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NC_021073.1__YP_007877975.1__VPDG_00002__00002

Bact-Vir

NC_021073.1__YP_007877975.1__VPDG_00002__00002

Identity

Accession:
NC_021073 ↗
Kingdom:
phage

Quality

71.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_henriette_12B8

TaxID: 573174

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 7-52
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1e7lA02 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.83 72.0 6.81e-01 100.0% 81.8%
3l0oA01 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.71 58.0 5.70e-01 100.0% 87.8%
2of5H00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.69 56.0 4.54e-01 100.0% 55.0%
4ojmX02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.66 53.0 4.29e-01 100.0% 61.9%
2p0tA02 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.65 52.0 4.67e-01 97.8% 97.2%
3s5wA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 56.0 3.27e-01 100.0% 36.6%
1vq8V00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 44.0 3.92e-01 78.3% 95.4%
1znnA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.58 47.0 2.98e-01 100.0% 17.6%
7y11B01 1.10.8.20 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › N-terminal domain of phosphatidylinositol transfer protein sec14p 0.57 41.0 3.79e-01 78.3% 76.2%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.55 34.0 3.22e-01 100.0% 50.0%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3611122 130.1.1.32 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP_RNF34_RFFL (DEPRECATED) 0.84 71.0 6.68e-01 93.5% 78.2%
3173158 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 73.0 7.18e-01 100.0% 92.0%
3127 130.1.1.7 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Endonuc-dimeris 0.83 72.0 6.85e-01 100.0% 83.3%
3943133 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.80 65.0 6.61e-01 91.3% 91.1%
3715853 130.1.1.31 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.80 69.0 6.82e-01 100.0% 93.8%
3336810 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.79 66.0 6.73e-01 100.0% 95.6%
4428371 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.79 67.0 6.84e-01 100.0% 97.8%
5053068 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.79 63.0 6.61e-01 87.0% 100.0%
3472431 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.79 61.0 6.45e-01 93.5% 100.0%
3880607 130.1.1.31 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.78 65.0 6.22e-01 97.8% 80.0%
3964225 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.78 67.0 6.05e-01 100.0% 70.8%
3881311 130.1.1.32 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP_RNF34_RFFL (DEPRECATED) 0.78 68.0 6.88e-01 97.8% 100.0%
3172891 130.1.1.16 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Ish1 0.77 65.0 6.42e-01 100.0% 90.0%
3712494 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.77 68.0 6.42e-01 100.0% 81.8%
4623858 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.77 64.0 6.46e-01 93.5% 95.6%
3797432 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.76 67.0 6.42e-01 100.0% 86.8%
3252664 130.1.1.31 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.76 63.0 6.06e-01 100.0% 81.8%
3198528 130.1.1.16 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Ish1 0.76 65.0 6.18e-01 100.0% 83.6%
4433184 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.76 65.0 6.17e-01 100.0% 81.8%
3511721 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.76 65.0 6.55e-01 97.8% 100.0%
3191284 130.1.1.16 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Ish1 0.75 60.0 5.96e-01 97.8% 88.0%
3614917 130.1.1.31 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › RNF34L-like_3rd 0.75 61.0 5.82e-01 97.8% 78.2%
3598653 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.75 61.0 6.17e-01 100.0% 97.8%
3440160 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.74 65.0 6.55e-01 97.8% 100.0%
3613361 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.74 63.0 6.19e-01 95.7% 94.0%
4292699 130.1.1.3 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › Rho_N 0.74 60.0 6.12e-01 97.8% 93.3%
4359663 3949.1.1.0 ↗ alpha arrays › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain › tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain 0.74 61.0 5.59e-01 100.0% 76.9%
3834246 145.1.1.1 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box 0.69 49.0 4.64e-01 91.3% 63.6%
3814674 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.67 49.0 4.95e-01 91.3% 80.0%
