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NC_015721.1__YP_004678854.1__BdPhPhi1402_gp27__00027

Bact-Vir

NC_015721.1__YP_004678854.1__BdPhPhi1402_gp27__00027

Identity

Accession:
NC_015721 ↗
Kingdom:
phage

Quality

94.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bdellovibrio_phage_phi1402

TaxID: 1035662

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 medium residues 1-93
PDB
Domain cluster: representative
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ajdA01 3.30.70.1170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Sun protein; domain 3 0.65 31.0 3.79e-01 83.9% 70.0%
4p72A04 3.30.56.10 Alpha Beta › 2-Layer Sandwich › Phenylalanyl-tRNA Synthetase; Chain B, domain 1 › 0.56 30.0 3.29e-01 84.9% 63.2%
1ewqB01 3.40.1170.10 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › DNA repair protein MutS, domain I 0.54 30.0 2.79e-01 91.4% 40.7%
2l48A00 3.30.70.2030 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 29.0 3.02e-01 86.0% 56.5%
1kmxA00 2.10.160.10 Mainly Beta › Ribbon › Vascular Endothelial Growth Factor-165, Heparin-binding Domain › Vascular endothelial growth factor, heparin-binding domain 0.51 28.0 3.38e-01 82.8% 89.1%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5010613 3696.1.1.0 ↗ a+b two layers › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related › DNA helicase UvsW N-terminal a+b domain-related 0.61 32.0 3.68e-01 91.4% 70.8%
4336912 5104.1.1.0 ↗ a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.58 31.0 3.05e-01 91.4% 44.8%
4990495 306.6.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.58 31.0 3.57e-01 91.4% 70.8%
5071804 242.4.1.2 ↗ a+b two layers › Homing endonucleases-like › DNA polymerase II large subunit DP2 central a+b domain › DNA polymerase II large subunit DP2 central a+b domain › PolC_DP2_central 0.57 31.0 3.15e-01 91.4% 52.2%
3602755 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 32.0 3.52e-01 91.4% 68.0%
5025092 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.56 30.0 3.26e-01 78.5% 61.3%
4034524 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.56 31.0 3.50e-01 92.5% 71.4%
4932736 4955.1.1.0 ↗ a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.54 33.0 3.57e-01 100.0% 73.3%
4575402 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.54 33.0 3.43e-01 93.5% 65.9%
4129052 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.53 30.0 3.07e-01 97.8% 52.6%
5083122 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.53 31.0 3.16e-01 96.8% 56.8%
4269197 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.53 31.0 3.30e-01 92.5% 65.0%
5082092 2006.1.1.11 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_3 0.52 37.0 2.88e-01 74.2% 32.3%
4194607 3016.1.1.10 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › GDC-P 0.52 30.0 3.31e-01 93.5% 71.4%
4108740 3016.1.1.10 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › GDC-P 0.52 30.0 2.92e-01 93.5% 47.6%
3511028 101.1.2.677 ↗ alpha arrays › HTH › HTH › winged helix domain › Sha_B_N 0.51 32.0 3.87e-01 92.5% 100.0%
1114523 3016.1.1.1 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.50 29.0 3.07e-01 92.5% 60.5%
4610155 3016.1.1.2 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_3 0.50 31.0 3.09e-01 92.5% 57.9%
D2 medium residues 94-148
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2aneH00 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.66 56.0 4.60e-01 100.0% 79.8%
7cayA01 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.61 51.0 4.32e-01 100.0% 78.0%
2fwrA01 3.40.1170.30 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › 0.60 46.0 4.62e-01 92.7% 82.5%
6wy9B02 2.40.110.10 Mainly Beta › Beta Barrel › Butyryl-CoA Dehydrogenase, subunit A; domain 2 › Butyryl-CoA Dehydrogenase, subunit A, domain 2 0.59 45.0 3.95e-01 90.9% 91.6%
2jbrA02 2.40.110.10 Mainly Beta › Beta Barrel › Butyryl-CoA Dehydrogenase, subunit A; domain 2 › Butyryl-CoA Dehydrogenase, subunit A, domain 2 0.58 45.0 3.94e-01 92.7% 91.6%
