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NC_025470.1__YP_009104102.1__S140_104__00101

Bact-Vir

NC_025470.1__YP_009104102.1__S140_104__00101

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

74.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

Singleton — not in a non-trivial cluster

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 2-53
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4il7A00 2.60.120.1300 Mainly Beta › Sandwich › Jelly Rolls › 0.73 48.0 4.12e-01 100.0% 42.4%
5cadA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.66 43.0 2.95e-01 100.0% 17.6%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.65 49.0 5.02e-01 100.0% 88.0%
3q8pB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.65 55.0 4.43e-01 100.0% 56.5%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.65 47.0 4.79e-01 100.0% 82.0%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.63 51.0 4.63e-01 100.0% 65.8%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.62 49.0 4.18e-01 100.0% 51.1%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.61 47.0 3.43e-01 100.0% 28.1%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.61 49.0 4.45e-01 100.0% 65.8%
2ig6A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 51.0 3.77e-01 100.0% 35.0%
4n0rA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 44.0 3.85e-01 100.0% 49.4%
4me3A03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.59 45.0 4.52e-01 100.0% 81.8%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.59 45.0 3.90e-01 100.0% 51.1%
1jx4A04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.58 46.0 3.97e-01 100.0% 55.1%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.56 48.0 3.86e-01 100.0% 53.2%
4ca1B02 2.60.210.10 Mainly Beta › Sandwich › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A 0.56 46.0 3.60e-01 100.0% 43.2%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.56 45.0 3.06e-01 100.0% 23.7%
2dtgE06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 40.0 3.38e-01 100.0% 43.7%
4m0wA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.54 46.0 3.46e-01 100.0% 40.1%
3tzgA00 2.40.160.150 Mainly Beta › Beta Barrel › Porin › 0.54 45.0 2.98e-01 100.0% 97.5%
3zq5A03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.53 38.0 2.86e-01 88.5% 27.5%
1wscA01 3.30.700.20 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › Hypothetical protein ph0010; domain 1 0.53 42.0 3.25e-01 100.0% 41.6%
6l4lA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.53 47.0 3.60e-01 100.0% 96.6%
1ks6A00 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.53 45.0 3.61e-01 100.0% 57.0%
1tm0A01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.52 46.0 3.24e-01 100.0% 88.4%
5wfiA01 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.52 45.0 3.46e-01 100.0% 43.8%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.52 36.0 2.71e-01 78.8% 24.4%
2ic2A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 43.0 3.57e-01 100.0% 50.0%
3kuzB00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 42.0 3.49e-01 100.0% 91.7%
1yq5A00 2.60.120.670 Mainly Beta › Sandwich › Jelly Rolls › Minor capsid protein. 0.51 43.0 3.17e-01 100.0% 34.7%
3qfgA00 2.60.40.1240 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 43.0 3.20e-01 100.0% 43.4%
1te5A00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.51 40.0 2.73e-01 100.0% 31.2%
3weeA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 40.0 2.97e-01 100.0% 70.5%
2joiA00 3.30.310.190 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.50 40.0 3.42e-01 96.2% 95.8%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995671 3115.1.1.12 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › PF30567 0.72 54.0 5.51e-01 100.0% 84.0%
3968768 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.66 59.0 5.20e-01 100.0% 94.7%
4969863 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 53.0 4.79e-01 100.0% 65.3%
5012895 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 52.0 5.17e-01 100.0% 87.3%
4939739 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.64 52.0 5.11e-01 100.0% 84.7%
3905094 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 0.64 55.0 4.12e-01 100.0% 43.0%
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.64 51.0 4.24e-01 100.0% 47.6%
4937773 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.64 52.0 5.06e-01 100.0% 86.2%
4996552 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.64 52.0 4.52e-01 100.0% 58.8%
2527501 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.63 51.0 4.21e-01 100.0% 48.1%
2831852 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.63 50.0 4.19e-01 100.0% 48.5%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.63 51.0 4.75e-01 100.0% 71.4%
3739303 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 0.63 53.0 4.20e-01 100.0% 46.7%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.62 49.0 4.82e-01 100.0% 83.3%
4990637 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.62 54.0 4.67e-01 100.0% 66.3%
4160542 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.61 49.0 4.78e-01 100.0% 86.2%
4442902 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.59 49.0 3.85e-01 100.0% 80.8%
3607227 4012.3.1.0 ↗ a+b two layers › SSHS domain › SSHS domain in CRISPR-associated endonuclease Cas9 › SSHS domain in CRISPR-associated endonuclease Cas9 0.58 49.0 4.96e-01 98.1% 100.0%
4030329 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.58 49.0 3.71e-01 100.0% 88.1%
3577630 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.58 47.0 3.68e-01 98.1% 39.2%
3725765 2008.1.1.147 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF29557 0.58 44.0 3.03e-01 86.5% 46.3%
3583046 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.57 45.0 4.52e-01 92.3% 89.1%
3800070 210.2.1.0 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain 0.57 44.0 2.68e-01 88.5% 13.9%
3626771 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.56 43.0 2.80e-01 88.5% 18.5%
3992154 1.1.2.7 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi › CDC48_N 0.55 44.0 4.29e-01 100.0% 80.0%
4001707 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.55 45.0 3.99e-01 100.0% 67.1%
4552838 304.150.1.1 ↗ a+b two layers › Alpha-beta plaits › Adapter protein mecA 2 C-terminal domain › Adapter protein mecA 2 C-terminal domain › MecA 0.55 49.0 4.04e-01 100.0% 63.4%
4591860 11.1.1.1125 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF30142 0.55 45.0 3.55e-01 100.0% 51.2%
5045852 302.4.1.1 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.55 46.0 3.72e-01 100.0% 47.3%
3738589 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.54 43.0 3.57e-01 100.0% 46.7%
3429114 221.1.1.7 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › UBX 0.54 47.0 3.31e-01 100.0% 44.7%
3670549 11.1.1.855 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF26102 0.54 44.0 3.48e-01 100.0% 44.0%
3681391 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 46.0 3.29e-01 100.0% 44.7%
3760983 3335.1.1.3 ↗ beta barrels › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › Handle domain in transferrin-binding protein B › KCTD18_C 0.54 43.0 3.70e-01 100.0% 95.0%
4367608 4139.1.1.1 ↗ a+b two layers › AMMECR1-like › AMMECR1-like › AMMECR1-like › AMMECR1 0.53 42.0 3.99e-01 100.0% 75.4%
5050481 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 40.0 3.04e-01 86.5% 33.1%
3817532 109.4.1.2179 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, DYW_deaminase, E_motif 0.53 44.0 2.54e-01 100.0% 14.8%
3592899 4081.1.1.0 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.53 43.0 2.98e-01 100.0% 60.5%
3217778 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.52 42.0 3.48e-01 100.0% 52.7%
3744530 302.4.1.1 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › Hydant_A_C 0.52 41.0 3.36e-01 100.0% 44.5%
4963275 223.1.1.191 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › DUF7285 0.51 37.0 3.24e-01 82.7% 76.7%
3302171 11.10.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › Sina_TRAF 0.51 41.0 3.22e-01 100.0% 45.2%
5021739 11.1.1.33 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arch_flagellin 0.51 42.0 3.06e-01 100.0% 51.2%
3176015 387.1.1.0 ↗ few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.51 41.0 4.25e-01 100.0% 100.0%