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NC_025470.1__YP_009104176.1__S140_178__00175

Bact-Vir

NC_025470.1__YP_009104176.1__S140_178__00175

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

90.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

View cluster (14 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 medium residues 57-115
PDB
Domain cluster: representative
CATH (57)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.78 69.0 4.83e-01 100.0% 89.4%
2k1gA00 3.90.1720.10 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) 0.72 62.0 4.90e-01 100.0% 70.5%
4b6eB01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.69 51.0 3.51e-01 79.7% 85.1%
3hlzA02 1.20.120.1090 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 47.0 3.73e-01 72.9% 86.8%
3qijB03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 49.0 4.34e-01 79.7% 85.4%
2j7qA00 3.90.70.120 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.67 55.0 3.84e-01 100.0% 74.9%
2f4mA01 3.10.620.30 Alpha Beta › Roll › C8orf32 fold › 0.66 56.0 3.85e-01 100.0% 30.0%
1wzoA01 2.30.30.370 Mainly Beta › Roll › SH3 type barrels. › FAH 0.65 42.0 4.72e-01 74.6% 100.0%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.64 46.0 3.59e-01 79.7% 33.6%
1i7dA03 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.64 48.0 3.64e-01 81.4% 92.9%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.64 40.0 4.03e-01 86.4% 60.7%
5d3xB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 49.0 3.82e-01 89.8% 80.1%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.62 47.0 3.91e-01 81.4% 61.5%
3gasB02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 47.0 3.40e-01 83.1% 32.7%
3fm8D03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 43.0 3.63e-01 76.3% 82.4%
3mb5A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.61 43.0 4.33e-01 78.0% 95.2%
3fssA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 45.0 4.04e-01 81.4% 89.5%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 45.0 3.55e-01 81.4% 44.4%
1m1hA02 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.60 41.0 3.71e-01 71.2% 68.3%
2fg9A01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 44.0 3.26e-01 81.4% 33.3%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 45.0 3.75e-01 83.1% 66.7%
2i51B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 45.0 3.13e-01 83.1% 30.9%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.59 45.0 4.14e-01 86.4% 93.8%
2a2jA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 45.0 3.07e-01 83.1% 27.6%
1a1rA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.59 41.0 3.72e-01 76.3% 55.3%
1u3eM02 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 0.59 44.0 4.29e-01 84.7% 89.7%
2fhqA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 43.0 3.37e-01 81.4% 40.7%
4ioyX02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 46.0 3.78e-01 89.8% 72.2%
1havB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 44.0 3.62e-01 81.4% 64.1%
3k6yA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.57 43.0 3.60e-01 83.1% 58.9%
4a4yA01 2.60.200.50 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.57 41.0 3.66e-01 83.1% 100.0%
1vw3C01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 43.0 3.34e-01 83.1% 39.7%
2ra2B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.56 42.0 4.25e-01 81.4% 100.0%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 39.0 3.97e-01 74.6% 83.1%
3loiA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 40.0 2.94e-01 81.4% 28.1%
1t9mA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 43.0 2.99e-01 86.4% 27.9%
1sg5A01 2.30.30.400 Mainly Beta › Roll › SH3 type barrels. › Rof-like 0.55 39.0 3.63e-01 76.3% 68.8%
3o4hA01 2.130.10.150 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Peptidase/esterase 'gauge' domain 0.55 41.0 2.71e-01 86.4% 18.3%
6j8yA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.54 46.0 3.07e-01 100.0% 25.3%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.54 39.0 3.79e-01 79.7% 74.2%
1dleB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 40.0 3.12e-01 83.1% 56.3%
2hq7B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 40.0 3.08e-01 83.1% 38.7%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.53 39.0 3.26e-01 81.4% 56.0%
3zpeA00 2.60.90.50 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › 0.53 39.0 3.07e-01 83.1% 42.8%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.52 37.0 3.06e-01 78.0% 99.2%
1h7zA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.52 40.0 2.86e-01 84.7% 35.1%
1yudA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 36.0 2.76e-01 81.4% 29.0%
2ijzA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.52 39.0 3.27e-01 83.1% 65.4%
2mvzA00 2.40.100.10 Mainly Beta › Beta Barrel › Cyclophilin › Cyclophilin-like 0.52 43.0 3.36e-01 100.0% 55.5%
4xuoA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 44.0 3.20e-01 93.2% 53.8%
6vtmB00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 37.0 3.23e-01 83.1% 47.9%
2imzA00 2.170.16.10 Mainly Beta › Beta Complex › Endonuclease - Pi-scei; Chain A, domain 1 › Hedgehog/Intein (Hint) domain 0.51 42.0 3.37e-01 100.0% 84.5%
1xf1A02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.51 42.0 3.25e-01 96.6% 85.8%
5h4eA02 3.30.920.50 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Beta-1,3-glucanase, C-terminal domain 0.51 36.0 3.03e-01 78.0% 65.5%
1yn3A00 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 35.0 3.00e-01 81.4% 42.9%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.50 36.0 3.51e-01 79.7% 74.2%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.50 36.0 3.20e-01 81.4% 58.3%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3290662 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.82 74.0 5.66e-01 100.0% 95.4%
