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NC_060137.1__YP_010246791.1__L3Y25_gp103__00132

Bact-Vir

NC_060137.1__YP_010246791.1__L3Y25_gp103__00132

Identity

Accession:
NC_060137 ↗
Kingdom:
phage

Quality

63.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Octobienvirus› Gordonia_phage_Syleon

TaxID: 2653718

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 14-76
PDB
Domain cluster: representative
CATH (33)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3c6kA01 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.63 49.0 4.36e-01 85.7% 58.5%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 49.0 3.65e-01 88.9% 95.2%
1xe7A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.61 39.0 2.76e-01 100.0% 22.6%
4m0wA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.61 49.0 3.82e-01 100.0% 40.9%
2qqzA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.59 45.0 3.76e-01 92.1% 46.1%
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 0.59 36.0 3.71e-01 96.8% 65.5%
4mjgA00 3.30.2030.30 Alpha Beta › 2-Layer Sandwich › TBP-like › 0.59 51.0 3.77e-01 100.0% 49.7%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.59 43.0 3.91e-01 82.5% 98.9%
4harA00 3.10.50.50 Alpha Beta › Roll › Chitinase A; domain 3 › Rubella virus capsid protein 0.58 51.0 4.42e-01 100.0% 94.9%
4fflA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.58 51.0 3.39e-01 100.0% 51.7%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.57 47.0 3.62e-01 100.0% 40.9%
5fl3A01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.57 51.0 4.33e-01 98.4% 85.0%
2r0cA02 3.30.9.10 Alpha Beta › 2-Layer Sandwich › D-Amino Acid Oxidase; Chain A, domain 2 › D-Amino Acid Oxidase, subunit A, domain 2 0.57 43.0 3.25e-01 100.0% 36.2%
3jvvA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.57 50.0 4.30e-01 98.4% 85.0%
2ewvA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.57 50.0 4.27e-01 98.4% 84.3%
6s6yD02 3.30.70.520 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 47.0 3.68e-01 100.0% 96.7%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.56 45.0 4.45e-01 96.8% 100.0%
3qwmA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 48.0 3.89e-01 100.0% 66.1%
4chmB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 47.0 3.86e-01 100.0% 66.1%
5axgA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 46.0 3.76e-01 96.8% 95.2%
3tw8A01 3.30.450.200 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin module 0.54 48.0 3.75e-01 100.0% 60.1%
1yudA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 38.0 2.88e-01 73.0% 56.1%
5itqA01 3.20.190.10 Alpha Beta › Alpha-Beta Barrel › N-terminal domain of MutM-like DNA repair proteins › MutM-like, N-terminal 0.54 43.0 3.53e-01 92.1% 75.0%
4dt4A02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.53 41.0 4.34e-01 100.0% 93.0%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.53 41.0 3.59e-01 100.0% 56.2%
3fg8A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.53 46.0 3.88e-01 98.4% 89.6%
3jrqA00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.53 42.0 2.97e-01 100.0% 98.5%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 43.0 3.88e-01 100.0% 82.1%
2iq1A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.52 44.0 3.00e-01 100.0% 97.3%
2kr7A02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.52 38.0 3.96e-01 100.0% 87.7%
1bnkA00 3.10.300.10 Alpha Beta › Roll › 3-methyladenine DNA Glycosylase; Chain A › Methylpurine-DNA glycosylase (MPG) 0.51 44.0 3.14e-01 100.0% 68.0%
2oo4A02 3.30.70.3310 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 39.0 3.36e-01 87.3% 72.1%
2grgA01 3.40.1840.10 Alpha Beta › 3-Layer(aba) Sandwich › Profilin-like › YNR034W-A-like 0.50 45.0 4.09e-01 100.0% 81.9%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3672678 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.74 41.0 3.73e-01 81.0% 41.2%
3991921 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 55.0 4.56e-01 100.0% 69.3%
3935486 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 54.0 4.34e-01 100.0% 68.8%
3597004 220.1.1.26 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Vps36_ESCRT-II 0.61 53.0 4.20e-01 100.0% 58.5%
4463006 3115.2.1.0 ↗ a+b two layers › GP2-like › GP2 › GP2 0.61 40.0 4.49e-01 100.0% 95.6%
3538314 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.59 51.0 4.18e-01 100.0% 60.8%
