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NC_070887.1__YP_010662406.1__PP938_gp256__00256

Bact-Vir

NC_070887.1__YP_010662406.1__PP938_gp256__00256

Identity

Accession:
NC_070887 ↗
Kingdom:
phage

Quality

72.6 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 medium residues 5-39
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.97 88.0 6.75e-01 100.0% 47.9%
7k3zG01 3.50.7.10 Alpha Beta › 3-Layer(bba) Sandwich › GroEL › GroEL 0.96 87.0 5.18e-01 100.0% 16.4%
5isuA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.94 81.0 4.86e-01 94.3% 15.6%
3rqtA02 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.94 78.0 4.64e-01 91.4% 15.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.93 82.0 6.75e-01 100.0% 61.3%
1sg2A00 3.30.910.20 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › Skp domain 0.92 82.0 5.33e-01 100.0% 24.8%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.92 80.0 7.27e-01 100.0% 72.9%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.92 80.0 5.51e-01 100.0% 30.7%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.92 81.0 7.14e-01 100.0% 74.5%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.92 80.0 6.15e-01 100.0% 45.5%
6epyA01 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.92 80.0 4.68e-01 100.0% 13.7%
3fseB02 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.91 79.0 5.16e-01 100.0% 24.3%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.91 79.0 5.07e-01 100.0% 22.9%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.91 80.0 6.60e-01 100.0% 56.5%
1wfdA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.90 78.0 5.69e-01 100.0% 37.6%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.89 76.0 4.74e-01 100.0% 18.7%
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.88 75.0 7.04e-01 100.0% 79.5%
1dpsA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.88 75.0 4.84e-01 100.0% 22.0%
2xkoC02 6.10.250.870 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.88 74.0 7.38e-01 97.1% 100.0%
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.88 73.0 5.63e-01 94.3% 80.3%
3zssA02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.88 75.0 5.81e-01 100.0% 44.3%
4hkaA02 1.10.287.3810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.88 74.0 6.63e-01 100.0% 68.6%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.87 72.0 5.29e-01 100.0% 36.1%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 73.0 4.86e-01 100.0% 45.9%
6dcjA02 1.25.40.650 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.85 71.0 5.07e-01 97.1% 32.7%
1vf6C00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.85 69.0 6.31e-01 100.0% 68.6%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.84 64.0 4.58e-01 100.0% 28.4%
1r9dA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.84 70.0 3.76e-01 100.0% 4.5%
3pvtA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 75.0 4.31e-01 100.0% 11.5%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.84 67.0 5.27e-01 97.1% 42.3%
1v0dA01 6.10.140.170 Special › Helix non-globular › Helix Hairpins › 0.83 68.0 6.16e-01 97.1% 67.3%
5a0uA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.83 69.0 3.69e-01 100.0% 4.4%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.81 66.0 5.15e-01 100.0% 42.4%
1dd9A03 1.20.50.20 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › DnaG, RNA polymerase domain, helical bundle 0.81 70.0 5.93e-01 100.0% 71.2%
4hb1A00 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 0.80 66.0 6.25e-01 100.0% 79.5%
2au3A04 1.20.50.30 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › 0.79 67.0 5.85e-01 100.0% 67.3%
5mmjn01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 63.0 4.87e-01 100.0% 39.3%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 62.0 4.22e-01 100.0% 24.3%
3q1pA01 6.10.250.1120 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.77 63.0 6.19e-01 97.1% 89.7%
4di1C02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.76 54.0 5.26e-01 80.0% 95.1%
2y4tA02 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.76 60.0 5.45e-01 100.0% 65.4%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.73 61.0 4.20e-01 100.0% 59.8%
7bi4A01 1.25.40.70 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Phosphatidylinositol 3-kinase, accessory domain (PIK) 0.70 52.0 3.34e-01 85.7% 21.5%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.68 52.0 3.50e-01 100.0% 20.3%
4jvtA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.66 53.0 5.06e-01 91.4% 95.1%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.66 52.0 4.88e-01 100.0% 70.2%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.64 52.0 3.70e-01 100.0% 38.9%
3sllA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.62 45.0 4.10e-01 100.0% 54.1%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3918963 2004.1.1.118 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AIG1 0.99 92.0 5.18e-01 100.0% 11.3%
3595966 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.98 91.0 7.06e-01 100.0% 51.5%
4991162 2484.1.1.302 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.98 90.0 5.32e-01 100.0% 16.3%
4576287 3755.3.1.471 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Paralemmin 0.97 89.0 5.58e-01 100.0% 22.6%
4115372 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.97 88.0 6.00e-01 100.0% 31.8%
4364457 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.97 89.0 8.07e-01 100.0% 77.8%
4040184 605.1.1.4 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.97 89.0 7.74e-01 100.0% 70.0%
