←Back to structures

NC_055856.1__YP_010109185.1__KNV14_gp11__00011

Bact-Vir

NC_055856.1__YP_010109185.1__KNV14_gp11__00011

Identity

Accession:
NC_055856 ↗
Kingdom:
phage

Quality

68.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Stackebrandtviridae› Vividuovirus› Gordonia_Phage_Barsten

TaxID: 2743907

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 5-50
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gnxA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.77 54.0 4.01e-01 73.9% 44.4%
3dueA00 3.40.1420.30 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › 0.75 51.0 3.69e-01 71.7% 32.3%
1whzA00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.71 48.0 4.22e-01 71.7% 60.9%
4a4yA01 2.60.200.50 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.71 56.0 4.49e-01 91.3% 73.5%
2ymsC00 2.40.10.480 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.69 56.0 4.71e-01 89.1% 88.0%
3dsoA00 2.40.10.300 Mainly Beta › Beta Barrel › Thrombin, subunit H › Copper resistance protein K 0.69 58.0 5.26e-01 100.0% 77.3%
2m3xC02 2.40.10.360 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.67 56.0 4.90e-01 93.5% 88.4%
4g7nA02 3.30.1120.130 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.67 54.0 4.37e-01 95.7% 48.5%
5lm7A02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.66 51.0 4.33e-01 84.8% 70.5%
2rf4E02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.66 46.0 3.84e-01 73.9% 83.1%
7o06C01 3.30.1470.10 Alpha Beta › 2-Layer Sandwich › Photosystem 1 Reaction Centre Subunit Ii; Chain: D; › Photosystem I PsaD, reaction center subunit II 0.66 49.0 3.92e-01 80.4% 87.9%
5cq2A02 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.65 45.0 4.69e-01 73.9% 79.1%
4ld1A00 2.60.450.20 Mainly Beta › Sandwich › lipopolysaccharide transport protein A fold › 0.65 45.0 3.13e-01 73.9% 33.1%
2gl5A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.64 53.0 3.94e-01 100.0% 91.7%
2vhjA02 2.30.270.20 Mainly Beta › Roll › duf1285 protein fold › 0.64 48.0 4.40e-01 82.6% 83.9%
3p34A02 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.63 52.0 4.21e-01 97.8% 76.3%
4c3iG02 2.40.50.1060 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.63 49.0 3.49e-01 87.0% 79.1%
2qdeA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.63 51.0 3.82e-01 100.0% 89.7%
4pswB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.62 53.0 3.15e-01 100.0% 38.5%
2ymsB00 2.40.10.480 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.62 54.0 4.61e-01 97.8% 82.4%
3jb9L00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.62 53.0 3.28e-01 100.0% 26.3%
3qwuA02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.61 49.0 3.46e-01 100.0% 71.1%
6ofsA03 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.61 46.0 3.01e-01 82.6% 90.2%
2jxwA00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.61 46.0 3.94e-01 82.6% 54.7%
1v9kA00 3.30.2350.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › Pseudouridine synthase 0.61 51.0 3.33e-01 97.8% 91.6%
2pulB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 45.0 3.65e-01 84.8% 70.7%
2yshA01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.59 37.0 4.03e-01 73.9% 87.9%
1bwzA01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.59 48.0 3.59e-01 95.7% 90.6%
3rheA00 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 47.0 3.64e-01 95.7% 81.6%
3le4A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.57 41.0 3.91e-01 78.3% 85.5%
2dl5A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 45.0 3.95e-01 100.0% 91.0%
4g6tA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.55 43.0 3.20e-01 89.1% 71.9%
1zq1A01 2.30.30.520 Mainly Beta › Roll › SH3 type barrels. › 0.55 43.0 3.73e-01 91.3% 74.0%
3eebA00 3.40.50.11050 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › MARTX cysteine protease (CPD) domain 0.53 44.0 2.98e-01 100.0% 79.0%
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 38.0 3.48e-01 82.6% 81.8%
2gfaB01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.51 39.0 3.66e-01 91.3% 83.9%
