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MW900438.1__QVJ07718.1__S1R3Y_000009__00009

Bact-Vir

MW900438.1__QVJ07718.1__S1R3Y_000009__00009

Identity

Accession:
MW900438 ↗
Kingdom:
phage

Quality

67.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_vB_ValP_VA-RY-3

TaxID: 2831177

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 4-59
PDB
Domain cluster: representative
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.94 69.0 6.72e-01 76.8% 71.7%
1l5jA03 3.40.1060.10 Alpha Beta › 3-Layer(aba) Sandwich › Aconitase; Domain 2 › Aconitase, Domain 2 0.88 63.0 4.32e-01 82.1% 24.3%
1zmbA02 6.10.170.10 Special › Helix non-globular › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.84 52.0 6.28e-01 80.4% 100.0%
3zxsC02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.82 60.0 4.29e-01 76.8% 98.7%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.81 58.0 5.27e-01 76.8% 55.8%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.81 58.0 5.32e-01 76.8% 62.2%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.81 60.0 4.66e-01 78.6% 38.8%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.77 70.0 5.17e-01 100.0% 50.7%
1rsoB00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.77 52.0 5.30e-01 80.4% 71.4%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.77 70.0 5.76e-01 100.0% 71.9%
1y74A00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.77 56.0 5.64e-01 78.6% 77.2%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.76 69.0 5.98e-01 100.0% 72.3%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.76 68.0 5.50e-01 100.0% 66.7%
2oezA02 1.10.3900.10 Mainly Alpha › Orthogonal Bundle › YacF-like › YacF-like 0.74 67.0 4.75e-01 100.0% 65.6%
3d2eA06 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.72 65.0 5.10e-01 100.0% 53.1%
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.71 49.0 3.78e-01 73.2% 56.2%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.70 63.0 4.75e-01 100.0% 52.4%
1ywmA02 1.20.1270.150 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Surface Active Protein 0.69 62.0 5.56e-01 100.0% 72.4%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.69 47.0 4.26e-01 71.4% 50.6%
1jalA03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.69 57.0 5.16e-01 100.0% 66.7%
3iylU02 1.10.287.1520 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 49.0 5.00e-01 76.8% 79.2%
2khmA01 1.10.10.1350 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain 0.67 47.0 3.81e-01 75.0% 58.3%
1ailA00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.66 47.0 4.38e-01 75.0% 60.0%
3ke6A02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.66 58.0 4.49e-01 100.0% 82.7%
2keyA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.65 47.0 3.83e-01 78.6% 41.1%
4cpgA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.63 43.0 4.08e-01 71.4% 58.0%
2wyhB04 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.63 51.0 4.40e-01 100.0% 70.3%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 3.97e-01 78.6% 60.7%
4finB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 41.0 2.71e-01 73.2% 15.4%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 50.0 3.57e-01 96.4% 87.0%
1j78A05 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.60 48.0 4.79e-01 92.9% 93.3%
4nleA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.59 51.0 4.71e-01 100.0% 73.7%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.54 41.0 3.79e-01 98.2% 64.0%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 44.0 3.85e-01 100.0% 95.8%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.98 72.0 5.39e-01 76.8% 36.1%
5036455 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.97 70.0 4.26e-01 75.0% 14.5%
3268365 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.96 71.0 4.81e-01 76.8% 25.3%
3187917 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.94 69.0 4.74e-01 78.6% 26.1%
3455580 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.94 71.0 4.43e-01 78.6% 18.0%
3555742 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.93 70.0 5.93e-01 78.6% 56.5%
3842812 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.87 65.0 4.23e-01 78.6% 20.9%
4641055 2004.1.1.6 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran,oligo_HPY 0.87 65.0 3.81e-01 78.6% 12.6%
3412555 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.85 63.0 4.99e-01 78.6% 40.9%
3218210 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.84 62.0 3.86e-01 78.6% 16.1%
3355246 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.83 60.0 5.28e-01 76.8% 53.8%
3457663 192.29.1.178 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › PF28703 0.82 74.0 5.98e-01 100.0% 63.8%
3171529 5025.1.1.7 ↗ extended segments › PetL subunit of the cytochrome b6f complex › PetL subunit of the cytochrome b6f complex › PetL subunit of the cytochrome b6f complex › Erv26 0.82 75.0 5.65e-01 100.0% 49.6%
4983736 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.82 77.0 6.25e-01 100.0% 73.7%
4291782 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.81 75.0 5.87e-01 100.0% 62.7%
4976222 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.81 75.0 5.88e-01 100.0% 63.6%
4114241 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.80 74.0 5.98e-01 100.0% 69.0%
4561725 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.80 74.0 5.86e-01 100.0% 65.7%
3972525 633.2.1.8 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein › PA2817 0.79 70.0 5.40e-01 100.0% 44.8%
3282520 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.79 63.0 5.83e-01 85.7% 82.9%
4290275 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.79 71.0 5.64e-01 100.0% 62.7%
5023598 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.78 72.0 5.81e-01 100.0% 66.0%
3810077 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.78 72.0 5.07e-01 100.0% 56.8%
4446572 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.77 71.0 5.59e-01 100.0% 62.7%
3365581 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.77 70.0 5.44e-01 100.0% 60.0%
4073103 4952.1.1.1 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_1 0.77 70.0 5.44e-01 100.0% 60.0%
4459277 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.76 68.0 5.69e-01 100.0% 70.5%
4231910 4168.1.1.1 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › HAMP 0.76 56.0 4.51e-01 78.6% 40.9%
3981585 5086.1.1.84 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_MFP_RND 0.76 54.0 4.95e-01 78.6% 57.3%
4457905 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.75 68.0 5.56e-01 100.0% 70.0%
3973636 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.75 53.0 4.90e-01 78.6% 57.3%
3783029 633.31.1.0 ↗ alpha bundles › Bromodomain-like › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase › Four-helical bundle insertion domain in pyruvate-ferredoxin oxidoreductase 0.75 59.0 5.26e-01 100.0% 61.3%
4251398 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.75 67.0 5.39e-01 100.0% 71.4%
3286824 632.2.1.17 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › DUF1707 0.73 54.0 5.92e-01 100.0% 97.8%
3621960 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.72 65.0 4.85e-01 100.0% 44.4%
3988447 5043.1.1.0 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.70 50.0 5.10e-01 80.4% 80.0%
3317228 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 50.0 4.40e-01 76.8% 52.9%
3282626 632.3.1.9 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain › DUF1707 0.69 51.0 5.57e-01 100.0% 97.8%
4124570 1054.1.1.1 ↗ alpha bundles › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arg_decarbox_C 0.68 48.0 5.15e-01 91.1% 93.3%
5043880 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.68 59.0 5.17e-01 100.0% 82.4%
3487550 101.1.1.64 ↗ alpha arrays › HTH › HTH › Three-helical HTH › tRNA_bind_2 0.60 37.0 3.55e-01 76.8% 51.6%
3479771 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.60 52.0 3.53e-01 98.2% 48.1%
3203010 605.1.1.139 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › LETM1_RBD 0.57 45.0 3.92e-01 98.2% 75.0%
D2 high residues 105-205
PDB
Domain cluster: representative