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NC_053249.1__YP_010002846.1__J1776_gp08__00008

Bact-Vir

NC_053249.1__YP_010002846.1__J1776_gp08__00008

Identity

Accession:
NC_053249 ↗
Kingdom:
phage

Quality

91.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Zitchvirus› Gordonia_phage_Verity

TaxID: 2591211

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 22-101
PDB
Domain cluster: representative
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3cxbB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.74 50.0 4.57e-01 70.0% 79.6%
2d9xA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.72 50.0 4.46e-01 71.2% 71.8%
1kz7C02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.71 49.0 4.02e-01 71.2% 65.7%
2y7bA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.69 47.0 3.94e-01 70.0% 78.4%
1ntyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 46.0 3.98e-01 70.0% 70.2%
3pnnA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.68 53.0 3.60e-01 96.2% 22.6%
1u5dA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 46.0 4.19e-01 71.2% 77.8%
1fx7B03 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.64 53.0 5.36e-01 88.7% 97.5%
2kr0A01 2.30.29.70 Mainly Beta › Roll › PH-domain like › Proteasomal ubiquitin receptor Rpn13/ADRM1 0.64 43.0 3.88e-01 70.0% 76.1%
2p0hA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 43.0 3.81e-01 71.2% 78.8%
5cxbA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.61 41.0 2.69e-01 70.0% 32.8%
3e1sA04 2.30.30.940 Mainly Beta › Roll › SH3 type barrels. › 0.60 43.0 4.59e-01 82.5% 88.4%
2imlA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.60 45.0 4.05e-01 81.2% 93.8%
4c5eC02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.60 41.0 3.91e-01 82.5% 60.4%
2vldB01 2.70.180.20 Mainly Beta › Distorted Sandwich › Protein Yojf; Chain: A; › 0.60 43.0 3.83e-01 77.5% 76.3%
5yjlD01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 44.0 3.65e-01 78.8% 80.3%
3h8zA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 41.0 4.44e-01 97.5% 92.2%
2ptfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 46.0 3.83e-01 88.7% 93.9%
4tkcA00 2.90.10.10 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › Bulb-type lectin domain 0.57 41.0 3.66e-01 76.2% 93.2%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.57 41.0 4.43e-01 88.7% 92.5%
2xzmR01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 39.0 2.61e-01 72.5% 43.0%
6pfzD02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 38.0 2.72e-01 70.0% 35.0%
5d5gA00 2.90.10.10 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › Bulb-type lectin domain 0.56 40.0 3.63e-01 75.0% 85.3%
1wczA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.56 46.0 4.17e-01 93.8% 81.7%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.55 43.0 3.51e-01 85.0% 88.1%
2vknA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 37.0 4.01e-01 70.0% 92.4%
3mezD00 2.90.10.10 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › Bulb-type lectin domain 0.55 39.0 3.52e-01 75.0% 87.5%
2kf2A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.55 40.0 3.26e-01 80.0% 73.7%
1jpcA00 2.90.10.10 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › Bulb-type lectin domain 0.54 38.0 3.50e-01 75.0% 88.0%
2as9B01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.53 44.0 4.16e-01 93.8% 85.1%
2digA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 35.0 3.71e-01 82.5% 80.9%
2eqjA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 35.0 3.84e-01 81.2% 84.8%
3zfnA02 2.30.140.40 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Pestivirus Npro endopeptidase C53, interaction domain 0.52 36.0 4.10e-01 83.7% 100.0%
3urgA02 2.30.30.530 Mainly Beta › Roll › SH3 type barrels. › Calcium binding protein CcbP, beta-barrel domain 0.52 36.0 3.93e-01 71.2% 92.1%
4oddA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 42.0 3.47e-01 90.0% 96.0%
3n91A02 2.40.128.420 Mainly Beta › Beta Barrel › Lipocalin › 0.52 40.0 3.48e-01 86.3% 90.4%
1c8zA00 3.20.90.10 Alpha Beta › Alpha-Beta Barrel › Tubby Protein; Chain A › Tubby Protein; Chain A 0.52 40.0 2.93e-01 88.7% 61.5%
1vwxf00 2.40.10.190 Mainly Beta › Beta Barrel › Thrombin, subunit H › translation elongation factor selb, chain A, domain 4 0.51 41.0 3.76e-01 90.0% 89.9%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 40.0 4.18e-01 91.3% 94.4%
4fr9A00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 42.0 3.57e-01 93.8% 87.9%
2qj8A00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.51 40.0 2.70e-01 85.0% 42.0%
1yqzA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.51 34.0 3.16e-01 70.0% 83.3%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3277493 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.76 51.0 4.60e-01 70.0% 81.8%
