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NC_031004.1__YP_009277932.1__BIZ68_gp14__00014

Bact-Vir

NC_031004.1__YP_009277932.1__BIZ68_gp14__00014

Identity

Accession:
NC_031004 ↗
Kingdom:
phage

Quality

83.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nyceiraevirus› Gordonia_phage_Nyceirae

TaxID: 1887651

Cluster

View cluster (247 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 57-124
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2jiiA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.75 47.0 3.95e-01 79.4% 39.1%
1p97A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.68 59.0 5.07e-01 100.0% 96.5%
4f3lA03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.65 54.0 4.58e-01 95.6% 87.7%
3rtyB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.65 52.0 4.55e-01 91.2% 99.1%
2vlgC00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.63 52.0 4.59e-01 92.6% 100.0%
3mcaA03 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.61 51.0 4.52e-01 94.1% 62.7%
2v0uA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.61 48.0 3.83e-01 88.2% 72.6%
4m4xA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.61 49.0 4.07e-01 91.2% 89.7%
2z6cA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.61 49.0 4.13e-01 91.2% 90.9%
5iu1B00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.60 48.0 4.16e-01 89.7% 91.1%
5ejlA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.60 51.0 4.25e-01 97.1% 83.1%
6pzjA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.60 47.0 3.78e-01 91.2% 77.0%
4r3aA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.59 48.0 3.70e-01 95.6% 62.5%
5svgC00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 48.0 4.15e-01 98.5% 99.2%
1go3E02 3.30.1490.120 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RNA polymerase Rpb7-like, N-terminal domain 0.58 48.0 4.55e-01 92.6% 90.1%
1bywA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 46.0 4.06e-01 92.6% 100.0%
7d58G01 3.30.1490.120 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RNA polymerase Rpb7-like, N-terminal domain 0.57 48.0 4.74e-01 97.1% 98.7%
1lfwA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 47.0 4.17e-01 95.6% 76.4%
3h9wA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 46.0 4.02e-01 92.6% 97.2%
2kr7A02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.57 40.0 4.22e-01 89.7% 91.2%
1nyrB02 3.30.980.10 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › Threonyl-trna Synthetase; Chain A, domain 2 0.57 45.0 3.59e-01 91.2% 97.3%
4hiaA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 43.0 3.32e-01 86.8% 60.2%
6kjuB01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 44.0 3.82e-01 91.2% 91.5%
3mr0A01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 44.0 3.88e-01 91.2% 91.8%
3sm3A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 47.0 3.32e-01 94.1% 45.3%
3fhwA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 38.0 3.42e-01 72.1% 98.0%
4mn5A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 43.0 3.87e-01 89.7% 90.3%
3pfeA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 44.0 3.74e-01 95.6% 76.2%
5uejA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 46.0 3.97e-01 98.5% 78.9%
3exzB00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.54 39.0 3.16e-01 80.9% 87.1%
4acvA00 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.54 43.0 3.71e-01 94.1% 60.5%
6lynD01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 37.0 3.50e-01 98.5% 58.6%
2iw3A05 2.40.50.990 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 39.0 3.37e-01 79.4% 50.5%
2h2qB01 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.53 40.0 2.89e-01 94.1% 26.9%
3ct9A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 44.0 3.88e-01 98.5% 83.2%
5k8mA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 45.0 3.69e-01 98.5% 80.9%
2cc6A00 3.30.1660.10 Alpha Beta › 2-Layer Sandwich › Dodecin subunit-like › Flavin-binding protein dodecin 0.52 41.0 4.22e-01 94.1% 96.9%
1cg2A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 43.0 3.80e-01 98.5% 75.5%
2ku7A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.52 42.0 3.44e-01 98.5% 45.7%
2rb7A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 43.0 3.81e-01 98.5% 81.3%
2hzmG01 3.30.310.180 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.51 43.0 3.71e-01 98.5% 71.3%
4k02A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.50 35.0 2.94e-01 73.5% 84.3%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4932654 284.4.1.1 ↗ a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain › FKBP26_IF 0.68 47.0 5.22e-01 91.2% 96.0%
4950576 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.66 57.0 4.48e-01 97.1% 76.6%
4950249 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.66 54.0 4.64e-01 91.2% 96.4%
4973551 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.66 55.0 4.58e-01 95.6% 88.0%
4951779 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.65 56.0 4.69e-01 97.1% 92.5%
3965192 1.1.13.67 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › DUF2460 0.65 54.0 4.61e-01 94.1% 86.8%
5003154 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.65 55.0 4.51e-01 95.6% 87.2%
4379553 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.64 53.0 4.36e-01 94.1% 81.5%
3484132 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.64 53.0 4.07e-01 95.6% 80.6%
