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NC_070789.1__YP_010652762.1__PP485_gp62__00062

Bact-Vir

NC_070789.1__YP_010652762.1__PP485_gp62__00062

Identity

Accession:
NC_070789 ↗
Kingdom:
phage

Quality

95.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nymphadoravirus› Gordonia_phage_ThankyouJordi

TaxID: 2571252

Cluster

View cluster (66 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 6-109
PDB
Domain cluster: rep: LacPavin_0818_WC55_scaffold_56344_prodigal-single.1__X__X__00048__D3-131
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.83 76.0 6.84e-01 100.0% 73.2%
2qxfA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.81 76.0 6.09e-01 100.0% 56.8%
4fzxC00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.78 65.0 5.47e-01 98.1% 55.8%
3ge2A00 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.58 33.0 3.51e-01 100.0% 64.0%
3cetB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 42.0 4.13e-01 100.0% 72.7%
1ci3M02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.56 29.0 3.72e-01 100.0% 87.9%
3n8bA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 29.0 3.42e-01 100.0% 73.3%
3t69A01 3.30.420.300 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, substrate binding domain 0.54 36.0 4.15e-01 94.2% 96.0%
3h51A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 31.0 2.82e-01 99.0% 43.0%
2d42A02 3.10.450.380 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 26.0 3.21e-01 100.0% 73.8%
5aguA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 30.0 2.85e-01 100.0% 46.0%
2yx6D01 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.50 35.0 3.60e-01 100.0% 75.5%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3988496 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.85 77.0 5.92e-01 100.0% 46.5%
4640906 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 77.0 6.11e-01 100.0% 51.8%
3280151 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 77.0 6.21e-01 100.0% 54.6%
5007230 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 77.0 6.10e-01 100.0% 51.8%
4033087 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 77.0 5.85e-01 100.0% 45.9%
4052322 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.84 77.0 6.13e-01 100.0% 53.2%
4037317 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.83 77.0 5.96e-01 100.0% 49.3%
4103309 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.83 76.0 5.90e-01 100.0% 48.1%
4176714 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.82 76.0 5.94e-01 100.0% 50.5%
1501363 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.81 77.0 4.84e-01 100.0% 23.3%
3941572 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.81 76.0 5.21e-01 100.0% 33.1%
4044377 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.81 76.0 4.79e-01 100.0% 23.2%
3947357 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.80 71.0 5.78e-01 100.0% 53.6%
5062283 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.80 75.0 5.89e-01 100.0% 52.0%
3942728 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.79 71.0 5.52e-01 100.0% 47.1%
3893443 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.79 75.0 5.68e-01 100.0% 48.6%
3988431 2484.1.1.13 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.78 70.0 5.72e-01 99.0% 55.0%
4290521 2484.1.1.91 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Exu_RNase_H_like 0.77 72.0 5.21e-01 100.0% 45.3%
4981192 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.76 58.0 4.23e-01 100.0% 32.2%
4028087 2484.1.1.20 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_A_exo1 0.66 50.0 3.95e-01 99.0% 38.6%
3383138 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.65 31.0 3.62e-01 94.2% 61.5%
5023018 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.65 59.0 4.67e-01 100.0% 51.0%
1148160 2484.1.1.23 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydantoinase_A 0.64 41.0 4.07e-01 98.1% 61.8%
4378664 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 50.0 3.72e-01 99.0% 36.2%
3719687 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 31.0 3.59e-01 93.3% 76.0%
4432262 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.54 31.0 2.96e-01 100.0% 49.2%
4648475 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.53 25.0 3.15e-01 91.3% 75.0%
4943476 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 47.0 3.47e-01 99.0% 53.8%
