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NC_010275.2__YP_001650879.1__kp_p14__00014

Bact-Vir

NC_010275.2__YP_001650879.1__kp_p14__00014

Identity

Accession:
NC_010275 ↗
Kingdom:
phage

Quality

74.0 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 11-67
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a0iA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.68 50.0 4.39e-01 100.0% 53.0%
3kenA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.65 54.0 3.44e-01 100.0% 26.4%
4qbuA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.61 52.0 5.03e-01 96.5% 100.0%
1pzxA02 2.20.28.50 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › DegV, N-terminal domain, peripheral subdomain 0.61 38.0 4.27e-01 94.7% 100.0%
1hwmB02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.60 49.0 3.97e-01 98.2% 99.2%
4pxdA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 50.0 4.01e-01 100.0% 95.7%
4hw8A02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 47.0 3.38e-01 98.2% 75.6%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.57 45.0 4.34e-01 100.0% 77.3%
1qupA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 47.0 4.43e-01 93.0% 91.4%
3n5fA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 49.0 3.96e-01 100.0% 95.6%
3tj8A02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.56 49.0 4.57e-01 100.0% 85.1%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 47.0 4.44e-01 94.7% 100.0%
2khoA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 43.0 3.24e-01 87.7% 81.1%
3tzyA02 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.55 47.0 4.44e-01 100.0% 91.4%
3ramA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 46.0 3.75e-01 100.0% 91.5%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.54 45.0 4.10e-01 100.0% 95.2%
5v7qZ00 3.30.1390.20 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L30/L7 0.53 45.0 4.50e-01 100.0% 100.0%
2v8pA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.53 45.0 3.69e-01 100.0% 96.5%
3fysA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 40.0 3.07e-01 87.7% 98.7%
2pw4A00 1.10.3300.10 Mainly Alpha › Orthogonal Bundle › Jann2411-like fold › Jann2411-like domain 0.53 43.0 3.06e-01 93.0% 74.3%
2jfdA03 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.52 43.0 4.21e-01 100.0% 93.9%
2crlA01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 43.0 4.10e-01 98.2% 97.1%
1cc8A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 42.0 4.00e-01 98.2% 95.8%
1vw4U00 3.30.1390.20 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L30; Chain: A, › Ribosomal protein L30/L7 0.51 43.0 3.89e-01 100.0% 73.2%
2aj0A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 42.0 3.99e-01 98.2% 95.8%
4ht4A00 3.30.930.30 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › 0.50 39.0 2.82e-01 89.5% 100.0%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587970 11.1.4.36 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.74 67.0 5.10e-01 100.0% 48.8%
3589021 11.1.4.36 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA 0.73 65.0 5.08e-01 100.0% 46.7%
4098712 304.14.1.0 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.64 56.0 5.16e-01 100.0% 96.0%
3216595 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.63 55.0 4.76e-01 100.0% 80.0%
4958814 3457.1.1.3 alpha bundles › GxGD membrane protease › GxGD membrane protease › GxGD membrane protease › Arc_PepC_II 0.62 49.0 3.29e-01 100.0% 20.4%
5025566 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.62 54.0 5.51e-01 96.5% 100.0%
5028844 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.61 54.0 4.94e-01 100.0% 100.0%
5078772 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.61 54.0 5.20e-01 100.0% 100.0%
4483441 304.14.1.0 a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.60 51.0 4.75e-01 100.0% 98.7%
4993535 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.59 51.0 4.54e-01 100.0% 100.0%
3338405 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 36.0 3.13e-01 82.5% 40.0%
3971965 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.58 49.0 4.60e-01 96.5% 97.1%
5023633 304.24.1.5 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.57 49.0 4.64e-01 100.0% 92.9%
3490910 304.107.1.1 a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain › GCV_T 0.56 47.0 3.39e-01 96.5% 91.4%
4319410 304.15.1.7 a+b two layers › Alpha-beta plaits › Viral DNA-binding domain › Viral DNA-binding domain › DUF5609 0.55 47.0 4.15e-01 96.5% 78.8%
3173015 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.54 47.0 4.33e-01 100.0% 96.0%
3604203 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 41.0 3.66e-01 94.7% 60.0%
5001137 821.1.1.4 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF123 0.53 48.0 3.55e-01 100.0% 49.3%
3187671 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 38.0 3.82e-01 100.0% 75.0%
3923662 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.52 42.0 4.05e-01 96.5% 97.1%
3699984 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 37.0 2.35e-01 78.9% 50.0%
4682714 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.51 41.0 3.97e-01 100.0% 98.6%
3975174 3253.1.1.0 a+b two layers › ferredoxin-like domain in flagellar biosynthesis protein flhA › ferredoxin-like domain in flagellar biosynthesis protein flhA › ferredoxin-like domain in flagellar biosynthesis protein flhA 0.50 38.0 4.01e-01 96.5% 100.0%
D2 high residues 76-145
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.79 55.0 4.69e-01 74.3% 47.2%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 53.0 5.61e-01 70.0% 96.8%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 53.0 5.03e-01 70.0% 71.6%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 57.0 4.90e-01 77.1% 83.2%
