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NC_070857.1__YP_010658499.1__PP751_gp100__00095

Bact-Vir

NC_070857.1__YP_010658499.1__PP751_gp100__00095

Identity

Accession:
NC_070857 ↗
Kingdom:
phage

Quality

78.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Xoxocotlavirus› Rhizobium_phage_RHph_X2_28B

TaxID: 2836086

Cluster

View cluster (36 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 3-74
PDB
Domain cluster: rep: OQ504960.1__WID41994.1__X__00022__D3-68
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4d7pA00 2.60.40.730 Mainly Beta › Sandwich › Immunoglobulin-like › SOR catalytic domain 0.67 45.0 4.14e-01 100.0% 53.1%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.63 47.0 4.29e-01 100.0% 59.4%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.63 42.0 3.84e-01 100.0% 51.0%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.63 42.0 4.75e-01 100.0% 92.5%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.63 43.0 3.32e-01 100.0% 30.5%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.63 46.0 3.61e-01 100.0% 37.1%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.62 49.0 4.28e-01 100.0% 56.9%
5z0uA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 43.0 3.61e-01 100.0% 42.7%
3r8qA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 39.0 3.63e-01 100.0% 51.1%
3qvnA02 3.55.40.20 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › Iron/manganese superoxide dismutase, C-terminal domain 0.61 42.0 3.65e-01 73.6% 85.5%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.60 43.0 4.24e-01 100.0% 72.4%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.60 40.0 4.17e-01 100.0% 75.8%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 45.0 3.29e-01 100.0% 30.4%
1blwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 38.0 3.43e-01 100.0% 46.1%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.57 37.0 3.15e-01 100.0% 40.0%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.56 35.0 3.12e-01 100.0% 41.7%
1u5tB02 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 0.56 36.0 3.67e-01 87.5% 68.1%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 42.0 3.89e-01 100.0% 62.5%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.55 37.0 3.98e-01 95.8% 85.0%
1ltlA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.54 35.0 4.14e-01 97.2% 98.0%
2ebfX01 3.10.670.10 Alpha Beta › Roll › Secreted effector protein ssei fold › Secreted effector protein ssei. 0.54 48.0 3.52e-01 100.0% 40.4%
5kycB02 2.20.210.10 Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › ubp-family deubiquitinating enzyme superfamily 0.53 37.0 4.14e-01 100.0% 98.1%
5lvxC02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 45.0 4.02e-01 100.0% 100.0%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.53 37.0 3.49e-01 100.0% 58.5%
3lmmA03 3.30.565.60 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › 0.53 41.0 3.18e-01 87.5% 61.4%
1dgsA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.52 35.0 3.30e-01 100.0% 53.7%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 47.0 3.42e-01 100.0% 50.3%
4qpwA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 46.0 3.71e-01 100.0% 50.7%
4nx9A02 2.60.40.4390 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 46.0 3.88e-01 100.0% 65.3%
2gfoA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.52 46.0 2.99e-01 100.0% 22.1%
4ksnA00 6.20.250.80 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.52 40.0 4.24e-01 100.0% 92.3%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.52 35.0 3.96e-01 98.6% 100.0%
1zq1A01 2.30.30.520 Mainly Beta › Roll › SH3 type barrels. › 0.52 37.0 3.73e-01 98.6% 74.0%
4hscX04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.52 33.0 2.95e-01 70.8% 42.7%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 44.0 2.98e-01 100.0% 24.0%
1cqxA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 43.0 3.76e-01 100.0% 61.3%
2e1qC01 3.10.20.30 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Beta-grasp domain 0.51 35.0 3.24e-01 100.0% 55.4%
8bs9A01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 44.0 2.96e-01 100.0% 24.7%
3i3tA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 43.0 2.94e-01 100.0% 24.1%
3tx8A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 43.0 3.81e-01 100.0% 100.0%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3508717 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.76 46.0 4.66e-01 100.0% 61.4%
4995672 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.72 46.0 5.35e-01 100.0% 94.0%
3508990 3115.3.1.2 ↗ a+b two layers › GP2-like › P56 › P56 › DUF2922 0.69 54.0 5.73e-01 100.0% 96.9%
4231372 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.68 57.0 5.84e-01 100.0% 100.0%
3972526 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.68 56.0 5.69e-01 98.6% 95.7%
4031235 3986.2.1.2 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd › DUF2922 0.67 51.0 5.25e-01 100.0% 87.1%