4325314 2004.1.1.100 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NTPase_1 0.52 38.0 3.25e-01 100.0% 46.2%
4159881 220.1.1.197 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF28623 0.52 35.0 3.67e-01 97.1% 74.7%
3313644 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.51 42.0 4.27e-01 100.0% 88.6%
4409039 2008.1.1.207 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_7 0.51 38.0 2.95e-01 77.9% 67.3%
D2 high residues 123-187
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ljcA02 1.20.58.1480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 57.0 4.61e-01 100.0% 57.1%
1kblA05 1.20.80.30 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.63 50.0 4.46e-01 100.0% 61.8%
2z3xA00 6.10.10.80 Special › Helix non-globular › Helicase, Ruva Protein; domain 3 › Small, acid-soluble spore protein, alpha/beta type-like 0.60 44.0 4.67e-01 100.0% 91.1%
2ph5A02 3.30.360.30 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › homospermidine synthase like 0.57 50.0 3.27e-01 100.0% 85.5%
3rq4A01 1.10.10.1700 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Histone-lysine N-methyltransferase 0.57 38.0 3.35e-01 89.2% 45.9%
1o3uA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.57 48.0 4.03e-01 100.0% 70.8%
2gk6A03 6.10.140.1240 Special › Helix non-globular › Helix Hairpins › 0.56 39.0 4.35e-01 81.5% 96.0%
4ev6A03 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.55 38.0 3.99e-01 90.8% 81.0%
1ivyB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 45.0 2.73e-01 92.3% 54.7%
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 45.0 4.22e-01 100.0% 73.2%
4ht4A00 3.30.930.30 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › 0.54 48.0 3.43e-01 100.0% 91.2%
1v1gA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 43.0 3.15e-01 100.0% 30.9%
2q9rA01 1.20.1590.10 Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like 0.54 46.0 3.32e-01 98.5% 53.8%
1uj8A00 1.10.10.600 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › IscX-like 0.53 34.0 3.34e-01 95.4% 57.5%
2p6pB01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.53 47.0 3.29e-01 100.0% 98.1%
3lxrF00 1.10.4120.20 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › 0.53 43.0 3.13e-01 89.2% 63.5%
4wxmB00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 46.0 3.72e-01 100.0% 96.9%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.52 42.0 2.70e-01 100.0% 38.0%
2kvcA01 1.10.150.430 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF3349, helical bundle 0.51 38.0 3.43e-01 80.0% 100.0%
3vkgA15 1.10.8.1220 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.50 42.0 3.83e-01 100.0% 80.9%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4021489 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.66 45.0 3.12e-01 70.8% 28.1%
3876480 3860.1.1.0 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm 0.62 42.0 3.20e-01 70.8% 32.0%
3201652 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.60 40.0 4.26e-01 95.4% 80.0%
3597463 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.59 37.0 3.49e-01 73.8% 51.2%
3702686 3525.1.1.0 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain 0.57 44.0 4.47e-01 98.5% 83.1%
4266989 7111.1.1.1 ↗ alpha bundles › Ubiquinol-cytochrome C chaperone, C-terminal domain › Ubiquinol-cytochrome C chaperone, C-terminal domain › Ubiquinol-cytochrome C chaperone, C-terminal domain › Ubiq_cyt_C_chap 0.55 41.0 3.09e-01 100.0% 32.1%
3400531 197.1.1.1 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › FERM_M 0.55 49.0 4.00e-01 100.0% 86.7%
5000686 862.1.1.1 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.54 42.0 2.79e-01 86.2% 21.1%
4117418 144.1.1.1 ↗ alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.54 42.0 4.37e-01 100.0% 96.7%
4967739 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.54 39.0 3.51e-01 76.9% 92.2%
3507024 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.52 45.0 2.91e-01 96.9% 92.0%
3638493 601.16.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase 0.52 41.0 3.06e-01 84.6% 73.1%
4951056 1085.1.1.1 ↗ few secondary structure elements › Archaea X-group 1085 › Archaea H-group 1085.1 › Archaea T-group 1085.1.1 › DHH_CID 0.51 46.0 4.19e-01 100.0% 89.4%
3213202 102.1.1.2 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › HRDC 0.51 39.0 3.58e-01 86.2% 93.3%
3369385 4070.1.1.1 ↗ alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like › Peptidase_M41 0.50 42.0 3.00e-01 93.8% 35.2%