3270570 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.76 51.0 4.52e-01 70.0% 70.4%
3271265 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.75 52.0 4.51e-01 71.2% 80.8%
3619467 220.1.1.84 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_15 0.74 50.0 4.48e-01 70.0% 77.3%
3699374 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.72 49.0 4.07e-01 70.0% 67.4%
4028300 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.71 49.0 4.40e-01 71.2% 73.6%
3574630 220.1.1.161 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26659 0.69 47.0 4.03e-01 71.2% 60.8%
3412833 220.1.1.161 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26659 0.67 46.0 4.04e-01 72.5% 65.0%
3223830 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 39.0 4.58e-01 78.8% 98.0%
4253206 4.1.1.127 ↗ beta barrels › SH3 › SH3 › SH3 › DtxR 0.63 54.0 5.24e-01 95.0% 94.4%
3445812 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 42.0 3.53e-01 70.0% 61.4%
1503651 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.62 43.0 4.33e-01 77.5% 72.5%
5034165 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.61 43.0 3.75e-01 75.0% 76.8%
4978571 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.61 47.0 3.88e-01 83.7% 94.5%
3414063 4.1.1.233 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_VII_N 0.60 40.0 4.55e-01 81.2% 98.2%
2362 71.2.1.1 ↗ beta meanders › Lipoprotein localization factors LolAB › PA1994-like › PA1994-like › Glycolipid_bind 0.60 49.0 3.82e-01 91.3% 55.9%
4938263 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.59 43.0 3.76e-01 77.5% 76.0%
4933308 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.59 46.0 3.76e-01 85.0% 86.5%
1549085 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.58 41.0 3.68e-01 76.2% 92.4%
1687168 2492.1.1.26 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › MPN_2A_DUB_like 0.58 43.0 3.38e-01 81.2% 85.3%
4945272 220.5.1.2 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_C 0.58 42.0 3.66e-01 77.5% 74.4%
4965160 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.57 39.0 3.76e-01 71.2% 85.3%
3648015 9.1.1.21 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Cyclin_D1_bind 0.57 44.0 3.51e-01 85.0% 95.3%
3259317 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.56 41.0 3.54e-01 76.2% 98.4%
3632407 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 44.0 3.93e-01 86.3% 81.2%
3857291 206.1.1.13 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Alpha_kinase 0.56 49.0 3.46e-01 98.8% 52.2%
1694856 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.56 39.0 3.48e-01 73.8% 88.2%
3523918 4.1.1.99 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_10 0.55 41.0 4.41e-01 86.3% 96.9%
3603402 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.55 44.0 4.32e-01 90.0% 88.9%
3619619 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 38.0 3.99e-01 76.2% 81.4%
5053266 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.55 40.0 3.27e-01 78.8% 93.8%
4029739 9.8.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Dipeptidyl peptidase I (cathepsin C), exclusion domain › Dipeptidyl peptidase I (cathepsin C), exclusion domain › CathepsinC_exc 0.55 41.0 3.62e-01 81.2% 93.3%
3928050 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 47.0 4.04e-01 100.0% 83.7%
3290160 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.54 44.0 4.47e-01 92.5% 97.5%
3841414 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.54 41.0 4.34e-01 92.5% 94.3%
3447771 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.54 45.0 3.28e-01 93.8% 88.7%
4583705 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.54 47.0 3.25e-01 100.0% 86.9%
4988761 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.54 43.0 4.22e-01 90.0% 92.2%
3414912 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.54 44.0 4.07e-01 100.0% 70.5%
3288935 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.54 40.0 3.63e-01 80.0% 91.8%
3808930 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.53 37.0 3.15e-01 73.8% 97.9%
5039819 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.53 44.0 3.87e-01 96.2% 92.3%
5042597 4.15.1.0 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.53 43.0 4.21e-01 91.3% 91.1%
4948685 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.53 43.0 3.91e-01 91.3% 87.6%
3803207 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.53 39.0 3.48e-01 78.8% 99.1%
3433881 5.3.1.2 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II › B_lectin 0.52 41.0 3.54e-01 88.7% 83.0%
4100088 5.3.1.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II 0.52 40.0 3.49e-01 83.7% 92.0%
3615787 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.51 43.0 3.14e-01 93.8% 88.0%