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NC_055809.1__YP_010103407.1__KNU67_gp029__00029

Bact-Vir

NC_055809.1__YP_010103407.1__KNU67_gp029__00029

Identity

Accession:
NC_055809 ↗
Kingdom:
phage

Quality

94.5 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 3-43
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.96 89.0 6.75e-01 100.0% 47.7%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.95 87.0 7.52e-01 100.0% 72.1%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.94 87.0 7.36e-01 100.0% 64.1%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.94 88.0 7.44e-01 100.0% 66.1%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.92 83.0 7.36e-01 100.0% 94.8%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.91 82.0 6.34e-01 100.0% 51.8%
4adzA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.91 81.0 6.21e-01 100.0% 48.9%
4abxA02 6.10.140.1090 Special › Helix non-globular › Helix Hairpins › 0.91 81.0 6.25e-01 100.0% 59.8%
3w5mA05 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.90 80.0 4.60e-01 100.0% 12.2%
3q18A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.89 80.0 5.66e-01 100.0% 35.3%
4wvaB00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.89 78.0 4.40e-01 100.0% 9.9%
3vw7A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.88 78.0 4.62e-01 100.0% 22.0%
2cwyA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.87 75.0 5.77e-01 100.0% 44.1%
1vpdA02 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 0.86 77.0 5.27e-01 100.0% 32.1%
5lbmA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.86 74.0 5.93e-01 100.0% 53.0%
5je8B02 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 0.86 76.0 5.27e-01 100.0% 34.4%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.85 74.0 6.38e-01 97.6% 92.1%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.84 74.0 6.07e-01 100.0% 60.8%
5zw7A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.84 71.0 4.84e-01 100.0% 38.8%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.84 73.0 7.03e-01 100.0% 93.6%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.84 72.0 5.51e-01 100.0% 44.9%
2y44A00 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.83 70.0 4.55e-01 100.0% 22.8%
2xppA00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.81 70.0 4.84e-01 100.0% 29.9%
2jifA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.80 66.0 4.54e-01 100.0% 27.3%
2wvxA04 1.20.1610.10 Mainly Alpha › Up-down Bundle › Glycosyl hydrolase family fold › alpha-1,2-mannosidases domains 0.80 68.0 4.49e-01 100.0% 24.9%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.79 65.0 5.49e-01 100.0% 59.2%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.79 67.0 4.57e-01 100.0% 44.4%
4cpgA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.77 67.0 5.66e-01 100.0% 60.9%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 66.0 5.63e-01 100.0% 60.3%
1qu3A04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.76 66.0 4.49e-01 100.0% 32.0%
5fmnA00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.76 61.0 4.87e-01 92.7% 47.7%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.76 66.0 5.36e-01 97.6% 63.2%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.73 59.0 4.87e-01 97.6% 68.3%
1pixA03 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.71 58.0 3.52e-01 97.6% 14.0%
2v57A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.71 56.0 3.69e-01 85.4% 22.8%
1t6cA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.71 60.0 4.20e-01 92.7% 38.4%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.70 55.0 5.15e-01 97.6% 100.0%
7d1tA01 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.69 55.0 3.75e-01 100.0% 52.7%
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.69 52.0 4.70e-01 97.6% 62.9%
3lupA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 49.0 3.30e-01 82.9% 92.3%
1sxjD03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.64 51.0 4.16e-01 100.0% 48.4%
4izzB02 1.10.10.1680 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › HetR, N-terminal DNA-binding domain 0.64 54.0 4.68e-01 100.0% 98.5%
2go7A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.62 48.0 4.17e-01 87.8% 86.6%
3g2bA00 1.10.10.1150 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD) 0.61 50.0 3.97e-01 97.6% 61.1%
1mw9X02 1.10.460.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 0.60 51.0 3.46e-01 100.0% 43.6%
4k7cA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.59 54.0 3.05e-01 100.0% 69.0%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.57 48.0 3.53e-01 100.0% 58.5%
5f64A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.57 48.0 4.04e-01 100.0% 66.7%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4268623 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 1.00 95.0 6.33e-01 100.0% 31.5%
4424778 605.2.1.3 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 1.00 95.0 6.62e-01 100.0% 37.3%
4555586 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 1.00 95.0 6.70e-01 100.0% 39.0%
4242072 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 1.00 95.0 6.53e-01 100.0% 35.7%
5027469 2004.1.1.29 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 1.00 95.0 5.18e-01 100.0% 8.5%
3932692 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 1.00 95.0 7.00e-01 100.0% 45.6%