4977960 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.63 54.0 3.12e-01 97.1% 17.2%
3967163 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.63 53.0 4.35e-01 95.6% 81.5%
5060588 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.63 53.0 4.52e-01 97.1% 87.5%
4999858 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.63 54.0 3.80e-01 97.1% 47.7%
4980675 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.63 53.0 4.49e-01 97.1% 93.3%
4930505 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.63 51.0 4.44e-01 92.6% 95.5%
3995035 223.1.1.29 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_11 0.63 54.0 4.23e-01 100.0% 71.6%
4960098 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.63 51.0 4.33e-01 92.6% 87.5%
4949125 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.63 54.0 4.22e-01 98.5% 73.3%
4945265 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.62 51.0 4.37e-01 94.1% 92.2%
4977587 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.62 51.0 4.31e-01 94.1% 89.2%
3946851 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.61 48.0 3.83e-01 91.2% 69.0%
3215667 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.61 41.0 3.47e-01 70.6% 89.2%
4077998 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.61 47.0 3.92e-01 88.2% 83.1%
3315652 243.5.1.1 ↗ a+b two layers › Cystatin-like › Amine oxidase N-terminal region › Amine oxidase N-terminal region › Cu_amine_oxidN2 0.60 42.0 3.47e-01 75.0% 63.8%
3521712 109.6.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF 0.60 43.0 2.79e-01 92.6% 15.0%
3175408 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.60 49.0 3.19e-01 94.1% 28.5%
3536617 223.1.1.29 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_11 0.60 48.0 4.03e-01 94.1% 86.9%
4938887 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.59 46.0 3.85e-01 91.2% 80.7%
4960006 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.59 50.0 4.34e-01 98.5% 69.7%
5002211 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.58 47.0 4.06e-01 92.6% 93.9%
3280248 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.58 46.0 3.86e-01 94.1% 82.2%
4961959 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.58 45.0 3.97e-01 89.7% 85.5%
4958534 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.58 46.0 4.30e-01 92.6% 100.0%
4930499 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.57 45.0 3.18e-01 89.7% 43.8%
4014614 223.1.1.24 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_8 0.57 47.0 3.77e-01 95.6% 80.0%
5034547 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.57 47.0 3.82e-01 95.6% 77.9%
3297973 4957.1.1.6 ↗ a+b complex topology › helical domain in yeast RNA-polymerases › third helical domain in yeast RNA-polymerase II beta-prime subunit › third helical domain in yeast RNA-polymerase II beta-prime subunit › PF31063 0.56 44.0 3.23e-01 92.6% 91.9%
3744748 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.56 49.0 4.41e-01 98.5% 74.7%
3798057 304.18.1.0 ↗ a+b two layers › Alpha-beta plaits › Anticodon-binding domain of PheRS › Anticodon-binding domain of PheRS 0.56 48.0 4.16e-01 98.5% 67.3%
3596773 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 46.0 3.83e-01 97.1% 86.2%
3513835 223.2.1.22 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Folliculin 0.55 46.0 3.48e-01 95.6% 58.9%
3625017 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 42.0 3.65e-01 83.8% 67.3%
3259208 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.55 45.0 3.77e-01 95.6% 66.9%
3795154 304.25.1.0 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain 0.55 47.0 4.08e-01 95.6% 71.4%
3740338 11.1.1.915 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF26111 0.54 44.0 3.63e-01 92.6% 57.7%
3224219 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 42.0 3.29e-01 91.2% 58.2%
3696704 11.1.1.915 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF26111 0.54 44.0 3.62e-01 92.6% 56.2%
4984209 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.53 45.0 3.82e-01 98.5% 75.0%
4961641 223.1.1.24 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_8 0.53 42.0 3.72e-01 92.6% 84.5%
4960088 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.53 41.0 3.55e-01 89.7% 86.7%
3711910 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.53 44.0 3.46e-01 97.1% 55.6%
4960103 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.53 43.0 3.43e-01 94.1% 73.3%
4012390 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.52 43.0 3.58e-01 95.6% 86.9%
3277097 223.2.1.6 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › uDENN 0.52 42.0 3.38e-01 92.6% 58.1%
146254 327.11.2.6 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_10 0.52 41.0 3.70e-01 98.5% 60.6%
3998555 327.11.2.6 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_10 0.52 43.0 4.16e-01 98.5% 87.5%
3924642 3850.1.1.0 ↗ few secondary structure elements › Protein-only RNase P Zn-binding domain › Protein-only RNase P Zn-binding domain › Protein-only RNase P Zn-binding domain 0.51 43.0 4.22e-01 95.6% 97.3%
3830339 11.10.1.5 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › MATH_2 0.51 39.0 3.19e-01 89.7% 92.7%
5039890 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.51 42.0 3.38e-01 97.1% 66.7%
3896233 331.3.1.72 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › FANCAA 0.51 40.0 3.51e-01 91.2% 81.8%
3552839 11.1.1.795 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › FANCAA 0.50 38.0 3.37e-01 85.3% 86.4%