2v1rA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.50 39.0 3.67e-01 100.0% 95.5%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3973165 818.1.1.0 ↗ a+b two layers › DNA topoisomerase I domain › DNA topoisomerase I domain › DNA topoisomerase I domain 0.81 60.0 4.91e-01 82.6% 45.0%
4944335 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.76 52.0 4.12e-01 71.7% 35.5%
3889662 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.76 51.0 4.58e-01 71.7% 80.0%
5075316 330.7.1.0 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain 0.74 51.0 4.37e-01 71.7% 61.4%
3660003 5.1.10.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed › ANAPC4_WD40 0.71 57.0 4.69e-01 87.0% 87.5%
5829 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.71 48.0 4.20e-01 71.7% 60.0%
147657 73.1.1.5 ↗ beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain › PrgH 0.71 56.0 4.21e-01 91.3% 59.0%
4947543 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.70 48.0 4.07e-01 71.7% 58.1%
3265851 64.1.1.1 ↗ beta meanders › WW domain-like › WW domain › WW domain › WW 0.69 55.0 5.82e-01 91.3% 100.0%
3624687 64.1.1.9 ↗ beta meanders › WW domain-like › WW domain › WW domain › WW_TCERG1 0.69 60.0 5.86e-01 97.8% 92.0%
5074928 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.69 47.0 4.22e-01 71.7% 55.4%
3388090 5.1.11.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed 0.68 61.0 3.65e-01 100.0% 31.0%
3648305 809.2.1.7 ↗ a+b two layers › BLIP-like › BT0923-like › BT0923-like › Beta-prop_IP5PC_F 0.68 56.0 4.44e-01 93.5% 73.7%
4928523 4.6.1.0 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain 0.67 50.0 4.68e-01 82.6% 87.9%
3981710 2004.1.1.417 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, AAA_21 0.66 54.0 3.49e-01 95.7% 20.4%
3211621 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.65 56.0 4.63e-01 100.0% 68.2%
4386761 292.2.1.3 ↗ a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › Plk4_PB2 0.65 54.0 4.34e-01 100.0% 66.0%
4149266 5.1.11.11 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 9-bladed › WD40 0.65 56.0 3.26e-01 100.0% 23.9%
3975292 7515.1.1.2 ↗ a/b three-layered sandwiches › Alkaline phosphatase-like › Alkaline phosphatase-like › Alkaline phosphatase-like › Sulfatase 0.64 56.0 3.34e-01 100.0% 31.1%
3223830 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 46.0 4.56e-01 78.3% 82.0%
4948537 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.63 51.0 3.14e-01 100.0% 17.4%
3163656 7515.1.1.2 ↗ a/b three-layered sandwiches › Alkaline phosphatase-like › Alkaline phosphatase-like › Alkaline phosphatase-like › Sulfatase 0.63 53.0 3.24e-01 100.0% 34.2%
5042381 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.63 52.0 3.05e-01 95.7% 13.3%
3897826 220.1.1.161 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26659 0.61 51.0 3.88e-01 95.7% 88.7%
3705938 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.61 53.0 3.92e-01 100.0% 66.7%
4375554 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.60 50.0 2.87e-01 100.0% 58.3%
3800040 5.1.4.422 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_Rol-3 0.60 51.0 3.24e-01 100.0% 19.6%
4964361 502.1.1.3 ↗ a+b two layers › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › DUF7348 0.60 50.0 4.40e-01 95.7% 78.6%
3790336 5.1.3.164 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_Rol-3 0.60 52.0 3.27e-01 100.0% 19.1%
3485745 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.54 41.0 3.84e-01 87.0% 93.3%
3924338 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.54 42.0 3.77e-01 89.1% 80.0%
3415045 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.52 42.0 3.73e-01 93.5% 80.0%
3987428 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.52 40.0 3.05e-01 82.6% 75.0%
3574613 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.52 40.0 3.26e-01 91.3% 47.0%
None — 0.51 40.0 2.12e-01 89.1% 3.6%
3649741 4.1.1.33 ↗ beta barrels › SH3 › SH3 › SH3 › Myosin_N 0.51 39.0 3.50e-01 91.3% 61.3%
None — 0.51 44.0 3.13e-01 100.0% 77.2%
None — 0.51 42.0 2.62e-01 100.0% 18.7%
5049906 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.51 36.0 3.39e-01 80.4% 61.7%