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NC_028676.1__YP_009189569.1__AU106_gp184__00184

Bact-Vir

NC_028676.1__YP_009189569.1__AU106_gp184__00184

Identity

Accession:
NC_028676 ↗
Kingdom:
phage

Quality

80.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Emnonavirus› Sinorhizobium_phage_phiM9

TaxID: 1636182

Cluster

View cluster (12 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 medium residues 10-75
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cv8A00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.67 58.0 4.27e-01 97.0% 38.7%
2kebA00 1.10.8.530 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › DNA polymerase alpha-primase, subunit B, N-terminal domain 0.66 56.0 5.36e-01 100.0% 98.7%
3kzqA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.65 56.0 3.92e-01 95.5% 65.0%
6dx5A00 3.90.70.80 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.63 55.0 4.12e-01 100.0% 56.8%
6pw7A02 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.60 40.0 3.92e-01 90.9% 63.4%
2l4eA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.59 43.0 4.46e-01 100.0% 93.0%
3idwA00 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.58 40.0 4.05e-01 72.7% 80.3%
1kl9A02 1.10.150.190 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 0.57 43.0 3.94e-01 83.3% 83.7%
1ichA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.57 40.0 3.77e-01 77.3% 88.5%
2a19A02 1.10.150.190 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 0.57 43.0 4.01e-01 83.3% 74.1%
3kezA03 1.25.40.900 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 36.0 3.05e-01 80.3% 37.6%
2o71A00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.55 40.0 3.70e-01 80.3% 82.4%
2kruA01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.55 40.0 4.26e-01 83.3% 100.0%
6dftJ00 3.40.910.10 Alpha Beta › 3-Layer(aba) Sandwich › Deoxyhypusine Synthase › Deoxyhypusine synthase 0.55 48.0 3.09e-01 100.0% 38.0%
3um7A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 38.0 3.34e-01 83.3% 48.5%
1sxjE02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.54 43.0 4.41e-01 95.5% 100.0%
1nxuA01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.54 39.0 3.78e-01 84.8% 68.4%
3s6jE02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 36.0 3.63e-01 80.3% 71.0%
4bxoA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.52 35.0 3.55e-01 72.7% 80.6%
7t2sA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 39.0 3.02e-01 89.4% 45.7%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3398102 148.1.3.5 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Pol_alpha_B_N 0.73 62.0 5.87e-01 95.5% 92.5%
4015710 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.72 63.0 5.83e-01 100.0% 91.8%
4191032 101.1.9.16 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain › HTH_17 0.68 47.0 5.19e-01 75.8% 94.0%
4545640 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 50.0 4.63e-01 80.3% 63.5%
3228016 219.1.1.15 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU 0.66 58.0 4.35e-01 100.0% 55.8%
4027373 108.1.1.28 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 0.65 48.0 4.65e-01 78.8% 69.3%
5005163 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.64 54.0 5.10e-01 95.5% 86.3%
5068773 148.1.3.50 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Cdc6_lid 0.61 50.0 4.70e-01 97.0% 88.2%
5029742 148.1.3.50 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Cdc6_lid 0.59 48.0 4.55e-01 95.5% 88.2%
4932585 148.1.3.50 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Cdc6_lid 0.59 48.0 4.72e-01 97.0% 100.0%
4134768 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.58 46.0 4.56e-01 90.9% 97.1%
4528489 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.51 38.0 3.39e-01 80.3% 83.2%
D2 medium residues 76-164
PDB
Domain cluster: rep: OX241576.1__CAH9016897.1__VP193E371_P0087__00087__D73-154
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wfpA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 38.0 3.73e-01 89.9% 54.1%
1y9qA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 40.0 3.98e-01 94.4% 61.3%
1g8kA04 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.60 42.0 3.66e-01 73.0% 89.6%
4el6A00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.58 42.0 4.11e-01 92.1% 69.1%
4jzjC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 38.0 4.20e-01 95.5% 87.1%
1xjaB00 2.60.120.280 Mainly Beta › Sandwich › Jelly Rolls › Regulatory protein AraC 0.56 39.0 3.25e-01 95.5% 40.9%
3pgvA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.55 41.0 4.00e-01 94.4% 71.3%
1yd0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.55 38.0 3.83e-01 70.8% 78.7%
1vajA02 3.30.1490.150 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Hypothetical protein ph0010; domain 2 0.54 41.0 4.40e-01 89.9% 100.0%
3sumB00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.53 43.0 3.79e-01 88.8% 96.3%
2yn3B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 34.0 3.76e-01 96.6% 81.7%
2ki8A01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.53 42.0 3.83e-01 87.6% 88.8%
4e2oA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 35.0 3.60e-01 89.9% 72.7%
1a3wB03 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.51 38.0 3.76e-01 79.8% 94.8%
2w3sA04 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.51 45.0 4.11e-01 95.5% 92.1%
2rftA02 3.90.209.20 Alpha Beta › Alpha-Beta Complex › Hemagglutinin (Ha1 Chain); Chain: A; domain 1 › Haemagglutinin, alpha/beta domain, HA1 chain 0.51 43.0 3.17e-01 93.3% 67.4%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.51 35.0 2.90e-01 74.2% 84.7%
4jcwA01 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.51 42.0 3.98e-01 89.9% 100.0%
1loxA02 2.60.60.20 Mainly Beta › Sandwich › Lipoxygenase-1 › PLAT/LH2 domain 0.50 35.0 3.33e-01 73.0% 64.0%
5l0qB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 41.0 3.92e-01 92.1% 87.0%
4n2kA01 2.60.40.1860 Mainly Beta › Sandwich › Immunoglobulin-like › Protein-arginine deiminase, N-terminal domain 0.50 44.0 4.01e-01 97.8% 79.0%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4930010 1.1.7.141 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MazE_antitoxin 0.60 52.0 5.12e-01 96.6% 92.6%
4125814 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.57 44.0 4.75e-01 94.4% 97.3%
4338601 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.57 43.0 4.35e-01 94.4% 80.0%
3515326 10.10.1.0 ↗ beta sandwiches › jelly-roll › Lipase/lipooxygenase domain (PLAT/LH2 domain) › Lipase/lipooxygenase domain (PLAT/LH2 domain) 0.54 38.0 3.31e-01 73.0% 78.5%
3610841 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 38.0 2.42e-01 75.3% 24.4%
2163476 1053.1.1.1 ↗ beta barrels › Factor H-binding protein (fHbp) N-terminal beta-barrel domain › Factor H-binding protein (fHbp) N-terminal beta-barrel domain › Factor H-binding protein (fHbp) N-terminal beta-barrel domain › FHBP_N 0.53 37.0 3.20e-01 73.0% 78.5%
5040464 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.52 42.0 4.15e-01 88.8% 100.0%
3399412 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.52 33.0 3.49e-01 92.1% 72.5%
3672526 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 42.0 3.82e-01 92.1% 95.2%
4115281 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.51 41.0 3.77e-01 87.6% 99.2%
3877800 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 42.0 3.95e-01 92.1% 76.4%
5022491 4.1.1.182 ↗ beta barrels › SH3 › SH3 › SH3 › DUF2097 0.51 41.0 4.25e-01 95.5% 95.3%
5017161 4.1.1.182 ↗ beta barrels › SH3 › SH3 › SH3 › DUF2097 0.50 42.0 4.32e-01 98.9% 98.8%