4043484 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 1.00 94.0 6.59e-01 100.0% 37.3%
4937169 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 94.0 6.55e-01 100.0% 37.3%
4470267 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 94.0 6.54e-01 100.0% 37.3%
3839273 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.53e-01 100.0% 37.3%
4335871 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.52e-01 100.0% 37.3%
4147453 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.52e-01 100.0% 37.3%
4120406 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.51e-01 100.0% 37.3%
4175087 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.51e-01 100.0% 37.3%
4300676 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.51e-01 100.0% 37.3%
5067071 604.17.1.0 alpha bundles › Spectrin repeat-like › MTH_863 C-terminal domain-like › MTH_863 C-terminal domain-like 0.99 93.0 7.73e-01 100.0% 63.1%
3809438 109.40.1.2 alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.99 93.0 6.35e-01 100.0% 34.2%
3693465 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.36e-01 100.0% 34.2%
3314722 109.40.1.2 alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Ctf4_C 0.99 93.0 6.27e-01 100.0% 32.8%
4231284 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.99 93.0 6.49e-01 100.0% 37.3%
3603648 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.98 92.0 6.89e-01 100.0% 46.6%
5044642 2484.1.1.302 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.98 92.0 5.42e-01 100.0% 16.1%
3705783 192.5.1.0 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.98 92.0 6.85e-01 100.0% 80.0%
4263341 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.98 92.0 6.38e-01 100.0% 35.7%
3934928 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.98 91.0 6.66e-01 100.0% 43.2%
4429194 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.97 91.0 6.38e-01 100.0% 37.3%
3497897 3939.1.1.0 alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.97 90.0 7.34e-01 100.0% 58.6%
4004623 192.5.1.15 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › FxsA 0.97 90.0 6.35e-01 100.0% 37.3%
3511388 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.97 88.0 7.93e-01 97.6% 75.5%
3241745 192.29.1.172 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › PF29678 0.97 89.0 5.78e-01 100.0% 26.5%
4136871 605.4.1.17 alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein › FxsA 0.97 89.0 6.36e-01 100.0% 39.0%
4061849 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.96 89.0 6.27e-01 100.0% 40.0%
3998985 4207.1.2.0 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.96 88.0 6.24e-01 100.0% 37.3%
3961597 7579.1.1.62 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_8 0.96 88.0 5.00e-01 100.0% 11.5%
3982352 4207.1.2.90 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › FxsA 0.95 87.0 6.17e-01 100.0% 37.3%
5007086 4336.1.1.1 alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF 0.94 86.0 6.11e-01 100.0% 37.3%
3575095 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.94 85.0 7.19e-01 100.0% 67.7%
3977161 605.1.1.332 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › FxsA 0.94 85.0 6.05e-01 100.0% 37.3%
3222267 375.1.9.27 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase › CCSMST1 0.93 85.0 6.20e-01 100.0% 42.0%
3680789 2004.1.1.505 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.93 84.0 4.74e-01 100.0% 10.0%
3953703 601.33.1.1 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain › CHAD 0.93 83.0 5.65e-01 100.0% 30.8%
4554324 3826.1.1.1 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.92 84.0 6.13e-01 100.0% 44.0%
4953534 3826.1.1.1 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.92 82.0 6.38e-01 100.0% 51.8%
3537261 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.90 82.0 4.81e-01 100.0% 14.6%
3285767 310.2.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.90 79.0 5.73e-01 100.0% 37.6%
2546344 3826.1.1.1 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Trns_repr_metal 0.89 79.0 6.96e-01 100.0% 73.3%
3576768 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.88 78.0 4.88e-01 100.0% 20.0%
4028650 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.87 78.0 6.85e-01 100.0% 68.3%
3403179 604.7.1.1 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.87 75.0 5.54e-01 100.0% 41.9%
3891038 633.6.1.1 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.81 67.0 5.19e-01 100.0% 42.0%
4305639 3826.1.1.25 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.78 63.0 5.08e-01 87.8% 54.7%
4067677 3826.1.1.25 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › GlutR_dimer 0.77 61.0 4.94e-01 87.8% 52.6%
4564711 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.77 61.0 4.97e-01 87.8% 54.7%
4518916 4144.1.1.8 alpha duplicates or obligate multimers › YejL-like › YejL-like › YejL-like › GlutR_dimer 0.77 61.0 4.96e-01 87.8% 54.7%
4267174 614.1.1.24 alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › GlutR_dimer 0.76 60.0 4.93e-01 87.8% 54.7%
4021036 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.76 63.0 4.91e-01 100.0% 41.0%
4980482 601.4.1.0 alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.70 56.0 4.13e-01 100.0% 33.1%
4952876 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.65 55.0 4.39e-01 100.0% 45.6%