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NC_070916.1__YP_010664323.1__PQA68_gp08__00008

Bact-Vir

NC_070916.1__YP_010664323.1__PQA68_gp08__00008

Identity

Accession:
NC_070916 ↗
Kingdom:
phage

Quality

86.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Peduoviridae› Duonihilunusvirus› Yersinia_phage_vB_YenM_06.16-2

TaxID: 2918920

Cluster

View cluster (33 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 4-92
PDB
Domain cluster: rep: GQ478086.1__ACZ64040.1__X__00021__D3-94
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF17399.8 best DUF5405 37.3 4.10e-09 100.0% 87.5%
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gccA00 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.66 43.0 4.91e-01 89.9% 92.1%
4fxdA05 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.64 37.0 3.34e-01 100.0% 43.6%
1lyvA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.62 56.0 3.91e-01 100.0% 69.6%
3ub8A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.62 37.0 3.09e-01 82.0% 33.8%
6krwA01 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.59 52.0 3.64e-01 98.9% 63.3%
1p1jA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.57 37.0 3.44e-01 96.6% 51.3%
4kz1A00 3.10.450.230 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › VirB8 protein 0.57 33.0 2.91e-01 95.5% 37.8%
5iu1B00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 36.0 3.42e-01 89.9% 51.8%
6d92A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 47.0 3.52e-01 96.6% 77.0%
5dynA01 3.40.50.11970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 48.0 4.56e-01 98.9% 82.1%
1vwxr00 3.30.390.110 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.54 47.0 4.27e-01 100.0% 71.2%
4uf7B00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.54 48.0 3.10e-01 100.0% 67.7%
3a7rA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.53 44.0 4.41e-01 98.9% 94.4%
4ibnA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 43.0 3.49e-01 95.5% 70.7%
4k3yC00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.52 42.0 2.81e-01 88.8% 50.7%
1v3eA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.51 46.0 2.94e-01 100.0% 50.1%
1ntyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 46.0 4.14e-01 100.0% 75.0%
1b7eA01 3.90.350.10 Alpha Beta › Alpha-Beta Complex › Transposase Inhibitor Protein From Tn5; Chain A, domain 1 › Transposase Inhibitor Protein From Tn5; Chain A, domain 1 0.51 43.0 3.19e-01 95.5% 41.9%
4bg7A00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.51 41.0 4.04e-01 91.0% 85.7%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.50 39.0 3.49e-01 86.5% 84.4%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3945393 7089.1.1.2 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › DUF5405 0.89 77.0 8.13e-01 94.4% 100.0%
4436313 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.68 49.0 4.93e-01 75.3% 77.8%
4936022 296.1.1.1 ↗ a+b three layers › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 › NIR_SIR 0.67 48.0 4.08e-01 74.2% 79.3%
3684699 7516.1.1.41 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glucan_synthase 0.64 52.0 3.26e-01 88.8% 57.6%
3664107 192.18.1.0 ↗ alpha bundles › Long alpha-hairpin › MxiH-like › MxiH-like 0.60 44.0 2.55e-01 76.4% 34.1%
5056218 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.59 43.0 4.74e-01 83.1% 97.1%
3206632 896.1.1.2 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › SRP14 0.59 40.0 4.09e-01 75.3% 72.9%
3328840 284.1.2.0 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases 0.58 44.0 4.50e-01 95.5% 84.7%
3342794 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.57 44.0 4.46e-01 96.6% 84.4%
4116893 7504.1.1.2 ↗ a/b three-layered sandwiches › ITPase-like › ITPase-like › ITPase-like › NTPase_I-T 0.57 39.0 3.22e-01 73.0% 80.0%
3707549 5.1.3.28 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › BNR_3 0.56 47.0 3.12e-01 95.5% 48.4%
3255279 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.55 44.0 2.86e-01 87.6% 36.6%
3409738 295.1.1.4 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain 0.55 35.0 3.95e-01 74.2% 89.2%
3317450 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 38.0 3.54e-01 71.9% 67.3%
3618860 223.1.1.29 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_11 0.54 37.0 3.25e-01 70.8% 55.7%
3216163 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 40.0 3.96e-01 78.7% 84.2%
3917310 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.54 36.0 3.99e-01 77.5% 95.4%
4015062 210.1.1.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits 0.54 47.0 3.45e-01 100.0% 63.9%
3952404 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.53 45.0 3.85e-01 95.5% 67.3%
4998983 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.53 39.0 2.40e-01 78.7% 59.8%
3453242 192.18.1.0 ↗ alpha bundles › Long alpha-hairpin › MxiH-like › MxiH-like 0.53 44.0 2.83e-01 95.5% 22.1%
3808306 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.53 45.0 3.10e-01 94.4% 97.5%
4958656 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 44.0 3.13e-01 95.5% 33.6%
3710325 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 36.0 3.77e-01 70.8% 93.8%
4958380 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 44.0 3.14e-01 94.4% 36.4%
4643206 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 43.0 3.53e-01 95.5% 55.6%
None — 0.52 43.0 2.88e-01 95.5% 68.3%
3986557 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 43.0 4.07e-01 96.6% 87.8%
4959188 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 43.0 3.43e-01 95.5% 50.0%
4370765 5.1.3.48 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Gmad1 0.52 47.0 3.27e-01 100.0% 47.9%
4530535 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.52 43.0 3.06e-01 94.4% 33.3%
3467186 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 43.0 2.77e-01 95.5% 20.6%
3756543 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.51 43.0 3.55e-01 93.3% 61.8%
3222389 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.51 44.0 3.36e-01 100.0% 67.7%
3382312 192.18.1.0 ↗ alpha bundles › Long alpha-hairpin › MxiH-like › MxiH-like 0.51 42.0 3.07e-01 95.5% 30.0%
3239000 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.51 35.0 3.21e-01 73.0% 92.3%
3347628 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 42.0 3.13e-01 95.5% 40.8%
3338071 2484.1.1.215 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27041 0.51 41.0 3.39e-01 89.9% 50.9%
4417589 2484.1.1.199 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Transposase_mut 0.50 43.0 3.50e-01 96.6% 55.0%
3427901 2484.1.1.215 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27041 0.50 43.0 3.25e-01 95.5% 50.2%
3433324 5.1.3.68 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF1618 0.50 44.0 2.96e-01 100.0% 84.0%
3925547 2484.1.1.157 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.50 42.0 3.35e-01 95.5% 51.8%
3212863 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.50 44.0 3.08e-01 100.0% 76.3%