3593981 302.1.1.0 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.67 50.0 4.43e-01 100.0% 55.2%
4448678 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.66 57.0 5.70e-01 100.0% 97.3%
3285401 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.66 43.0 4.30e-01 100.0% 64.0%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 47.0 5.00e-01 100.0% 96.7%
3622256 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.63 45.0 3.55e-01 100.0% 34.8%
3574971 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.63 40.0 4.57e-01 100.0% 92.0%
3414928 382.1.1.6 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › QVR 0.63 43.0 4.08e-01 100.0% 59.1%
3874464 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.63 48.0 3.11e-01 100.0% 17.2%
4927529 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.62 47.0 4.17e-01 100.0% 56.3%
3588755 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 53.0 5.29e-01 100.0% 90.5%
3573883 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.62 49.0 4.10e-01 100.0% 49.6%
5061487 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.61 39.0 3.15e-01 100.0% 34.1%
3879743 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 42.0 4.16e-01 100.0% 68.0%
5063433 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 39.0 4.46e-01 100.0% 94.0%
3956576 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.60 43.0 3.52e-01 100.0% 39.3%
4928817 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.60 42.0 3.37e-01 100.0% 36.0%
4175825 387.1.1.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.59 41.0 4.31e-01 100.0% 80.0%
4931814 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.59 44.0 3.59e-01 100.0% 41.4%
3284911 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.59 46.0 3.64e-01 100.0% 40.7%
3284585 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.59 45.0 3.71e-01 100.0% 45.7%
3738951 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.57 44.0 3.85e-01 100.0% 54.5%
3280574 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.57 42.0 3.46e-01 100.0% 41.4%
4956437 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.57 37.0 3.02e-01 100.0% 35.6%
5065473 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.57 35.0 2.60e-01 88.9% 20.5%
4983067 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.57 37.0 4.32e-01 100.0% 98.0%
3290002 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.55 41.0 3.33e-01 100.0% 39.3%
3927698 11.1.1.905 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_ILCR1 0.55 40.0 3.19e-01 100.0% 36.8%
3276514 1169.1.1.2 ↗ a+b complex topology › Procyclic specific surface antigen-2 › Procyclic specific surface antigen-2 › Procyclic specific surface antigen-2 › DDB_G0273449 0.54 37.0 3.15e-01 70.8% 96.8%
4185009 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.54 38.0 3.94e-01 95.8% 81.5%
3362301 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.54 47.0 3.08e-01 100.0% 22.8%
4505797 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.54 39.0 4.06e-01 98.6% 84.6%
3731972 1.1.7.7 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.54 46.0 3.80e-01 100.0% 53.1%
4015499 1.1.5.9 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx,PNP_phzG_C 0.54 44.0 3.10e-01 100.0% 28.3%
4927303 525.1.1.1 ↗ a+b two layers › Urease, gamma-subunit › Urease, gamma-subunit › Urease, gamma-subunit › Urease_gamma 0.54 47.0 4.01e-01 100.0% 88.3%
5041452 303.1.1.1 ↗ a+b four layers › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › Pyruvoyl-dependent histidine and arginine decarboxylases › PvlArgDC 0.54 45.0 3.57e-01 100.0% 44.4%
5004476 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.53 37.0 3.85e-01 98.6% 80.0%
4490994 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.52 45.0 2.90e-01 100.0% 23.7%
3236126 10.10.1.1 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) › PLAT 0.52 48.0 3.94e-01 100.0% 73.6%
4104821 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.52 38.0 3.77e-01 98.6% 74.7%
3928350 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.52 45.0 3.15e-01 100.0% 30.8%
3699091 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.52 45.0 2.84e-01 100.0% 27.4%
3709104 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.51 45.0 2.86e-01 100.0% 29.2%
3859192 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.51 36.0 3.39e-01 100.0% 60.0%
2640865 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 36.0 3.97e-01 98.6% 100.0%
5067513 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 36.0 4.04e-01 95.8% 100.0%
3646906 304.8.1.0 ↗ a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.50 43.0 3.98e-01 100.0% 94.7%
3231920 11.10.1.4 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › TRAF-mep_MATH 0.50 44.0 3.28e-01 100.0% 38.4%
3289833 1.1.5.15 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › F420H2_quin_red 0.50 44.0 3.54e-01 100.0% 55.2%