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NC_054725.1__YP_010059380.1__KHQ85_gp130__00130

Bact-Vir

NC_054725.1__YP_010059380.1__KHQ85_gp130__00130

Identity

Accession:
NC_054725 ↗
Kingdom:
phage

Quality

88.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Skogvirus› Gordonia_phage_Skog

TaxID: 2704033

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 16-81
PDB
Domain cluster: representative
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2fnqA02 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.65 51.0 3.10e-01 86.4% 66.3%
4zgfA00 2.40.128.270 Mainly Beta › Beta Barrel › Lipocalin › 0.59 46.0 3.68e-01 87.9% 67.4%
1qviA01 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.58 41.0 3.49e-01 81.8% 43.5%
5eriA00 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 0.57 45.0 3.51e-01 87.9% 60.8%
4djhA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 47.0 3.21e-01 100.0% 24.7%
4nreA02 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.56 48.0 2.91e-01 95.5% 15.4%
2fiaB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 40.0 3.05e-01 75.8% 67.9%
1loxA01 1.20.245.10 Mainly Alpha › Up-down Bundle › Lipoxygenase-1; domain 5 › Lipoxygenase-1; Domain 5 0.56 47.0 2.91e-01 95.5% 17.4%
3mhsA01 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.56 48.0 3.87e-01 95.5% 70.1%
2rdpA00 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 0.55 47.0 3.67e-01 93.9% 95.7%
4bqqB02 3.90.1750.20 Alpha Beta › Alpha-Beta Complex › Hect, E3 ligase catalytic domain fold › Putative Large Serine Recombinase; Chain B, Domain 2 0.55 42.0 3.10e-01 86.4% 50.5%
3g12B00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.54 24.0 2.06e-01 83.3% 20.4%
1p4xA01 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 0.54 45.0 3.69e-01 95.5% 80.3%
3akjA02 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.54 45.0 3.32e-01 98.5% 83.6%
5yuyA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.53 43.0 3.54e-01 89.4% 68.9%
1vkcA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.53 40.0 3.11e-01 80.3% 80.6%
2pdoA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.52 39.0 3.15e-01 80.3% 78.2%
4jndA02 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 43.0 2.94e-01 100.0% 73.0%
8d3mA02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.51 45.0 3.09e-01 100.0% 28.7%
7l9pK01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.51 36.0 2.97e-01 78.8% 41.2%
1k8kF00 3.30.1460.20 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.50 42.0 3.27e-01 100.0% 88.6%
3t5tB01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 45.0 2.94e-01 100.0% 41.8%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3827853 7579.1.1.6 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.75 43.0 2.79e-01 77.3% 14.1%
3954346 2006.1.6.15 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.75 41.0 2.58e-01 84.8% 12.2%
4303957 2006.1.6.15 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › DUF58 0.74 40.0 2.99e-01 84.8% 23.2%
3740226 5051.1.1.7 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Nramp 0.68 59.0 3.55e-01 98.5% 90.2%
4311291 109.4.1.2202 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27584, PF27595 0.67 54.0 2.97e-01 89.4% 8.9%
3170889 109.4.1.148 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › EST1_DNA_bind,EST1 0.66 59.0 3.40e-01 100.0% 31.3%
3881144 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.65 57.0 3.68e-01 100.0% 36.6%
3483955 386.1.1.6 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › ARS2 0.64 44.0 4.10e-01 72.7% 62.4%
3593362 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.64 56.0 5.09e-01 95.5% 74.1%
4155531 377.1.1.15 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › YacG 0.63 34.0 3.89e-01 71.2% 70.0%
3600149 1021.1.1.0 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases 0.63 41.0 3.57e-01 95.5% 45.0%
3863157 109.4.1.423 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PP4R3 0.62 50.0 2.98e-01 93.9% 22.0%
4929483 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.61 52.0 4.33e-01 97.0% 96.7%
4978596 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.60 51.0 4.21e-01 97.0% 88.0%
3932471 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.60 44.0 2.80e-01 78.8% 92.1%
3178364 319.1.1.19 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › PF29696 0.57 39.0 3.43e-01 72.7% 68.6%
3281159 4107.1.1.1 ↗ alpha arrays › Jann2411-like › Jann2411-like › Jann2411-like › ABATE,zf-CGNR 0.57 45.0 3.31e-01 86.4% 33.9%
5041715 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.57 48.0 4.12e-01 97.0% 90.9%
3925884 3226.1.1.3 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › HCO3_cotransp 0.56 46.0 2.74e-01 90.9% 12.6%
3168940 109.4.1.64 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › GET4 0.56 49.0 3.14e-01 98.5% 27.7%
3314358 1021.1.1.2 ↗ a+b two layers › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › C-terminal domain in RNA helicases › RNA_hel_CTD 0.56 40.0 3.73e-01 77.3% 71.8%
3506749 633.21.1.23 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CD20 0.55 46.0 3.51e-01 95.5% 38.2%
3287378 601.23.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III 0.55 42.0 2.96e-01 89.4% 81.2%
4026778 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.55 45.0 4.25e-01 89.4% 76.2%
3491910 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.54 47.0 4.52e-01 97.0% 94.7%
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 0.54 44.0 2.80e-01 89.4% 36.9%
3743505 213.1.1.1 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1 0.54 41.0 3.13e-01 80.3% 69.4%
5014365 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.52 44.0 2.72e-01 98.5% 56.4%
None — 0.52 41.0 3.06e-01 87.9% 50.3%
143476 2011.1.1.6 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M20 0.52 42.0 3.13e-01 89.4% 50.6%
3788807 4009.1.1.3 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › KTI12 0.52 43.0 3.79e-01 90.9% 86.3%
4025879 632.2.1.42 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › CLPTM1 0.51 44.0 3.41e-01 93.9% 42.8%
5043001 101.1.2.135 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2 0.51 41.0 3.56e-01 90.9% 77.1%
4997639 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 37.0 3.20e-01 78.8% 51.4%
3255441 376.1.1.5 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-UBP 0.50 44.0 3.51e-01 95.5% 73.6%
3331838 386.1.1.4 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-BED 0.50 30.0 3.35e-01 87.9% 78.0%
3570056 198.1.1.4 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › DUF3456 0.50 36.0 3.32e-01 75.8% 67.1%