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KX581096.3__AOT26807.1__pVa5_0052__00051

Bact-Vir

KX581096.3__AOT26807.1__pVa5_0052__00051

Identity

Accession:
KX581096 ↗
Kingdom:
phage

Quality

84.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_vB_VspP_pVa5_12Jun

TaxID: 2890992

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 7-70
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 59.0 5.00e-01 89.1% 89.4%
1jvmB00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 55.0 4.73e-01 82.8% 93.0%
4h33A00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 55.0 4.87e-01 84.4% 94.5%
3spcA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 53.0 4.24e-01 81.2% 92.1%
4wpcA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.70 55.0 3.58e-01 85.9% 19.8%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.69 52.0 5.15e-01 79.7% 80.3%
3nvoB02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.68 55.0 4.54e-01 89.1% 78.4%
3bg2A03 1.10.3410.10 Mainly Alpha › Orthogonal Bundle › putative deoxyguanosinetriphosphate triphosphohydrolase fold › putative deoxyguanosinetriphosphate triphosphohydrolase like domain 0.66 51.0 4.49e-01 84.4% 70.8%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 51.0 4.46e-01 84.4% 78.7%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.65 50.0 4.63e-01 84.4% 97.6%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 53.0 4.44e-01 93.8% 56.2%
3fcnA00 1.20.1220.20 Mainly Alpha › Up-down Bundle › Malate Synthase G; Chain: A; Domain 4 › Uncharcterised protein PF01724 0.63 52.0 3.99e-01 95.3% 61.4%
3behB01 1.20.120.540 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels 0.63 54.0 4.40e-01 93.8% 88.0%
4gx0A01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 50.0 4.22e-01 85.9% 80.6%
4ivfA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 51.0 4.31e-01 95.3% 61.2%
3craA02 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.62 47.0 3.79e-01 82.8% 48.4%
8b6jF01 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.62 44.0 4.41e-01 76.6% 74.6%
3mzvA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.61 52.0 3.39e-01 95.3% 70.6%
2qksA01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 48.0 4.09e-01 85.9% 80.2%
8ctsB01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 46.0 4.23e-01 84.4% 95.4%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 46.0 3.90e-01 87.5% 51.7%
1wjzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.59 48.0 4.27e-01 90.6% 71.3%
1gwcA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 49.0 3.83e-01 93.8% 45.4%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.58 47.0 4.49e-01 92.2% 80.8%
4hteA03 1.10.167.30 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › 0.52 42.0 3.97e-01 93.8% 72.5%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3489761 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.76 59.0 3.97e-01 82.8% 35.6%
3668287 601.2.1.5 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › Ctr 0.75 64.0 5.31e-01 93.8% 56.4%
3968965 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.74 61.0 5.44e-01 90.6% 73.3%
3595101 3718.1.1.0 ↗ alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.73 52.0 4.29e-01 73.4% 42.7%
3315495 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.73 58.0 5.29e-01 85.9% 65.9%
4174467 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 0.73 56.0 4.95e-01 81.2% 97.8%
3929377 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.73 59.0 5.37e-01 89.1% 83.5%
5077926 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.72 53.0 4.13e-01 78.1% 44.4%
3740332 1128.1.1.0 ↗ alpha bundles › LYR protein › LYR protein › LYR protein 0.71 48.0 4.49e-01 70.3% 82.5%
3734403 1065.1.1.1 ↗ alpha bundles › SPX domain › SPX domain › SPX domain › SPX 0.71 60.0 4.32e-01 93.8% 55.1%
3628093 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.71 58.0 4.96e-01 90.6% 73.3%
2739406 3945.1.1.0 ↗ alpha superhelices › N-terminal fragment of dynein heavy chain › N-terminal fragment of dynein heavy chain › N-terminal fragment of dynein heavy chain 0.70 50.0 3.84e-01 75.0% 33.8%
3500290 101.1.12.0 ↗ alpha arrays › HTH › HTH › HTH motif inserted in other structures 0.70 56.0 5.20e-01 85.9% 83.7%
3079134 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.70 55.0 3.46e-01 84.4% 17.8%
3994910 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.69 56.0 4.25e-01 89.1% 48.7%
4180563 3978.1.1.1 ↗ alpha complex topology › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › Integral membrane Acyl-CoA desaturase › FA_desaturase 0.68 57.0 3.63e-01 92.2% 21.3%
3797019 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.68 56.0 3.63e-01 90.6% 25.3%
4942757 606.1.1.1 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.68 57.0 4.79e-01 90.6% 75.2%
3396400 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 58.0 4.59e-01 92.2% 67.2%
3900923 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 55.0 4.81e-01 92.2% 71.0%
4013428 246.2.1.0 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases 0.68 60.0 3.82e-01 100.0% 29.2%
3503770 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.67 56.0 4.32e-01 92.2% 55.2%
3648687 604.12.1.89 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › CDP-OH_P_transf 0.67 57.0 5.09e-01 100.0% 90.5%
3495199 109.4.1.1197 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TNPO3_IPO13_4th 0.66 58.0 3.61e-01 98.4% 41.4%
5055919 159.1.1.4 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › PRA-PH 0.66 50.0 4.52e-01 82.8% 73.3%
