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NC_010495.1__YP_001742077.1VIP004000040

Bact-Vir

NC_010495.1__YP_001742077.1__VIP0040__00040

Identity

Accession:: NC_010495 ↗
Kingdom:: phage

Quality

84.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Macdonaldcampvirus› Salmonella_phage_Vi_II-E1

TaxID: 424716

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 29-73

PDB

Domain cluster: rep: OP889247.1__WAX22170.1__AVP1_0060__00060__D14-51

D2 high residues 81-158

PDB

Domain cluster: rep: MH719082.1__AXY86119.1__X__00064__D210-266

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF18668.7 best	Tail_spike_N	48.3	1.20e-12	75.6%	77.1%

D3 high residues 161-418

PDB

Domain cluster: rep: NC_041929.1__YP_009601433.1__FDH46_gp170__00308__D30-40_212-440

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03629.25 best	SASA	53.7	3.20e-14	91.1%	95.1%

CATH (26)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1zmbA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.87	76.0	7.82e-01	96.1%	93.9%
2aeaA00	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.83	75.0	7.79e-01	94.6%	98.0%
6hfzA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.80	59.0	6.45e-01	97.7%	90.2%
4q9aA00	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.75	60.0	6.54e-01	95.3%	97.7%
3rjtA00	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.73	59.0	6.43e-01	96.9%	99.1%
4k7jA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.73	58.0	6.16e-01	97.7%	92.5%
7toiA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.72	57.0	6.19e-01	93.8%	96.7%
2o14A02	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.72	55.0	6.15e-01	94.2%	98.5%
3milB00	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.69	55.0	5.75e-01	94.6%	88.2%
3t1oA00	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.69	47.0	5.39e-01	94.2%	92.7%
7br2D01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.68	54.0	5.91e-01	94.6%	97.2%
3l2oB02	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.67	45.0	5.37e-01	93.0%	99.4%
7ztnA01	3.40.50.1110	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase	0.66	58.0	5.48e-01	92.2%	100.0%
2csuA03	3.40.50.261	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains	0.64	40.0	4.86e-01	95.0%	94.6%
1oizA02	3.40.525.10	Alpha Beta › 3-Layer(aba) Sandwich › Phosphatidylinositol Transfer Protein Sec14p › CRAL-TRIO lipid binding domain	0.60	36.0	4.13e-01	79.5%	77.7%
3i5xA01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.57	36.0	3.73e-01	81.8%	64.8%
2py6A03	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.56	36.0	4.22e-01	93.0%	91.7%
5jipA01	3.20.20.80	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases	0.54	43.0	4.59e-01	91.9%	93.4%
3c0kA03	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.53	36.0	3.96e-01	94.6%	82.2%
3ndoA00	3.20.20.70	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I	0.53	40.0	4.29e-01	93.0%	89.3%
1y1pA01	3.40.50.720	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain	0.52	47.0	4.37e-01	95.7%	91.4%
3oa3A00	3.20.20.70	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I	0.52	40.0	4.04e-01	91.9%	79.4%
1vcvA00	3.20.20.70	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I	0.51	40.0	4.30e-01	94.2%	94.7%
3ragB00	3.40.50.410	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain	0.50	42.0	4.45e-01	96.1%	99.6%
1reqB01	3.20.20.240	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Methylmalonyl-CoA mutase	0.50	44.0	3.67e-01	92.2%	58.4%
4mj3B00	3.40.50.1820	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain	0.50	42.0	3.97e-01	86.8%	95.4%

ECOD (28)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3452250	2007.5.1.3 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA	0.87	75.0	7.71e-01	94.2%	91.2%
10060	2007.5.1.3 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA	0.87	76.0	7.38e-01	96.5%	82.6%
3683753	2007.5.1.3 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA	0.83	76.0	7.79e-01	94.6%	96.8%
4319241	2007.5.1.3 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA	0.79	72.0	7.29e-01	93.8%	98.0%
1298650	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.75	60.0	6.54e-01	95.3%	97.7%
1144534	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.73	59.0	6.37e-01	96.5%	97.3%
4105192	2007.1.3.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like	0.73	37.0	4.54e-01	94.6%	75.2%
4478613	2007.5.1.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase	0.70	56.0	6.16e-01	93.4%	100.0%
4380093	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.70	56.0	6.16e-01	93.8%	100.0%
4213770	2007.5.1.1 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL	0.69	63.0	6.16e-01	95.0%	97.5%
2724001	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.69	57.0	6.13e-01	94.2%	98.6%
3589770	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.69	63.0	6.42e-01	96.5%	96.8%
4175296	2004.1.1.0 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases	0.65	47.0	5.09e-01	94.6%	86.4%
4490519	2003.1.1.120 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD-bd_HRPKS_sdrA	0.63	41.0	4.95e-01	96.9%	97.6%
4019941	2007.5.1.8 ↗	a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2	0.63	57.0	5.74e-01	94.6%	93.5%
4947989	2007.1.3.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like	0.62	33.0	4.42e-01	93.4%	98.5%
3608380	7579.1.1.23 ↗	a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › PAF-AH_p_II	0.61	51.0	4.27e-01	88.0%	81.1%
3712837	2004.1.1.0 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases	0.57	41.0	4.64e-01	93.8%	94.0%
3688465	2007.12.1.0 ↗	a/b three-layered sandwiches › Flavodoxin-like › Beta-D-glucan exohydrolase, C-terminal domain › Beta-D-glucan exohydrolase, C-terminal domain	0.57	40.0	4.49e-01	100.0%	90.2%
5010988	2004.1.1.67 ↗	a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CbiA	0.56	51.0	5.11e-01	96.5%	100.0%
3782622	2003.1.1.42 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_binding_2	0.56	43.0	4.76e-01	100.0%	98.5%
4982163	2002.1.1.44 ↗	a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › TatD_DNase	0.55	41.0	4.06e-01	95.0%	71.6%
4479041	2002.1.1.76 ↗	a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DeoC	0.54	40.0	4.39e-01	93.0%	92.1%
3689880	2003.1.1.20 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase	0.53	49.0	4.29e-01	97.7%	88.1%
4930325	7579.1.1.0 ↗	a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases	0.53	48.0	4.40e-01	97.7%	83.9%
3708205	2003.1.1.0 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains	0.52	48.0	4.42e-01	99.2%	90.7%
3501950	2002.1.1.13 ↗	a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Aldo_ket_red	0.51	38.0	3.79e-01	83.3%	72.6%
4022050	7579.1.1.51 ↗	a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DUF676	0.50	45.0	4.41e-01	95.3%	89.3%