4542815 223.1.1.12 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_2 0.57 51.0 3.87e-01 98.4% 66.4%
5011354 316.1.1.39 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF2204 0.57 48.0 3.51e-01 98.4% 40.5%
3249490 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.56 50.0 4.10e-01 100.0% 60.9%
5067362 221.1.1.50 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF4430 0.56 44.0 3.84e-01 88.9% 94.2%
4866061 223.1.1.12 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_2 0.56 50.0 4.23e-01 98.4% 91.2%
3609512 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.56 50.0 3.82e-01 100.0% 49.7%
3955760 810.1.1.3 ↗ a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › AIG2_2 0.56 43.0 3.44e-01 88.9% 71.7%
3279290 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.56 39.0 4.20e-01 81.0% 98.0%
3273132 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.55 41.0 3.02e-01 90.5% 28.1%
3237220 220.1.1.84 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_15 0.55 46.0 3.91e-01 100.0% 81.7%
3286341 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.55 49.0 3.83e-01 100.0% 50.4%
2529893 284.2.1.0 ↗ a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.55 44.0 4.39e-01 100.0% 100.0%
3472026 220.1.1.27 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_RBD 0.54 47.0 3.89e-01 100.0% 64.2%
4275468 223.1.1.95 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › NtrY_N 0.54 48.0 3.53e-01 100.0% 41.8%
3329328 1.1.11.1 ↗ beta barrels › cradle loop barrel › RIFT-related › Type II restriction endonuclease effector domain › B3 0.54 47.0 3.85e-01 98.4% 95.0%
3225059 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.53 48.0 4.03e-01 100.0% 61.0%
4031519 3425.1.1.1 ↗ a+b three layers › Two-component system yycF/yycG regulatory protein yycH-like › YycH N-terminal domain › YycH N-terminal domain › YycH 0.53 47.0 3.61e-01 100.0% 57.9%
2528374 284.4.1.0 ↗ a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain 0.53 41.0 3.87e-01 100.0% 68.8%
5033424 284.4.1.0 ↗ a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain 0.52 41.0 4.19e-01 100.0% 88.3%
3599873 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.52 46.0 3.11e-01 100.0% 28.2%
4004520 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.52 45.0 3.61e-01 96.8% 69.6%
3707456 223.2.1.10 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Gtr1_RagA 0.52 46.0 3.45e-01 100.0% 73.5%
5076995 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.52 36.0 3.39e-01 100.0% 58.7%
4951165 284.4.1.0 ↗ a+b two layers › FKBP-like › Archaeal FKBP insertion domain › Archaeal FKBP insertion domain 0.52 40.0 4.21e-01 100.0% 96.4%
3953435 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 44.0 3.23e-01 100.0% 39.5%
197693 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.51 36.0 3.13e-01 100.0% 46.5%
3955812 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.51 42.0 3.87e-01 100.0% 82.8%
3476370 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 45.0 3.47e-01 100.0% 44.8%
4317800 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 45.0 3.51e-01 100.0% 45.0%
3217758 207.1.1.52 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FBA_2 0.51 42.0 2.87e-01 96.8% 34.5%
3280174 223.5.1.0 ↗ a+b three layers › Profilin-like › YNR034W-A-like › YNR034W-A-like 0.51 45.0 4.13e-01 100.0% 92.9%
3593387 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 45.0 3.54e-01 100.0% 63.4%
3581513 4357.1.1.1 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.51 42.0 4.00e-01 100.0% 80.0%
5079486 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 45.0 3.50e-01 100.0% 55.7%
4358998 223.3.1.2 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Peptidase_S11 0.51 39.0 3.14e-01 87.3% 73.3%
3711668 4357.1.1.1 ↗ beta barrels › WWE domain › WWE domain › WWE domain › WWE 0.51 41.0 3.78e-01 100.0% 75.6%
3267853 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.50 38.0 2.75e-01 87.3% 26.8%
4156259 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 44.0 2.85e-01 100.0% 21.0%
3928228 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.50 42.0 2.93e-01 100.0% 75.0%
3953386 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 43.0 3.21e-01 100.0% 44.1%
4932930 221.1.1.50 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DUF4430 0.50 38.0 3.09e-01 90.5% 66.0%