3664931 101.1.9.0 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain 0.62 44.0 4.30e-01 82.6% 70.0%
3578362 101.1.1.4 ↗ alpha arrays › HTH › HTH › Three-helical HTH › PAX 0.60 43.0 3.75e-01 76.1% 53.3%
3507860 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 47.0 3.71e-01 100.0% 40.0%
4027588 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.58 43.0 2.95e-01 93.5% 23.1%
3789626 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.57 42.0 3.85e-01 80.4% 61.5%
5034422 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.57 51.0 4.80e-01 100.0% 100.0%
3494018 137.1.1.1 ↗ alpha bundles › A DNA-binding domain in eukaryotic transcription factors › A DNA-binding domain in eukaryotic transcription factors › A DNA-binding domain in eukaryotic transcription factors › bZIP_Maf 0.56 40.0 3.77e-01 89.1% 60.0%
3502023 605.1.1.201 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › BPD_transp_1 0.55 40.0 3.58e-01 100.0% 52.9%
D2 high residues 298-373
PDB
D3 medium residues 128-277
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1x8zB00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.67 36.0 3.71e-01 70.0% 53.1%
2dg8D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.60 42.0 4.00e-01 71.3% 70.5%
1m56C02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.59 38.0 3.48e-01 70.7% 50.0%
1zk8B02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 41.0 4.38e-01 72.0% 93.2%
1orsC00 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.57 34.0 3.65e-01 72.0% 65.9%
3qkxB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 40.0 3.76e-01 71.3% 91.7%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 40.0 4.00e-01 74.0% 70.8%
2f07B00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.56 40.0 3.69e-01 72.7% 70.4%
4mo7A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 37.0 3.87e-01 70.0% 91.5%
3c1yA02 1.20.1260.110 Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region 0.54 44.0 4.46e-01 93.3% 86.5%
4u72A01 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.54 39.0 3.39e-01 73.3% 90.1%
3axjB01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.54 39.0 3.88e-01 73.3% 81.3%
1ah7A00 1.10.575.10 Mainly Alpha › Orthogonal Bundle › P1 Nuclease › P1 Nuclease 0.53 44.0 3.78e-01 89.3% 89.8%
5tgzA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 45.0 3.62e-01 92.7% 59.2%
3uonA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 45.0 3.64e-01 92.7% 62.7%
7eq1R01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 41.0 3.36e-01 84.7% 62.1%
2fbnA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 38.0 3.80e-01 100.0% 75.2%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4943812 3579.1.1.0 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J 0.71 35.0 3.37e-01 70.0% 41.8%
3686594 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.68 34.0 4.51e-01 70.7% 88.7%
3788202 109.10.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Translin › Translin › Translin 0.65 47.0 3.95e-01 74.7% 49.4%
3593141 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 45.0 3.82e-01 84.0% 49.2%
3290284 601.18.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Oxygen-evolving enhancer protein 3 › Oxygen-evolving enhancer protein 3 0.58 34.0 4.05e-01 72.7% 88.4%
3949818 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.56 41.0 4.07e-01 74.0% 93.5%
2644092 3281.1.1.2 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N 0.56 50.0 3.30e-01 98.7% 52.2%
4356766 5069.1.1.15 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_C_asm 0.55 38.0 3.67e-01 71.3% 61.7%
4083434 5069.1.1.53 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › UPF0182 0.54 40.0 3.81e-01 76.7% 78.3%
3279896 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.54 38.0 3.62e-01 72.7% 66.7%
3581031 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.53 40.0 3.80e-01 77.3% 77.1%
3616841 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.53 39.0 3.11e-01 76.0% 46.9%
4998888 604.39.1.0 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters 0.53 41.0 3.91e-01 81.3% 88.3%
3711874 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 41.0 4.45e-01 86.0% 99.2%
3229344 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.52 36.0 3.36e-01 71.3% 66.3%
3238734 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.51 43.0 3.23e-01 92.0% 47.0%
4464661 601.3.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.51 39.0 4.15e-01 79.3% 93.3%