixa B: [236418]
    automated match to d2z33a1
Streptococcus pyogenes [TaxId:1314] [226362] (1 PDB entry)
- Domain for 3rjp:
  - Domain d3rjpa_: 3rjp A: [215897]
    automated match to d1gxpb_
Escherichia coli [TaxId:83333] [315476] (2 PDB entries)
1. Domains for 4uht:
  1. Domain d4uhta_: 4uht A: [315477]
    automated match to d3q9vb_
    complexed with cl
  2. Domain d4uhtb_: 4uht B: [315478]
    automated match to d3q9vb_
    complexed with cl
2. Domain for 5ju7:
  - Domain d5ju7a1: 5ju7 A:2-107 [333480]
    Other proteins in same PDB: d5ju7a2
    automated match to d4nhjb_
    complexed with zn
Streptococcus agalactiae [TaxId:1311] [319313] (1 PDB entry)
- Domains for 5dcm:
  1. Domain d5dcmb1: 5dcm B:127-221 [319314]
    Other proteins in same PDB: d5dcma2, d5dcmb2
    automated match to d2jpba_
  2. Domain d5dcma1: 5dcm A:128-221 [319339]
    Other proteins in same PDB: d5dcma2, d5dcmb2
    automated match to d3q9vb_
Acinetobacter baumannii [TaxId:575584] [328679] (1 PDB entry)
- Domain for 2naz:
  - Domain d2naza_: 2naz A: [328680]
    automated match to d4nhjb_

More info for Protein automated matches from a.4.6.0: automated matches

Timeline for Protein automated matches from a.4.6.0: automated matches:

Protein automated matches from a.4.6.0: automated matches first appeared in SCOPe 2.01
Protein automated matches from a.4.6.0: automated matches appears in SCOPe 2.05