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MH925092.1__QAY01979.1__VpaJT1_50__00049

Bact-Vir

MH925092.1__QAY01979.1__VpaJT1_50__00049

Identity

Accession:
MH925092 ↗
Kingdom:
phage

Quality

92.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_VpaJT_1

TaxID: 2484247

Cluster

View cluster (2 members)

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 38-97
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3cisH00 3.40.50.12370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 49.0 3.24e-01 85.0% 46.8%
2zyzC00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.65 45.0 3.86e-01 100.0% 45.8%
2w3sB03 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.63 42.0 3.62e-01 100.0% 42.6%
4yt9A01 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.63 53.0 3.34e-01 95.0% 87.0%
2y0cB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 50.0 3.56e-01 93.3% 97.5%
2zgiD02 3.20.10.10 Alpha Beta › Alpha-Beta Barrel › D-amino Acid Aminotransferase; Chain A, domain 2 › D-amino Acid Aminotransferase, subunit A, domain 2 0.61 38.0 2.95e-01 100.0% 26.0%
3gm8A03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.60 51.0 3.25e-01 96.7% 34.4%
6x50A03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 47.0 3.32e-01 90.0% 53.8%
1zbrA00 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.59 49.0 3.09e-01 95.0% 90.6%
1qhlA00 3.40.1140.10 Alpha Beta › 3-Layer(aba) Sandwich › N-terminal domain of mukB › 0.58 43.0 2.99e-01 80.0% 91.1%
3r3pB00 3.40.960.10 Alpha Beta › 3-Layer(aba) Sandwich › Endonuclease; Chain A › VSR Endonuclease 0.58 40.0 3.44e-01 71.7% 58.2%
5e0sB00 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.58 47.0 3.31e-01 91.7% 29.9%
4mfiA00 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 46.0 2.83e-01 91.7% 76.9%
3laxA00 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.56 47.0 3.95e-01 95.0% 62.3%
1dljA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 45.0 3.17e-01 90.0% 94.1%
3nd5A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 48.0 3.61e-01 98.3% 71.1%
8inpA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.55 46.0 3.16e-01 100.0% 39.4%
4g1iA02 3.30.300.170 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.55 46.0 4.38e-01 95.0% 90.1%
3bt7A02 2.40.50.1070 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 46.0 3.50e-01 96.7% 94.5%
3wxmB02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.53 47.0 3.71e-01 98.3% 92.6%
1wotA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.53 45.0 3.85e-01 95.0% 75.5%
2g9zA02 3.40.50.10240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin pyrophosphokinase, catalytic domain 0.53 46.0 3.37e-01 100.0% 50.6%
4q5tA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.53 42.0 3.25e-01 90.0% 91.8%
4aq4A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.53 43.0 3.00e-01 90.0% 52.5%
1g01A00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 43.0 2.75e-01 96.7% 41.7%
4njhA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 43.0 3.10e-01 100.0% 74.2%
4gqoA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 41.0 2.97e-01 91.7% 81.5%
1hv8A02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 44.0 3.34e-01 98.3% 98.0%
6opmD01 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.51 38.0 2.60e-01 81.7% 81.1%
1nnnA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.51 43.0 3.46e-01 96.7% 54.5%
4nl4H03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 38.0 2.82e-01 88.3% 55.6%
1jflA02 3.40.50.1860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 43.0 3.61e-01 98.3% 67.9%
3fysA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.50 45.0 3.50e-01 100.0% 79.1%
6upsA01 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.50 39.0 3.06e-01 91.7% 59.4%
4zs9A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 40.0 3.01e-01 91.7% 90.9%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3252046 316.1.1.56 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PF26128 0.85 68.0 4.46e-01 98.3% 22.1%
3268750 316.1.1.56 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PF26128 0.84 67.0 4.68e-01 100.0% 29.1%
3274698 316.1.1.56 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PF26128 0.79 66.0 4.36e-01 98.3% 22.9%
4167187 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.71 48.0 4.99e-01 100.0% 76.4%
3715693 2003.1.1.17 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_Gly3P_dh_N 0.69 55.0 3.69e-01 90.0% 94.2%
4837880 316.1.1.1 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PolyA_pol 0.67 57.0 4.51e-01 100.0% 52.6%
3989293 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.64 47.0 3.81e-01 100.0% 40.9%
5001172 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.63 50.0 4.12e-01 100.0% 49.5%
4502519 2004.1.1.33 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C,RecQ_Zn_bind 0.62 42.0 2.88e-01 71.7% 49.4%
3910441 2004.1.1.33 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C,RecQ_Zn_bind 0.62 42.0 3.03e-01 71.7% 60.0%
5029665 327.7.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like 0.62 50.0 5.23e-01 95.0% 96.4%
3935176 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.62 43.0 2.98e-01 73.3% 65.7%
4117435 2004.1.1.33 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C,RecQ_Zn_bind 0.61 42.0 2.85e-01 71.7% 49.6%
3867423 2004.1.1.364 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD+Helicase_C 0.61 47.0 2.81e-01 86.7% 30.8%
1523629 7523.1.1.9 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.60 39.0 3.21e-01 70.0% 33.6%
3962967 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 41.0 2.75e-01 71.7% 61.2%
3990580 2004.1.1.364 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD+Helicase_C 0.59 45.0 2.74e-01 86.7% 34.2%
3635498 2004.1.1.364 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD+Helicase_C 0.58 44.0 2.66e-01 86.7% 31.9%
3458011 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.58 44.0 3.11e-01 90.0% 62.6%
4068026 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.57 38.0 2.78e-01 70.0% 24.9%
3833823 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.55 45.0 3.00e-01 91.7% 66.5%
4014985 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.55 41.0 2.45e-01 81.7% 27.4%
4977853 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 44.0 3.17e-01 91.7% 58.9%
5047895 327.5.1.10 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › PF27533 0.54 46.0 3.98e-01 95.0% 64.2%
3380943 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.54 42.0 2.84e-01 86.7% 68.6%
5064964 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.54 45.0 3.94e-01 95.0% 74.7%
4120130 2005.1.1.13 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CTP_transf_like 0.53 45.0 3.40e-01 98.3% 67.9%
3570604 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.53 44.0 3.57e-01 98.3% 95.4%
3491980 2004.1.1.29 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD 0.53 44.0 3.00e-01 98.3% 46.5%
4260774 2007.1.19.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › FabD/lysophospholipase-like › SAT 0.52 45.0 2.93e-01 98.3% 96.6%
5019592 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.52 43.0 2.99e-01 96.7% 92.2%
4598966 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 43.0 3.19e-01 96.7% 89.9%
3815755 2005.1.1.3 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.51 40.0 3.13e-01 96.7% 87.6%
3679686 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 44.0 3.05e-01 100.0% 48.4%
3483530 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 42.0 2.88e-01 96.7% 46.5%
5045955 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 43.0 3.05e-01 100.0% 64.2%
3280681 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 41.0 2.82e-01 95.0% 83.2%
2137648 2004.1.1.24 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom,Helicase_C 0.51 44.0 3.04e-01 98.3% 51.9%
3426410 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 42.0 3.03e-01 96.7% 85.3%
4937972 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 44.0 2.86e-01 98.3% 31.9%
3950210 323.1.1.0 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.50 37.0 2.96e-01 81.7% 75.6%
3594466 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 42.0 3.18e-01 98.3% 93.1%
3987781 327.13.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system 0.50 41.0 3.81e-01 95.0% 75.0%
4992362 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.50 40.0 3.32e-01 95.0% 55.8%