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NC_015721.1__YP_004678840.1__BdPhPhi1402_gp13__00013

Bact-Vir

NC_015721.1__YP_004678840.1__BdPhPhi1402_gp13__00013

Identity

Accession:
NC_015721 ↗
Kingdom:
phage

Quality

72.8 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 high residues 49-146
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3if8B02 1.20.58.730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 45.0 4.50e-01 74.5% 62.0%
1t6jA03 1.10.274.20 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3 0.67 47.0 4.62e-01 79.6% 68.0%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.62 45.0 4.71e-01 76.5% 85.7%
2vzbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.59 46.0 3.92e-01 85.7% 77.2%
2dzlA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.58 29.0 3.42e-01 85.7% 66.7%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 41.0 3.59e-01 76.5% 69.5%
2hytA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 42.0 3.43e-01 81.6% 56.5%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 38.0 3.55e-01 73.5% 71.7%
2wglA00 1.10.4190.10 Mainly Alpha › Orthogonal Bundle › Urease accessory protein UreF › Urease accessory protein UreF 0.53 46.0 3.66e-01 98.0% 57.4%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.52 39.0 3.86e-01 91.8% 75.7%
1z67A00 1.10.10.690 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › YidB-like 0.50 38.0 3.58e-01 82.7% 91.3%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030263 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.67 49.0 4.27e-01 77.6% 88.0%
3874750 101.1.1.249 ↗ alpha arrays › HTH › HTH › Three-helical HTH › SGIII 0.65 45.0 4.89e-01 74.5% 86.3%
3285853 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.65 50.0 4.82e-01 81.6% 78.2%
3705785 3050.1.1.30 ↗ alpha bundles › Ribosomal protein L19 (L19e) C-terminal domain › Ribosomal protein L19 (L19e) C-terminal domain › Ribosomal protein L19 (L19e) C-terminal domain › TMEM254 0.63 42.0 4.27e-01 78.6% 69.5%
4029677 3291.1.1.219 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PF30356 0.62 42.0 3.61e-01 73.5% 43.2%
3712322 3050.1.1.0 ↗ alpha bundles › Ribosomal protein L19 (L19e) C-terminal domain › Ribosomal protein L19 (L19e) C-terminal domain › Ribosomal protein L19 (L19e) C-terminal domain 0.62 45.0 3.94e-01 76.5% 82.7%
4030633 524.1.1.1 ↗ alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC 0.62 46.0 4.03e-01 80.6% 61.3%
4296683 604.3.1.2 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › ABA4-like 0.61 41.0 3.54e-01 83.7% 46.2%
4971262 7014.1.1.1 ↗ alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA 0.60 46.0 4.36e-01 80.6% 74.8%
4386768 5045.1.1.1 ↗ alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.55 49.0 3.59e-01 100.0% 62.6%
4120512 172.2.1.1 ↗ alpha complex topology › Citrate synthase-like › Urease accessory protein ureF › Urease accessory protein ureF › UreF 0.55 48.0 3.75e-01 99.0% 80.9%
3163951 172.2.1.1 ↗ alpha complex topology › Citrate synthase-like › Urease accessory protein ureF › Urease accessory protein ureF › UreF 0.54 47.0 3.69e-01 100.0% 81.3%
4162408 172.2.1.1 ↗ alpha complex topology › Citrate synthase-like › Urease accessory protein ureF › Urease accessory protein ureF › UreF 0.53 46.0 3.60e-01 100.0% 80.0%
3473135 601.16.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › FAT domain of focal adhesion kinase › FAT domain of focal adhesion kinase › Focal_AT 0.53 44.0 4.15e-01 94.9% 100.0%
3229891 5057.1.1.0 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.52 45.0 4.02e-01 93.9% 95.6%
4290066 172.2.1.1 ↗ alpha complex topology › Citrate synthase-like › Urease accessory protein ureF › Urease accessory protein ureF › UreF 0.52 45.0 3.54e-01 100.0% 77.3%
4231284 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.51 42.0 4.04e-01 88.8% 93.6%
3197246 3721.1.1.0 ↗ alpha bundles › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain › Protein regulator of cytokinesis 1 (PRC1) dimerization domain 0.50 33.0 3.73e-01 96.9% 94.3%
D2 high residues 153-205
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lxjA00 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 48.0 4.00e-01 100.0% 78.6%
1q8bA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 44.0 3.87e-01 94.3% 92.5%
6mrmC01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.56 46.0 3.37e-01 100.0% 67.5%
1ou8A00 2.30.30.220 Mainly Beta › Roll › SH3 type barrels. › SspB-like 0.54 43.0 3.68e-01 100.0% 72.6%
4r4xA02 2.60.120.1570 Mainly Beta › Sandwich › Jelly Rolls › Peptide-N-glycosidase F, N-terminal domain 0.53 36.0 2.57e-01 73.6% 87.8%
2xueA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.53 42.0 2.80e-01 100.0% 40.9%
2y26A01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.52 41.0 2.67e-01 100.0% 37.7%
2h0eB00 2.60.40.180 Mainly Beta › Sandwich › Immunoglobulin-like › Transthyretin/hydroxyisourate hydrolase domain 0.51 41.0 3.42e-01 100.0% 52.2%
5k0uB00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.50 40.0 2.78e-01 100.0% 54.0%
1s6lA02 3.15.10.60 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Alkylmercury lyase 0.50 39.0 3.11e-01 94.3% 39.5%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032640 601.19.1.3 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Phage_Mu_F 0.74 64.0 3.97e-01 100.0% 18.7%
4237650 3325.1.1.1 ↗ a+b two layers › UvrB-binding domain of UvrA › UvrB-binding domain of UvrA › UvrB-binding domain of UvrA › UvrA_inter 0.57 49.0 3.90e-01 100.0% 78.3%
5059885 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.53 44.0 3.19e-01 100.0% 45.6%
4030071 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.51 39.0 3.80e-01 94.3% 81.7%
3590783 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.50 39.0 3.08e-01 100.0% 53.8%