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NC_020877.1__YP_007677608.1__QLX36_gp104__00104

Bact-Vir

NC_020877.1__YP_007677608.1__QLX36_gp104__00104

Identity

Accession:
NC_020877 ↗
Kingdom:
phage

Quality

92.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Silviavirus› Staphylococcus_phage_vB_SauM_Romulus

TaxID: 1235660

Cluster

View cluster (4 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 2-48
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3puaA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.74 53.0 3.19e-01 97.9% 12.6%
4bwxA03 1.10.287.3700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 51.0 4.36e-01 89.4% 78.8%
3wt0A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 50.0 3.63e-01 95.7% 38.1%
1g5hB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.62 54.0 4.18e-01 100.0% 67.3%
4xr7F02 1.10.287.3700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 47.0 3.92e-01 87.2% 66.7%
3pvlA05 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 50.0 4.42e-01 97.9% 77.6%
1qe0A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.61 50.0 4.17e-01 100.0% 80.2%
4m4zA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.60 49.0 4.91e-01 89.4% 100.0%
1nj1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.60 51.0 4.00e-01 100.0% 66.3%
5i4eA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.59 46.0 4.73e-01 85.1% 91.3%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.59 48.0 4.59e-01 89.4% 83.3%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 42.0 3.26e-01 93.6% 34.0%
2q5iA03 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.58 48.0 3.69e-01 100.0% 58.7%
4wi1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.58 49.0 3.68e-01 100.0% 56.9%
4a2aA04 3.90.640.10 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 0.58 44.0 4.16e-01 93.6% 92.3%
1lckA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 46.0 4.32e-01 89.4% 91.5%
3netB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.58 49.0 3.96e-01 100.0% 70.4%
2kxcA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 46.0 4.16e-01 91.5% 86.6%
1adjB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 48.0 3.91e-01 100.0% 72.3%
5xilA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 47.0 3.56e-01 100.0% 55.5%
1httA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.57 47.0 3.85e-01 100.0% 72.4%
2i4lB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.56 47.0 3.79e-01 100.0% 68.3%
2yrvA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 50.0 3.74e-01 100.0% 53.1%
2j3lA01 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.56 46.0 3.64e-01 100.0% 60.2%
1khcA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 50.0 4.49e-01 100.0% 87.7%
1uebA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 42.0 3.85e-01 83.0% 82.5%
2lw7A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.56 45.0 3.57e-01 100.0% 61.4%
1r5tA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.55 39.0 2.84e-01 76.6% 69.5%
1juvA00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.55 42.0 2.96e-01 93.6% 39.4%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 47.0 4.11e-01 100.0% 67.1%
2diqA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 47.0 3.72e-01 100.0% 52.0%
4ljiB00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.53 35.0 2.61e-01 100.0% 23.7%
3f8dA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 42.0 3.23e-01 95.7% 98.4%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.53 40.0 3.85e-01 100.0% 71.9%
4divV01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.52 38.0 2.88e-01 85.1% 85.4%
1fl2A02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 39.0 3.09e-01 95.7% 98.4%
1fvuB00 3.10.100.10 Alpha Beta › Roll › Mannose-Binding Protein A; Chain A › Mannose-Binding Protein A, subunit A 0.51 43.0 3.28e-01 100.0% 73.6%
2kqrA01 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.50 37.0 3.35e-01 87.2% 77.0%
4m0hA01 2.60.120.1440 Mainly Beta › Sandwich › Jelly Rolls › 0.50 39.0 2.97e-01 95.7% 82.0%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3592370 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.81 71.0 5.29e-01 100.0% 43.3%
3598807 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.81 71.0 6.25e-01 100.0% 78.3%
3712524 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.79 57.0 5.45e-01 78.7% 78.2%
3605531 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.79 68.0 5.67e-01 100.0% 65.5%
4778018 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.65 51.0 4.28e-01 87.2% 73.2%
2321219 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.63 53.0 3.89e-01 97.9% 57.5%
4562754 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.63 53.0 4.27e-01 100.0% 77.0%
3514631 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.63 52.0 3.97e-01 100.0% 78.2%
3739884 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.63 52.0 3.94e-01 100.0% 70.5%
4163844 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.62 51.0 4.25e-01 100.0% 73.7%
3489207 221.4.1.1 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX 0.62 51.0 3.19e-01 95.7% 60.1%
