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NC_055862.1__YP_010109747.1__KNV20_gp19__00019

Bact-Vir

Identity

Accession:: NC_055862 ↗
Kingdom:: phage

Quality

90.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Peduoviridae› Valbvirus› Vibrio_phage_ValB1MD-2

TaxID: 2759177

Cluster

View cluster (5 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 high residues 14-106_194-218

PDB

Domain cluster: rep: MH238466.1__AWY03247.1__X__00024__D19-153

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF05069.19 best	Phage_tail_S	35.0	1.80e-08	97.5%	59.5%

CATH (9)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4e1pA00	3.30.60.230	Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain	0.68	19.0	2.80e-01	83.1%	49.1%
1xexB00	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.65	43.0	3.85e-01	84.7%	49.1%
1whyA01	3.30.70.330	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain	0.57	30.0	3.63e-01	73.7%	80.6%
2y3mA02	3.30.1370.130	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 ›	0.56	28.0	3.66e-01	93.2%	96.4%
7kfuC02	1.20.120.920	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain	0.55	49.0	3.95e-01	99.2%	99.1%
7sk7A01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.55	41.0	3.19e-01	78.0%	96.8%
5unhA02	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.54	39.0	3.00e-01	75.4%	93.5%
1t6jA03	1.10.274.20	Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Phenylalanine ammonia-lyase 1; domain 3	0.52	40.0	4.19e-01	83.1%	100.0%
4djhA01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.51	40.0	3.01e-01	82.2%	93.7%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4480316	7502.1.1.0 ↗	a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS	0.61	25.0	2.98e-01	89.8%	55.0%
4305577	327.11.2.1 ↗	a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1	0.56	32.0	3.40e-01	89.8%	64.0%
3903882	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.55	40.0	2.94e-01	76.3%	87.4%
5011097	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	30.0	3.58e-01	90.7%	81.3%
4335820	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	32.0	3.62e-01	91.5%	77.6%
4809625	11.1.1.243 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › RET_CLD4	0.55	35.0	3.81e-01	96.6%	81.3%
3899209	5001.1.1.1 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1	0.54	37.0	3.11e-01	90.7%	42.1%
3714994	633.23.1.0 ↗	alpha bundles › Bromodomain-like › Claudin › Claudin	0.54	40.0	3.41e-01	78.0%	89.2%
3982462	4132.1.1.1 ↗	alpha bundles › IpaD-like › IpaD-like › IpaD-like › T3SS_TC	0.54	39.0	2.93e-01	76.3%	85.3%
5000805	327.11.2.3 ↗	a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_6	0.53	30.0	3.33e-01	89.8%	71.6%
None	—		0.51	39.0	2.94e-01	79.7%	90.5%
4417273	5054.1.1.6 ↗	alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TrkH	0.50	43.0	4.05e-01	94.1%	93.8%

D2 high residues 123-190

PDB

Domain cluster: rep: KY045851.1__APM00242.1__C5a_32__00032__D123-186

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3dsqA01	1.10.287.540	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.65	42.0	4.43e-01	79.4%	72.6%
3td7A02	1.20.120.1250	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sulfhydryl oxidase R596, ORFan domain	0.57	42.0	3.37e-01	79.4%	80.1%
2pqxA00	3.90.730.10	Alpha Beta › Alpha-Beta Complex › Ribonuclease Rh; Chain A › Ribonuclease T2-like	0.54	43.0	2.90e-01	85.3%	88.6%
1lbuA01	1.10.101.10	Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD	0.53	42.0	4.03e-01	94.1%	73.8%
1gep001	3.30.413.10	Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1	0.53	40.0	2.96e-01	80.9%	46.6%
2l9fA00	1.10.1200.10	Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like	0.53	43.0	3.74e-01	88.2%	60.8%
2mf4A01	1.10.1200.10	Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like	0.51	39.0	3.75e-01	88.2%	70.7%
1q5nA02	1.20.200.10	Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain)	0.51	37.0	2.71e-01	83.8%	88.1%
3eqvA03	3.40.710.10	Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily	0.51	41.0	3.14e-01	94.1%	85.1%
2pb2B01	3.90.1150.10	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1	0.50	36.0	2.89e-01	76.5%	62.7%
4uobA01	1.10.1670.10	Mainly Alpha › Orthogonal Bundle › Endonuclease Iii, domain 2 › Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)	0.50	36.0	3.05e-01	76.5%	45.7%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3219743	7060.1.1.1 ↗	alpha arrays › ELMO domain › ELMO domain › ELMO domain › ELMO_CED12	0.63	53.0	3.70e-01	89.7%	57.4%
3597964	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.56	47.0	3.10e-01	94.1%	83.6%
3958056	3016.1.1.0 ↗	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	0.54	39.0	3.31e-01	77.9%	65.3%
3932020	59.1.1.2 ↗	beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like › RNA_pol_Rpc4	0.53	36.0	3.11e-01	95.6%	41.7%
4977673	69.1.1.0 ↗	beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint	0.53	43.0	3.04e-01	91.2%	32.0%
5058154	131.1.1.0 ↗	alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like	0.52	44.0	3.13e-01	100.0%	77.4%
4934922	101.1.9.0 ↗	alpha arrays › HTH › HTH › Putative DNA-binding domain	0.51	38.0	3.73e-01	80.9%	92.0%
3716917	2484.1.1.45 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › CAF1	0.51	41.0	2.75e-01	94.1%	87.8%
4291953	101.1.9.5 ↗	alpha arrays › HTH › HTH › Putative DNA-binding domain › B5	0.51	41.0	3.63e-01	89.7%	93.0%
4277689	2002.1.1.56 ↗	a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Dus	0.50	40.0	2.52e-01	92.6%	71.5%