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NC_025470.1__YP_009104174.1__S140_176__00173

Bact-Vir

NC_025470.1__YP_009104174.1__S140_176__00173

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

76.1 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 12-155
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1f1mA00 1.20.120.240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Lipoprotein, type 6 0.73 57.0 5.52e-01 82.6% 92.0%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.72 53.0 5.91e-01 76.4% 96.5%
2p7vA00 1.20.120.1370 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Regulator of RNA polymerase sigma(70) subunit, domain 4 0.69 56.0 5.60e-01 86.8% 94.0%
2e87A01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.68 53.0 5.18e-01 81.9% 93.1%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.68 54.0 5.59e-01 82.6% 95.5%
1zzpA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.68 48.0 5.38e-01 71.5% 96.3%
5cy5B00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.68 47.0 4.72e-01 70.8% 100.0%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.68 53.0 5.75e-01 85.4% 99.2%
5h5mA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 50.0 5.23e-01 76.4% 100.0%
1st6A04 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 47.0 5.16e-01 71.5% 100.0%
1qkrB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 56.0 5.19e-01 88.9% 82.8%
4w8pA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 51.0 5.38e-01 80.6% 96.2%
7yu4A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.66 55.0 4.55e-01 88.9% 85.6%
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.65 51.0 5.12e-01 81.9% 93.7%
2j9wB00 1.20.120.1130 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vps28 C-terminal domain 0.65 43.0 4.97e-01 84.7% 97.0%
2kbbA00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.64 51.0 4.78e-01 82.6% 73.6%
2kmfA01 1.20.58.810 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Photosystem II Pbs27 0.64 44.0 5.06e-01 77.1% 99.0%
2hz8A00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.63 48.0 5.28e-01 84.7% 100.0%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.63 51.0 5.42e-01 87.5% 96.9%
7akwA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.62 51.0 4.42e-01 88.2% 91.4%
3k29A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 33.0 3.17e-01 84.0% 45.3%
3ug9A02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.61 50.0 4.32e-01 87.5% 88.4%
6h2dS01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.60 41.0 3.60e-01 70.1% 95.5%
8etcb01 1.20.120.1190 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.59 48.0 4.81e-01 86.1% 97.9%
3f0cA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 44.0 4.45e-01 80.6% 87.5%
4dvyP03 1.20.120.1270 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CagA exotoxin domain III 0.57 47.0 4.56e-01 93.8% 78.0%
3pf0A00 1.20.1420.20 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › M75 peptidase, HXXE motif 0.57 49.0 3.80e-01 92.4% 98.1%
3kkbA00 1.20.120.880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Histidine kinase (KinB), sensor domain 0.56 44.0 4.68e-01 84.7% 92.9%
4fp4A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.56 50.0 4.27e-01 100.0% 96.3%
2fm8C01 1.10.4150.10 Mainly Alpha › Orthogonal Bundle › SipA N-terminal domain-like › SipA N-terminal domain-like 0.56 41.0 3.67e-01 75.0% 77.3%
1jfaB00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.56 49.0 3.74e-01 97.2% 64.0%
3lwjA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 38.0 3.53e-01 70.1% 59.1%
2np3A00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 39.0 3.98e-01 77.1% 74.6%
4g12A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 38.0 3.82e-01 71.5% 79.9%
3g7rA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 41.0 3.73e-01 80.6% 61.9%
1zk8B02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 37.0 3.88e-01 71.5% 80.3%
3syvA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 38.0 3.20e-01 75.7% 80.4%
3fppA03 6.10.140.1990 Special › Helix non-globular › Helix Hairpins › 0.52 30.0 3.78e-01 80.6% 93.2%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 38.0 4.23e-01 99.3% 98.2%
4hkaA01 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 45.0 3.59e-01 95.1% 81.3%
4kc9A02 1.20.120.1750 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.51 40.0 3.49e-01 83.3% 99.5%
6humG01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.50 38.0 3.69e-01 77.8% 77.5%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3415815 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.72 57.0 5.42e-01 82.6% 83.6%
4018342 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.70 49.0 5.53e-01 91.0% 93.6%
3393867 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.69 53.0 5.69e-01 80.6% 99.2%
3796225 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.69 52.0 5.56e-01 79.9% 91.2%
3966605 601.4.1.84 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › KinB_sensor 0.68 53.0 5.73e-01 85.4% 96.7%
3511227 601.15.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › Proteasome activator reg(alpha) › Proteasome activator reg(alpha) › PA28_C 0.68 53.0 4.83e-01 81.9% 94.7%
3247154 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.67 54.0 5.12e-01 88.2% 72.7%
3959788 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.67 48.0 5.01e-01 75.7% 79.3%
3303755 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.67 49.0 5.17e-01 76.4% 92.3%
4195415 3755.3.1.363 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › T1-F 0.67 47.0 5.05e-01 87.5% 84.0%
3593997 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.66 52.0 5.43e-01 95.1% 91.5%
4463061 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.66 48.0 5.30e-01 75.7% 100.0%
3275304 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.65 52.0 5.54e-01 84.0% 96.0%
3061928 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 51.0 4.66e-01 81.9% 91.5%
4399455 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.65 50.0 4.95e-01 81.9% 89.0%
3967393 601.4.1.3 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › 4HB_MCP_1 0.65 51.0 4.61e-01 84.0% 70.0%
3441289 3684.1.1.19 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › DUF1110 0.65 51.0 4.82e-01 84.0% 94.3%
3231243 4177.1.1.10 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › GMIP-like_FCH 0.64 45.0 3.59e-01 72.2% 84.5%
5038395 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.63 50.0 4.95e-01 83.3% 85.8%
3226092 5001.1.1.41 ↗ 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_Srw 0.63 52.0 4.06e-01 88.9% 89.1%
3411948 601.1.1.43 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Serendipity_A 0.63 48.0 5.16e-01 78.5% 97.5%
3327074 5001.1.1.122 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › PF27754 0.63 52.0 4.07e-01 88.2% 85.2%
3282142 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.63 53.0 5.31e-01 88.2% 91.0%
4145320 601.1.1.15 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › DUF697 0.63 54.0 4.72e-01 93.8% 62.3%
4137645 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.62 49.0 4.97e-01 81.9% 95.0%
4260979 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.61 30.0 2.46e-01 81.2% 24.5%
3596950 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.61 53.0 4.72e-01 96.5% 89.5%
4966374 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.60 33.0 3.14e-01 82.6% 45.1%
5035080 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.58 47.0 4.64e-01 91.7% 81.3%
3627226 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.57 41.0 3.71e-01 73.6% 92.0%
4284037 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.57 44.0 3.63e-01 81.9% 86.0%
3211541 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.57 48.0 4.19e-01 93.8% 68.3%
5005724 3755.3.1.637 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF7121 0.56 36.0 3.04e-01 100.0% 38.3%
4374346 3579.1.1.0 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J 0.53 39.0 3.95e-01 75.0% 76.4%
3435257 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 35.0 3.71e-01 91.7% 76.0%
3286634 109.3.1.160 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › EccD 0.52 45.0 3.47e-01 95.1% 62.1%
3532071 109.4.1.937 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_EDRF1 0.51 43.0 3.63e-01 88.9% 87.6%