←Back to structures

NC_048765.1__YP_009845743.1__HWC21_gp087__00087

Bact-Vir

NC_048765.1__YP_009845743.1__HWC21_gp087__00087

Identity

Accession:
NC_048765 ↗
Kingdom:
phage

Quality

74.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Vapseptimavirus› Vibrio_phage_VAP7

TaxID: 2584487

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 medium residues 1-91
PDB
Domain cluster: rep: MT074142.1__QIG64294.1__DAC23_16__00016__D45-128
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4oifA02 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.60 39.0 3.02e-01 95.6% 28.1%
1kwgA02 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.54 36.0 2.79e-01 92.3% 30.5%
1iw4A00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.54 32.0 3.88e-01 71.4% 98.2%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3964437 3430.1.1.1 ↗ a+b complex topology › Primosome assembly protein PriA 3' DNA-binding domain › Primosome assembly protein PriA 3' DNA-binding domain › Primosome assembly protein PriA 3' DNA-binding domain › PriA_3primeBD 0.65 40.0 3.76e-01 78.0% 50.0%
D2 medium residues 92-165
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.88 60.0 5.96e-01 70.3% 74.0%
2ch7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.87 59.0 3.78e-01 70.3% 97.4%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.86 58.0 5.70e-01 70.3% 76.2%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.84 57.0 5.68e-01 70.3% 96.1%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.83 57.0 6.17e-01 71.6% 92.2%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.82 59.0 5.22e-01 74.3% 55.9%
1fs0G02 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.82 56.0 5.24e-01 70.3% 76.4%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.78 60.0 4.64e-01 89.2% 39.7%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 52.0 4.33e-01 70.3% 43.9%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 68.0 6.22e-01 94.6% 97.8%
2b5uA02 1.10.287.620 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix Hairpins 0.75 57.0 4.39e-01 81.1% 93.2%
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.75 52.0 4.51e-01 73.0% 69.9%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.74 51.0 4.19e-01 71.6% 45.1%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 66.0 6.26e-01 97.3% 100.0%
1vb5A01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.69 47.0 4.38e-01 90.5% 55.3%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.69 55.0 4.94e-01 89.2% 62.1%
1ugoA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.69 61.0 5.46e-01 94.6% 78.8%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.69 62.0 5.97e-01 97.3% 90.5%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 60.0 4.91e-01 94.6% 82.0%
3eabE00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.68 57.0 5.41e-01 91.9% 93.0%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 57.0 5.15e-01 94.6% 95.2%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 45.0 5.01e-01 71.6% 91.2%
4ivfA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.67 46.0 3.98e-01 70.3% 54.3%
4ijjB00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.66 49.0 4.12e-01 79.7% 70.8%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.66 57.0 5.44e-01 95.9% 86.2%
2i0mA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.66 57.0 5.09e-01 97.3% 86.8%
7odyC01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.64 49.0 4.55e-01 95.9% 65.2%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.63 43.0 4.52e-01 83.8% 81.5%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 42.0 3.56e-01 70.3% 51.9%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 53.0 4.77e-01 94.6% 92.2%
3k3uA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.62 54.0 4.49e-01 100.0% 96.4%
3fb2A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 53.0 4.77e-01 97.3% 93.3%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.61 56.0 4.12e-01 100.0% 65.0%
3ns4A00 1.10.357.110 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Vacuolar protein sorting-associated protein 53, C-terminus 0.60 50.0 3.75e-01 97.3% 63.9%
4fjvA02 1.20.1300.20 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Peptidase C65 Otubain, subdomain 2 0.59 45.0 3.63e-01 81.1% 84.7%
2gsvA00 6.10.140.40 Special › Helix non-globular › Helix Hairpins › 0.59 48.0 5.03e-01 94.6% 98.5%
2l3lA01 1.20.58.1250 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Tubulin Binding Cofactor C, N-terminal domain 0.58 48.0 4.38e-01 97.3% 67.9%
2ipcA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.55 48.0 3.33e-01 95.9% 73.1%
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.55 46.0 4.10e-01 94.6% 89.8%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.54 44.0 3.86e-01 90.5% 75.4%