2469820 219.1.1.49 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C70 0.77 68.0 5.01e-01 100.0% 85.7%
3524963 219.1.1.122 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › PF28648 0.73 65.0 4.07e-01 100.0% 79.4%
3684527 221.1.5.3 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Chemotaxis inhibitory protein CHIPS › DUF7734 0.71 53.0 4.57e-01 81.4% 54.8%
2770320 219.1.1.39 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF1175 0.69 60.0 4.23e-01 100.0% 76.6%
4024877 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.69 52.0 3.89e-01 81.4% 80.7%
7413 219.1.1.24 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Herpes_teg_N 0.67 55.0 3.83e-01 100.0% 74.6%
3971733 11.9.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › FAH › FAH 0.66 49.0 3.08e-01 79.7% 69.4%
3519122 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.66 50.0 4.38e-01 83.1% 64.4%
3769507 4.1.1.31 ↗ beta barrels › SH3 › SH3 › SH3 › Spin-Ssty 0.66 48.0 4.54e-01 78.0% 74.3%
3438163 4135.1.1.1 ↗ beta duplicates or obligate multimers › MAL13P1.257-like › MAL13P1.257-like › MAL13P1.257-like › CXXC_Zn-b_euk 0.66 50.0 3.64e-01 83.1% 61.8%
3411284 270.1.1.2 ↗ beta barrels › FMT C-terminal domain-like › FMT C-terminal domain-related › FMT C-terminal domain-related › Formyl_trans_C 0.63 49.0 3.97e-01 83.1% 95.5%
3280641 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.63 48.0 4.05e-01 83.1% 57.0%
4207197 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 47.0 3.95e-01 81.4% 65.0%
5034126 375.1.3.3 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF5817 0.62 45.0 4.56e-01 79.7% 76.7%
3973332 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 46.0 4.29e-01 81.4% 64.0%
4959767 375.1.3.3 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF5817 0.62 45.0 4.52e-01 79.7% 76.7%
4953373 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.61 46.0 3.54e-01 81.4% 40.6%
4950325 375.1.3.1 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF1922 0.61 44.0 3.88e-01 78.0% 52.9%
3266485 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 47.0 3.65e-01 86.4% 58.6%
4120506 243.11.1.4 ↗ a+b two layers › Cystatin-like › NP_346341.1 protein › NP_346341.1 protein › PF29632 0.60 50.0 4.65e-01 100.0% 90.0%
3593931 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 46.0 3.47e-01 88.1% 51.2%
5060529 375.1.3.3 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF5817 0.59 43.0 4.09e-01 79.7% 65.7%
3989019 1.1.7.19 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D2 0.59 42.0 3.49e-01 78.0% 54.5%
1161323 1.1.5.14 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Peptidase_S29 0.59 42.0 2.96e-01 76.3% 26.0%
3211769 376.1.6.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › IBR domain 0.58 49.0 4.88e-01 94.9% 93.3%
3512735 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.58 44.0 3.10e-01 88.1% 66.2%
3466459 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.57 45.0 3.52e-01 89.8% 59.3%
5025279 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 42.0 3.49e-01 81.4% 59.1%
3785886 1.1.5.18 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › FMN_bind_2 0.57 43.0 2.97e-01 81.4% 28.8%
4617429 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 45.0 4.64e-01 89.8% 98.2%
3436491 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.57 47.0 3.57e-01 100.0% 50.6%
4389625 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.56 43.0 4.45e-01 86.4% 96.4%
1489671 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.56 44.0 4.55e-01 89.8% 96.4%
3516743 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.56 43.0 3.17e-01 86.4% 48.8%
3605286 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.55 40.0 3.55e-01 83.1% 69.0%
5030549 375.1.3.1 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF1922 0.55 38.0 3.95e-01 78.0% 81.8%
3760926 227.1.1.12 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.55 46.0 3.63e-01 100.0% 50.4%
4947213 375.1.3.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 0.54 38.0 3.92e-01 78.0% 81.8%
4239498 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.54 42.0 4.31e-01 88.1% 100.0%
4032992 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.54 40.0 3.32e-01 81.4% 55.5%
3625037 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.54 45.0 3.58e-01 100.0% 52.6%
3507499 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.54 45.0 3.55e-01 100.0% 54.8%
4013297 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.53 40.0 2.89e-01 83.1% 69.7%
3772640 10.21.1.1 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.53 38.0 3.15e-01 79.7% 47.2%
4991529 375.1.3.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 0.53 38.0 3.79e-01 79.7% 76.7%
3528111 10.21.1.0 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 0.53 38.0 3.11e-01 79.7% 46.4%
3244229 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.52 44.0 3.58e-01 100.0% 52.0%
3254772 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.52 39.0 2.78e-01 86.4% 81.4%
3427234 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.52 43.0 2.97e-01 100.0% 90.2%
4120366 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.52 40.0 4.10e-01 88.1% 98.2%
5041477 375.1.3.3 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Hypothetical protein MTH1184 › DUF5817 0.52 36.0 3.66e-01 79.7% 76.7%
1563470 10.32.1.8 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CBM_4_9 0.52 44.0 3.16e-01 93.2% 51.5%
3406312 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.52 43.0 3.53e-01 100.0% 51.2%
4981108 375.1.1.331 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF5817 0.51 35.0 3.78e-01 78.0% 100.0%
3579802 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 36.0 3.27e-01 78.0% 55.3%
5057963 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.50 42.0 3.28e-01 100.0% 49.7%
3219185 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.50 37.0 2.86e-01 81.4% 78.6%