3260931 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.66 59.0 3.65e-01 100.0% 19.7%
3952598 150.7.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE 0.66 51.0 4.60e-01 84.4% 84.4%
4946099 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.65 46.0 4.21e-01 73.4% 56.6%
3471396 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.65 54.0 4.77e-01 93.8% 69.5%
3328264 109.4.1.46 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IBN_N 0.65 56.0 3.36e-01 98.4% 24.9%
3593998 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.64 51.0 4.11e-01 89.1% 52.3%
4444553 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.64 49.0 3.16e-01 84.4% 17.2%
4015549 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 55.0 3.42e-01 100.0% 20.5%
3992612 604.6.1.1 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.62 52.0 4.73e-01 95.3% 73.3%
3909490 109.1.1.16 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_6 0.62 52.0 3.84e-01 93.8% 34.7%
3408830 864.1.1.2 ↗ a+b two layers › DLC › DLC › DLC › Tctex-1 0.62 41.0 3.52e-01 71.9% 41.3%
3651522 3016.1.1.14 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Met_gamma_lyase 0.61 45.0 3.67e-01 78.1% 76.0%
3288128 1079.1.1.7 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › SfLAP 0.60 47.0 3.51e-01 89.1% 85.0%
3190136 109.4.1.570 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vps8 0.58 50.0 3.75e-01 100.0% 47.1%
3437734 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.57 44.0 4.42e-01 82.8% 83.1%
3600867 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.54 37.0 3.35e-01 81.2% 51.1%
3260526 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.51 39.0 3.55e-01 89.1% 65.3%
D2 high residues 82-208
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1w53A00 1.10.1240.30 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain 0.66 34.0 4.07e-01 75.6% 73.8%
3m03B00 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.64 44.0 4.97e-01 99.2% 93.7%
3nbiA01 1.10.8.1020 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › RecQ-mediated genome instability protein 1, N-terminal domain 0.60 26.0 3.84e-01 84.3% 91.4%
1sqgA01 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.59 43.0 4.23e-01 99.2% 68.8%
1jkwA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.59 39.0 3.59e-01 96.1% 48.3%
1m2vB01 1.20.120.730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sec23/Sec24 helical domain 0.56 39.0 3.58e-01 71.7% 65.1%
4dveA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.56 48.0 4.26e-01 95.3% 69.8%
1gcvA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.56 40.0 3.96e-01 98.4% 69.3%
1kqpA00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.56 43.0 3.40e-01 82.7% 80.1%
4tkrA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.54 45.0 4.06e-01 92.1% 97.3%
4kk2B00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.54 46.0 3.38e-01 92.1% 66.7%
1q8cA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.53 38.0 3.79e-01 80.3% 70.5%
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.53 32.0 3.60e-01 99.2% 77.9%
2isyA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.50 34.0 3.32e-01 99.2% 62.3%
4fp4A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.50 41.0 3.39e-01 89.8% 74.1%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4665476 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.64 52.0 4.33e-01 99.2% 51.2%
3675163 3881.1.1.1 ↗ alpha bundles › CNOT9 binding domain CN9BD (DUF3819) › CNOT9 binding domain CN9BD (DUF3819) › CNOT9 binding domain CN9BD (DUF3819) › DUF3819 0.62 54.0 4.72e-01 95.3% 80.5%
5034766 604.40.1.2 ↗ alpha bundles › Spectrin repeat-like › Predicted bacterial vitamin B12 uptake system BtuM › Predicted bacterial vitamin B12 uptake system BtuM › DUF6580 0.58 52.0 4.38e-01 97.6% 67.0%
3699448 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.58 34.0 3.18e-01 95.3% 44.2%
5071122 3896.1.1.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase 0.56 48.0 4.29e-01 94.5% 83.8%
3924301 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.56 34.0 3.57e-01 71.7% 66.1%
5063669 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.55 26.0 3.26e-01 93.7% 72.0%
4390743 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.53 34.0 3.13e-01 73.2% 48.5%
3601251 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 45.0 3.56e-01 92.9% 74.1%
3581883 5048.1.1.0 ↗ alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like 0.52 39.0 3.48e-01 77.2% 60.6%
3929962 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.52 39.0 3.15e-01 78.0% 87.8%
3743063 633.24.1.0 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain 0.52 36.0 4.00e-01 70.9% 98.0%
4283760 1203.1.2.7 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › GNVR 0.52 41.0 4.01e-01 86.6% 76.4%
3969345 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.52 39.0 3.29e-01 80.3% 77.3%
3585742 102.1.2.18 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › OGG_N 0.51 35.0 2.84e-01 94.5% 35.4%
3782021 5081.1.1.4 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › DUF1751 0.51 46.0 3.93e-01 100.0% 98.6%
3648828 198.1.1.4 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › DUF3456 0.51 38.0 3.76e-01 79.5% 80.7%
3879763 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.50 35.0 2.83e-01 71.7% 72.1%
4030861 5051.1.1.10 ↗ alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › AA_permease_2 0.50 44.0 3.07e-01 98.4% 73.2%