2c42A03 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.53 43.0 3.25e-01 95.9% 90.6%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 38.0 4.04e-01 89.2% 96.7%
3d6jA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.51 36.0 3.83e-01 100.0% 80.6%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4038778 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.88 61.0 5.11e-01 71.6% 54.8%
3904566 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.87 59.0 4.16e-01 70.3% 26.3%
3855328 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.86 60.0 5.42e-01 71.6% 58.9%
3757869 4006.1.1.0 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain 0.85 59.0 5.39e-01 71.6% 58.9%
4579811 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.85 59.0 5.16e-01 71.6% 53.3%
3808476 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.84 64.0 6.60e-01 78.4% 91.4%
3793286 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.83 57.0 4.07e-01 71.6% 78.5%
4596937 605.1.1.247 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › PCRF 0.83 57.0 5.11e-01 71.6% 56.0%
4136151 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.82 57.0 5.10e-01 71.6% 56.0%
5055329 3004.1.1.0 ↗ alpha bundles › Hypothetical protein YfhH, N-terminal domain › Hypothetical protein YfhH, N-terminal domain › Hypothetical protein YfhH, N-terminal domain 0.81 56.0 5.62e-01 71.6% 70.7%
4099744 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.79 55.0 4.93e-01 71.6% 58.0%
3585459 109.4.1.2716 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CTNNBL, TFCD_C, ARM_TBCD_2nd 0.78 61.0 3.39e-01 90.5% 6.3%
3500901 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.78 54.0 3.91e-01 71.6% 29.5%
3693906 192.22.1.5 ↗ alpha bundles › Long alpha-hairpin › Ral binding domain of RLIP76 › Ral binding domain of RLIP76 › Tho2 0.76 58.0 5.27e-01 79.7% 81.1%
5070891 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.76 65.0 6.36e-01 97.3% 85.0%
4927922 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.76 55.0 6.15e-01 83.8% 93.3%
3931056 633.16.1.0 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like 0.75 65.0 5.82e-01 97.3% 87.6%
5027312 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.74 62.0 5.52e-01 89.2% 93.2%
3704489 109.4.1.308 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vps39_1 0.74 65.0 3.80e-01 95.9% 34.4%
3738337 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.72 63.0 5.59e-01 95.9% 80.0%
1145704 604.5.1.3 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_1_C 0.72 64.0 6.32e-01 98.6% 98.7%
3277002 3252.1.1.0 ↗ alpha arrays › SHQ1 C-terminal domain-like › SHQ1 C-terminal domain › SHQ1 C-terminal domain 0.72 58.0 4.00e-01 87.8% 60.8%
3658236 604.12.1.69 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › SRP68 0.71 63.0 5.26e-01 95.9% 57.6%
4005523 3860.1.1.167 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm › MscS_porin 0.71 49.0 3.88e-01 73.0% 57.5%
3314530 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.71 61.0 5.46e-01 91.9% 74.0%
3768254 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.71 63.0 5.80e-01 97.3% 96.8%
3704748 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.71 56.0 5.67e-01 89.2% 100.0%
3408094 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 61.0 4.96e-01 94.6% 83.7%
3479953 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.70 63.0 5.96e-01 95.9% 90.6%
3526105 604.3.1.18 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › PF27519 0.70 60.0 5.63e-01 94.6% 86.7%
3911608 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.70 62.0 5.79e-01 95.9% 83.3%
4667113 604.5.1.3 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_1_C 0.70 60.0 6.17e-01 94.6% 100.0%
3409714 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.69 62.0 5.57e-01 97.3% 78.0%
4862803 4246.1.1.2 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_1 0.69 63.0 4.25e-01 98.6% 51.6%
3294784 3755.3.1.54 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › THOC7 0.69 46.0 3.67e-01 73.0% 33.5%
4024049 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.67 59.0 5.93e-01 97.3% 96.0%
4030059 3903.1.1.0 ↗ alpha duplicates or obligate multimers › Reticulocyte binding protein 5 › Reticulocyte binding protein 5 › Reticulocyte binding protein 5 0.65 55.0 3.80e-01 98.6% 87.5%
4958436 2008.1.1.217 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › UvrD-helicase 0.65 55.0 3.10e-01 100.0% 13.5%
3594310 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.64 53.0 5.26e-01 95.9% 93.8%
3486453 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.63 55.0 4.91e-01 98.6% 95.2%
3511170 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.60 46.0 4.62e-01 94.6% 82.7%
3516452 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.58 43.0 3.09e-01 81.1% 56.1%