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NC_020868.1__YP_007676516.1__VPMG_00026__00026

Bact-Vir

NC_020868.1__YP_007676516.1__VPMG_00026__00026

Identity

Accession:
NC_020868 ↗
Kingdom:
phage

Quality

86.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Stoningtonvirus› Vibrio_phage_VBP32

TaxID: 754072

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 high residues 10-69
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vl9B00 2.60.120.180 Mainly Beta › Sandwich › Jelly Rolls › Glycoside hydrolase family 11/12, catalytic domain 0.59 40.0 2.76e-01 83.3% 19.0%
1xa6A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 40.0 3.46e-01 78.3% 85.6%
2l2nA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 40.0 3.79e-01 75.0% 84.5%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 40.0 3.84e-01 76.7% 81.7%
1eotA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 44.0 4.26e-01 96.7% 75.7%
2d8iA01 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.56 41.0 3.73e-01 81.7% 84.1%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 41.0 3.50e-01 81.7% 63.8%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.56 46.0 3.65e-01 96.7% 69.9%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 40.0 3.79e-01 76.7% 81.9%
1ogyA01 3.30.200.210 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › 0.55 46.0 3.79e-01 100.0% 84.7%
1bf5A04 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.55 41.0 3.48e-01 83.3% 74.3%
2epbA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 41.0 4.06e-01 95.0% 82.4%
3sluA02 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 38.0 3.02e-01 78.3% 90.5%
1sfeA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.52 42.0 3.85e-01 100.0% 66.7%
8in8C01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 40.0 2.76e-01 90.0% 80.5%
5wceA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 42.0 3.43e-01 96.7% 79.1%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 40.0 3.56e-01 95.0% 57.7%
7uzsX02 3.90.260.10 Alpha Beta › Alpha-Beta Complex › Coagulation Factor XIII; Chain A, domain 2 › Transglutaminase-like 0.51 43.0 2.84e-01 100.0% 51.7%
1vkwA01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.51 35.0 2.87e-01 71.7% 37.2%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5039125 375.1.1.83 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-TFIIB 0.77 47.0 4.60e-01 70.0% 56.9%
5038361 4294.1.1.13 ↗ few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › Zn_ribbon_TFIIB 0.73 45.0 5.00e-01 70.0% 82.2%
5030311 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.71 44.0 4.60e-01 70.0% 67.3%
3819021 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.61 41.0 2.74e-01 71.7% 46.2%
4972532 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.60 40.0 3.60e-01 70.0% 73.3%
3818314 3202.1.1.1 ↗ a+b two layers › Alr2454 protein › Alr2454 protein › Alr2454 protein › DUF3067 0.60 40.0 3.43e-01 70.0% 86.7%
3883088 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.59 41.0 3.98e-01 75.0% 95.7%
4117020 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.59 37.0 3.75e-01 78.3% 63.3%
3419351 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.59 43.0 4.28e-01 78.3% 75.4%
4992408 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.59 37.0 4.04e-01 70.0% 84.4%
3510695 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 43.0 4.00e-01 80.0% 73.8%
3927652 2484.5.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase 0.59 47.0 4.01e-01 93.3% 82.7%
5071179 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.59 39.0 3.94e-01 70.0% 68.3%
3967506 300.1.1.8 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PLDc_2 0.58 43.0 2.90e-01 80.0% 60.8%
3866247 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.58 41.0 3.96e-01 83.3% 65.7%
3612106 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.55 42.0 4.02e-01 90.0% 70.7%
3970048 4292.2.1.0 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain 0.54 42.0 3.88e-01 86.7% 74.4%
3651210 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.54 36.0 3.63e-01 70.0% 70.0%
5056316 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.53 43.0 2.75e-01 98.3% 94.1%
3388135 4292.2.1.1 ↗ a+b two layers › FlaG-like › MAGUK binding stalk (MBS) domain › MAGUK binding stalk (MBS) domain › FlaG 0.53 41.0 3.84e-01 86.7% 78.7%
3232550 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 42.0 3.80e-01 90.0% 63.5%
4930970 375.1.1.338 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF7479 0.53 35.0 3.61e-01 70.0% 74.5%
3299579 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 37.0 3.52e-01 73.3% 67.1%
4952072 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.52 36.0 3.86e-01 75.0% 98.0%
4944756 3604.1.1.0 ↗ a+b two layers › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain › Uncharacterized protein MK0293 C-terminal domain 0.52 36.0 3.61e-01 75.0% 90.0%
4954522 878.1.1.1 ↗ a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › DUF3194 0.51 35.0 3.11e-01 71.7% 69.1%
3823787 220.1.1.74 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PIG-H 0.51 41.0 3.31e-01 96.7% 61.4%
3503356 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.51 36.0 3.14e-01 75.0% 65.3%
4889522 3321.1.1.2 ↗ a+b two layers › Meander beta sheet domain in fatty acid synthase subunit beta › Meander beta sheet domain in fatty acid synthase subunit beta › Meander beta sheet domain in fatty acid synthase subunit beta › DNA_pol_B_N 0.51 36.0 2.93e-01 75.0% 61.6%