5081385 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.62 54.0 3.16e-01 100.0% 16.2%
4969848 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.62 49.0 3.71e-01 91.5% 69.2%
2321841 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.62 51.0 3.78e-01 100.0% 64.1%
4532648 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.61 52.0 4.17e-01 100.0% 67.7%
3843756 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.61 47.0 3.79e-01 91.5% 43.2%
3170397 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.60 49.0 4.16e-01 91.5% 76.2%
4439755 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.60 50.0 4.04e-01 100.0% 73.0%
3164004 2484.1.1.245 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA, PilM_2, FtsA 0.60 46.0 2.83e-01 97.9% 15.9%
4299923 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 51.0 4.20e-01 100.0% 77.5%
5029138 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 50.0 4.12e-01 100.0% 76.7%
3566431 389.1.2.1 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.59 47.0 4.50e-01 97.9% 81.7%
4130309 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 50.0 4.19e-01 100.0% 82.4%
4462675 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 50.0 4.03e-01 100.0% 70.4%
4570210 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.59 50.0 4.05e-01 100.0% 73.7%
4947286 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.59 49.0 3.80e-01 100.0% 59.1%
4427469 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 48.0 3.57e-01 97.9% 92.6%
4595963 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.58 49.0 4.00e-01 100.0% 71.6%
3314214 7502.1.1.7 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon2 0.58 49.0 3.84e-01 100.0% 64.5%
4011699 4224.1.1.0 ↗ few secondary structure elements › CHY zinc finger › CHY zinc finger › CHY zinc finger 0.58 40.0 3.74e-01 74.5% 75.0%
4381621 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 48.0 3.26e-01 100.0% 35.9%
4419877 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 48.0 3.63e-01 100.0% 55.2%
3628455 109.4.1.102 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › WAPL 0.57 50.0 2.84e-01 100.0% 12.8%
4238930 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 48.0 3.87e-01 100.0% 77.0%
4932528 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 48.0 4.02e-01 100.0% 75.6%
5080553 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 47.0 3.87e-01 100.0% 70.4%
4240279 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 48.0 3.70e-01 100.0% 60.0%
4125289 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 47.0 3.88e-01 100.0% 73.4%
4394756 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 47.0 3.79e-01 100.0% 68.0%
4683191 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.57 47.0 3.82e-01 100.0% 73.0%
4469100 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.56 47.0 3.84e-01 97.9% 77.7%
4994848 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.56 47.0 3.77e-01 100.0% 68.6%
4068744 875.1.1.1 ↗ a+b two layers › Chorismate synthase, AroC › Chorismate synthase, AroC › Chorismate synthase, AroC › Chorismate_synt 0.56 43.0 2.60e-01 89.4% 82.7%
4381486 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.56 44.0 3.69e-01 91.5% 100.0%
4528204 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.56 45.0 3.71e-01 100.0% 73.0%
4345074 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.55 45.0 3.67e-01 100.0% 67.0%
4054592 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.55 45.0 3.67e-01 100.0% 68.0%
4046713 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.54 46.0 3.80e-01 100.0% 76.7%
3255317 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 38.0 3.89e-01 76.6% 97.8%
3976043 209.1.1.6 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › InvE_AD 0.54 46.0 3.33e-01 97.9% 53.3%
4315674 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.54 44.0 3.66e-01 100.0% 71.6%
3296910 386.1.1.207 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED_2 0.54 38.0 3.98e-01 89.4% 85.0%
5060760 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.53 43.0 4.02e-01 100.0% 78.5%
3693567 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.53 35.0 2.91e-01 95.7% 34.4%
3920343 209.1.1.1 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › Lectin_C 0.52 43.0 3.15e-01 100.0% 70.0%
4547689 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.52 43.0 3.62e-01 100.0% 61.1%
3211001 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.52 41.0 3.46e-01 95.7% 65.6%
4639808 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.52 42.0 3.57e-01 100.0% 81.1%
4286261 875.1.1.1 ↗ a+b two layers › Chorismate synthase, AroC › Chorismate synthase, AroC › Chorismate synthase, AroC › Chorismate_synt 0.51 39.0 2.41e-01 93.6% 67.6%
4608282 2484.1.1.70 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.51 40.0 2.45e-01 93.6% 15.3%
3188771 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.51 40.0 2.56e-01 91.5% 18.4%
D2 high residues 62-180
PDB
Domain cluster: rep: LacPavin_0818_WC40_scaffold_193576_prodigal-single.1__X__X__00294__D106-220