4kktA02 2.40.30.170 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Efflux pump adaptor protein, beta barrel domain 0.58 46.0 3.90e-01 96.4% 75.2%
5af7B02 2.40.110.10 Mainly Beta › Beta Barrel › Butyryl-CoA Dehydrogenase, subunit A; domain 2 › Butyryl-CoA Dehydrogenase, subunit A, domain 2 0.57 45.0 3.83e-01 100.0% 90.4%
3d37B01 2.30.300.10 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Baseplate protein-like domain - beta roll fold 0.57 45.0 3.35e-01 96.4% 40.2%
3ocjA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.56 43.0 2.74e-01 85.5% 37.7%
3qw9B00 2.60.40.4100 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-C domain 0.55 41.0 3.07e-01 87.3% 59.0%
2pliA00 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.55 41.0 3.62e-01 83.6% 95.2%
1j71A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.54 44.0 3.19e-01 92.7% 54.7%
7ocxC01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 39.0 3.66e-01 83.6% 61.8%
3gqhA01 2.40.300.10 Mainly Beta › Beta Barrel › Virus Head Decoration Protein; Chain: A, › Head decoration protein D 0.54 40.0 3.24e-01 85.5% 86.2%
2k8qA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 42.0 3.27e-01 89.1% 59.7%
5os9A00 2.40.330.10 Mainly Beta › Beta Barrel › At1g16640 B3 domain › DNA-binding pseudobarrel domain 0.53 44.0 3.62e-01 100.0% 92.2%
3h6eA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 38.0 2.64e-01 81.8% 91.9%
6eugA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 37.0 2.35e-01 78.2% 89.9%
2pb7A01 2.30.280.10 Mainly Beta › Roll › PUA domain-like › SRA-YDG 0.52 42.0 3.14e-01 100.0% 88.7%
2eaqA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.52 37.0 3.24e-01 76.4% 87.6%
3n0vA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.52 40.0 3.54e-01 87.3% 56.0%
4cj0A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 42.0 3.69e-01 98.2% 80.0%
1y0hB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 37.0 3.15e-01 78.2% 65.3%
4dn9B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 37.0 3.16e-01 78.2% 63.9%
2nzcB00 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.51 38.0 3.45e-01 83.6% 59.3%
2e9hA01 3.30.30.170 Alpha Beta › 2-Layer Sandwich › Defensin A-like › 0.51 41.0 3.33e-01 92.7% 69.9%
5z62B02 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.51 41.0 3.19e-01 94.5% 87.5%
1twfB07 2.40.50.150 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II, Rpb2 subunit, wall domain 0.50 37.0 3.00e-01 83.6% 91.1%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4210619 323.1.1.33 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › PF27279 0.59 49.0 3.02e-01 100.0% 66.5%
4402697 1.1.5.25 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.59 46.0 3.82e-01 96.4% 66.7%
3211296 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 44.0 3.53e-01 85.5% 61.7%
3604610 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.57 43.0 4.15e-01 87.3% 100.0%
3734783 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.56 40.0 2.51e-01 80.0% 95.3%
3836146 1.1.9.4 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › SAD_SRA 0.55 45.0 3.48e-01 100.0% 91.7%
3504295 1.1.5.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin 0.55 43.0 3.33e-01 98.2% 55.6%
3512547 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.53 42.0 3.12e-01 96.4% 87.2%
3445182 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.53 37.0 2.99e-01 76.4% 36.0%
5039158 50.1.1.3 ↗ beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S78 0.53 38.0 2.80e-01 78.2% 84.4%
3570820 304.112.1.10 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › Med13_N 0.53 38.0 2.66e-01 78.2% 84.1%
3871812 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.52 37.0 2.33e-01 81.8% 30.7%
4045808 708.1.1.22 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › DUF5575_N 0.52 38.0 3.11e-01 83.6% 91.6%
3302927 1.1.9.4 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › SAD_SRA 0.52 42.0 2.86e-01 100.0% 58.8%
3651466 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 39.0 2.81e-01 89.1% 55.3%
4240079 304.4.1.4 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.50 35.0 3.03e-01 76.4% 58.0%