D4 high residues 467-581

PDB

Domain cluster: rep: SRR1747023_scaffold_5_prodigal-single.1__X__X__00146__D455-587

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3wp8A02	2.150.10.10	Mainly Beta › 2 Solenoid › Alkaline Protease, subunit P, domain 1 › Serralysin-like metalloprotease, C-terminal	0.77	73.0	6.54e-01	99.1%	75.0%
2xqhA01	2.150.10.10	Mainly Beta › 2 Solenoid › Alkaline Protease, subunit P, domain 1 › Serralysin-like metalloprotease, C-terminal	0.76	70.0	6.59e-01	98.3%	85.2%
3tv0A00	2.160.10.10	Mainly Beta › 3 Solenoid › UDP N-Acetylglucosamine Acyltransferase; domain 1 › Hexapeptide repeat proteins	0.69	60.0	5.62e-01	95.7%	93.0%
4n27A00	2.160.10.10	Mainly Beta › 3 Solenoid › UDP N-Acetylglucosamine Acyltransferase; domain 1 › Hexapeptide repeat proteins	0.67	60.0	5.26e-01	99.1%	81.7%
2yo0A01	2.150.10.10	Mainly Beta › 2 Solenoid › Alkaline Protease, subunit P, domain 1 › Serralysin-like metalloprotease, C-terminal	0.63	58.0	5.13e-01	99.1%	71.1%
3oh3A02	2.160.10.30	Mainly Beta › 3 Solenoid › UDP N-Acetylglucosamine Acyltransferase; domain 1 ›	0.53	37.0	3.53e-01	72.2%	100.0%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5055775	208.2.1.0 ↗	beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Adhesin YadA, collagen-binding domain › Adhesin YadA, collagen-binding domain	0.75	71.0	5.50e-01	100.0%	58.7%

D5 high residues 630-689_762-794

PDB

Domain cluster: rep: OP558001.1__WJJ58412.1__NDO71_orf046__00046__D533-638

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF13884.12 best	Peptidase_S74	37.3	3.70e-09	49.5%	70.7%

D6 high residues 692-757

PDB

Domain cluster: representative

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3vwoA02	2.10.70.40	Mainly Beta › Ribbon › Complement Module; domain 1 › peptidoglycan hydrolase	0.70	32.0	3.59e-01	93.9%	51.0%
3ksrA01	6.20.370.100	Special › Other non-globular › Rhinovirus 14, subunit 4 ›	0.62	30.0	3.69e-01	100.0%	100.0%
2b9dA01	3.30.160.330	Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain ›	0.62	30.0	3.60e-01	97.0%	66.7%
4f0aB02	3.30.2460.20	Alpha Beta › 2-Layer Sandwich › Endo-n-acetylneuraminidase fold › Wnt (Wingless and Int-1), C-terminal domain	0.61	36.0	3.61e-01	97.0%	55.9%
4ec7A00	2.10.90.10	Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines	0.54	35.0	3.08e-01	90.9%	40.7%
4bqqB02	3.90.1750.20	Alpha Beta › Alpha-Beta Complex › Hect, E3 ligase catalytic domain fold › Putative Large Serine Recombinase; Chain B, Domain 2	0.51	37.0	2.73e-01	78.8%	28.4%

ECOD (8)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5029482	295.1.1.0 ↗	a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain	0.63	34.0	3.24e-01	74.2%	42.5%
None	—		0.61	33.0	2.69e-01	100.0%	27.2%
3926492	385.1.1.0 ↗	few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines	0.59	38.0	3.02e-01	86.4%	29.5%
3218183	385.1.1.0 ↗	few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines	0.59	37.0	2.86e-01	83.3%	26.2%
3794286	385.1.1.0 ↗	few secondary structure elements › Cystine-knot cytokines › Cystine-knot cytokines › Cystine-knot cytokines	0.58	37.0	3.21e-01	83.3%	40.0%
3717787	206.1.1.1 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase	0.53	36.0	2.32e-01	74.2%	94.6%
5071965	512.1.1.1 ↗	a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st	0.51	34.0	3.16e-01	97.0%	48.4%
4990821	7571.1.1.1 ↗	a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N	0.50	38.0	2.52e-01	81.8%	74.9%