7sgrA02 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.77 55.0 3.49e-01 74.3% 18.1%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.76 51.0 3.72e-01 74.3% 27.4%
2ke4A00 6.10.140.470 Special › Helix non-globular › Helix Hairpins › 0.75 53.0 4.73e-01 74.3% 56.1%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.74 50.0 4.59e-01 70.0% 54.4%
6bl6B01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.73 65.0 4.21e-01 100.0% 78.8%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 49.0 4.83e-01 70.0% 70.7%
2dnxA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 57.0 4.65e-01 87.1% 66.9%
1m4rB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.71 64.0 5.03e-01 100.0% 50.4%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.70 56.0 4.69e-01 85.7% 87.4%
1kqfC00 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.70 57.0 4.04e-01 90.0% 70.8%
1yz5B00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.70 56.0 3.86e-01 87.1% 26.6%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.69 54.0 4.64e-01 85.7% 93.0%
7zm7601 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.69 51.0 3.84e-01 78.6% 67.7%
1i4dA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.67 46.0 3.38e-01 71.4% 63.8%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.67 47.0 4.16e-01 74.3% 88.6%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.67 47.0 4.72e-01 74.3% 77.5%
2gl2B00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 46.0 4.02e-01 74.3% 46.8%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 44.0 4.44e-01 70.0% 74.6%
3vnxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.65 58.0 4.20e-01 100.0% 36.4%
3zgxA02 6.10.140.1720 Special › Helix non-globular › Helix Hairpins › 0.64 43.0 4.00e-01 70.0% 81.3%
6iknD01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 43.0 2.90e-01 70.0% 19.5%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 43.0 4.31e-01 71.4% 70.8%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 58.0 4.42e-01 100.0% 46.7%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.62 48.0 4.05e-01 87.1% 75.2%
3owaB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 42.0 3.31e-01 72.9% 33.8%
1z6oA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.58 51.0 3.67e-01 100.0% 38.2%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.58 46.0 3.73e-01 84.3% 88.1%
4gzrB00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.56 37.0 3.69e-01 74.3% 63.6%
1i36A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.54 45.0 4.04e-01 92.9% 85.9%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4219218 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.85 58.0 4.88e-01 70.0% 44.5%
4024277 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.82 55.0 5.44e-01 70.0% 65.3%
3973453 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.80 57.0 5.45e-01 74.3% 90.0%
4983118 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.79 57.0 5.05e-01 74.3% 69.5%
5050139 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.79 56.0 5.53e-01 74.3% 88.0%
5011532 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.79 56.0 5.00e-01 74.3% 84.2%
3712411 3939.1.1.0 alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.78 56.0 3.72e-01 74.3% 24.4%
3737505 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.78 55.0 5.43e-01 74.3% 88.0%
4945931 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.78 55.0 5.58e-01 74.3% 74.3%
4062183 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.77 55.0 5.41e-01 74.3% 88.0%
4406698 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.77 55.0 4.93e-01 74.3% 54.7%
3469701 3755.1.1.0 alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.76 55.0 3.72e-01 74.3% 22.8%
3559003 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.76 55.0 4.78e-01 74.3% 52.0%
3699098 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 54.0 5.20e-01 74.3% 65.0%
4414254 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.76 54.0 3.50e-01 74.3% 18.6%
3390898 192.1.1.0 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.76 68.0 6.04e-01 100.0% 91.0%
4017285 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.75 51.0 3.69e-01 70.0% 26.3%
3280988 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.74 50.0 4.82e-01 70.0% 61.3%
4163282 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.74 53.0 3.79e-01 74.3% 28.1%
3459313 616.1.1.1 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.73 58.0 5.35e-01 87.1% 67.8%
3497930 5001.1.1.0 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.72 57.0 3.62e-01 85.7% 72.2%
5028679 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.71 49.0 4.29e-01 74.3% 48.5%
3795605 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.68 47.0 3.57e-01 74.3% 30.0%
3365763 170.1.1.0 alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.65 55.0 4.87e-01 95.7% 63.8%
3795070 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.65 47.0 3.84e-01 84.3% 38.6%
3585102 1128.1.1.0 alpha bundles › LYR protein › LYR protein › LYR protein 0.65 47.0 3.88e-01 84.3% 40.0%
3399861 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.64 44.0 3.60e-01 72.9% 39.3%
3638639 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.59 44.0 3.94e-01 78.6% 59.0%
3734404 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.59 42.0 4.03e-01 78.6% 65.0%
3267527 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.55 41.0 4.03e-01 84.3% 77.3%
3538309 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.54 41.0 4.01e-01 90.0% 75.0%
3654553 2004.1.1.16 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.51 39.0 2.69e-01 81.4% 61.8%
4344927 1128.1.1.2 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR_2 0.51 36.0 3.69e-01 84.3% 77.1%