3220374 5001.1.1.84 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srz 0.96 87.0 5.06e-01 100.0% 14.0%
3258150 192.17.1.0 alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.96 87.0 8.32e-01 100.0% 87.5%
4024442 2488.1.1.7 a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › EMG1 0.96 87.0 5.09e-01 100.0% 14.7%
3527193 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.96 86.0 4.94e-01 100.0% 12.1%
4954852 101.1.2.136 alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.96 86.0 5.33e-01 100.0% 20.2%
3369775 5076.2.1.10 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.95 85.0 4.90e-01 100.0% 12.3%
5029333 4207.1.2.114 alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › CHAD 0.95 85.0 6.27e-01 100.0% 41.2%
3885251 904.1.1.0 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain 0.95 85.0 5.20e-01 100.0% 18.9%
3492118 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.95 85.0 4.93e-01 100.0% 13.5%
3857330 904.1.1.0 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain 0.95 85.0 5.33e-01 100.0% 21.9%
3418094 604.12.1.1 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT 0.95 85.0 6.35e-01 100.0% 43.8%
3565241 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.95 84.0 4.68e-01 100.0% 8.9%
3394272 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.95 84.0 5.22e-01 100.0% 20.0%
3638713 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.94 84.0 4.58e-01 100.0% 7.0%
3599922 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.94 86.0 4.80e-01 100.0% 10.0%
3219646 3826.1.1.0 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.94 83.0 7.13e-01 100.0% 63.6%
3629711 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.94 83.0 5.59e-01 100.0% 29.2%
4979981 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.94 83.0 5.73e-01 100.0% 31.8%
4408580 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.94 84.0 7.73e-01 100.0% 77.8%
3996264 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.94 83.0 5.18e-01 100.0% 20.6%
3612124 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.94 85.0 4.74e-01 100.0% 9.9%
5048590 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.94 82.0 5.68e-01 100.0% 31.8%
3600065 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.93 82.0 4.52e-01 100.0% 7.6%
3498716 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.93 82.0 5.65e-01 100.0% 31.8%
5016885 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.93 82.0 6.60e-01 100.0% 53.8%
3718848 1132.1.1.0 extended segments › Mitochondrial complex I, B16.6 subunit › Mitochondrial complex I, B16.6 subunit › Mitochondrial complex I, B16.6 subunit 0.93 81.0 5.69e-01 100.0% 33.3%
3570403 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.93 81.0 5.43e-01 100.0% 28.0%
3640083 2004.1.1.185 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11,AAA_12 0.93 81.0 4.59e-01 100.0% 10.0%
3249106 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.93 81.0 7.20e-01 100.0% 70.0%
3423915 6132.1.1.10 alpha bundles › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › R3H-assoc 0.92 81.0 6.95e-01 100.0% 63.6%
4983057 4163.1.1.0 alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.92 81.0 5.72e-01 100.0% 35.0%
3690329 2004.1.1.473 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII, AAA_11 0.92 81.0 4.55e-01 100.0% 9.6%
3724988 2004.1.1.184 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.92 81.0 4.54e-01 100.0% 9.5%
5081365 601.33.1.0 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.92 80.0 5.19e-01 100.0% 24.1%
4034237 5055.1.1.0 extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.92 79.0 5.43e-01 100.0% 30.4%
3509080 2484.8.1.0 mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) 0.91 79.0 4.75e-01 100.0% 15.6%
3290879 3922.1.1.155 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DUF4349 0.91 79.0 6.27e-01 100.0% 50.0%
4419515 150.1.1.59 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Coat_F 0.91 79.0 5.99e-01 100.0% 43.8%
3302917 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 0.91 78.0 4.42e-01 100.0% 10.6%
3323007 2004.1.1.29 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 0.91 79.0 4.56e-01 100.0% 11.7%
3902068 109.4.1.1369 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MA3, MIF4G 0.90 78.0 4.22e-01 100.0% 6.2%
3785919 109.4.1.72 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vps16_C 0.90 78.0 4.74e-01 100.0% 17.1%
3414767 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.90 77.0 5.92e-01 100.0% 43.8%
3976663 3812.1.1.1 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › T3SS_needle_E 0.90 76.0 6.28e-01 100.0% 53.8%
3247204 103.1.1.0 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.90 77.0 6.47e-01 100.0% 58.3%
3226372 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.90 79.0 5.53e-01 100.0% 33.3%
4366957 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.88 75.0 7.03e-01 100.0% 77.8%
3635782 3291.1.1.53 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › CENPU 0.88 74.0 4.63e-01 100.0% 18.4%
3224742 3755.3.1.9 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › SH3BP5 0.88 74.0 4.53e-01 100.0% 16.3%
3881211 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.88 74.0 4.23e-01 100.0% 10.3%
3216709 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.87 73.0 5.45e-01 100.0% 38.9%
3385229 2003.1.9.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.87 71.0 4.06e-01 100.0% 9.6%
3920380 904.1.1.1 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain › zf-B_box 0.82 67.0 4.22e-01 100.0% 18.5%