Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	Q	T	S	A	F	H	F	E	S	L	V	W	D	W	P	I	A	I	Y	L	F	L	I	G	I	S	A	G	L	V	T	L	A	V	L	L	R	R	F	Y	P	Q	A	G	G	A	D	S	T	L	L	R	T	T	L	I	V	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																				?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	G	A	V	I	L	G	L	L	I	L	V	F	H	L	T	R	P	W	T	F	W	K	L	M	F	H	Y	S	F	T	S	V	M	S	M	G	V	M	L	F	Q	L	Y	M	V	V	L	V	L	W	L	A	K	I	F	E	H	D	L
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	A	L	Q	Q	R	W	L	P	K	L	G	I	V	Q	K	V	L	S	L	L	T	P	V	H	R	G	L	E	T	L	M	L	V	L	A	V	L	L	G	A	Y	T	G	F	L	L	S	A	L	K	S	Y	P	F	L	N	N	P	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?		?	?	?				?	?																																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	P	V	L	F	L	F	S	G	I	S	S	G	A	A	V	A	L	I	A	M	A	I	R	Q	R	S	N	P	H	S	T	E	A	Q	F	V	H	R	M	E	I	P	V	V	W	G	E	I	F	L	L	V	A	F	F	V	G	L	A
Secondary structure
SS confidence
Disorder																									?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	G	D	D	G	K	V	R	A	L	V	A	A	L	G	G	G	F	W	T	W	W	F	W	L	G	V	A	G	L	G	L	I	V	P	M	L	L	K	P	W	V	N	R	S	S	G	I	P	A	V	L	A	A	C	G	A	S	L	V
Secondary structure
SS confidence
Disorder																																											?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.
Sequence		G	V	L	M	L	R	F	F	I	L	Y	A	G	Q	L	T	V	A
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2vpz chain G Region: 11 - 314 Aligned: 235 Modelled: 252 Confidence: 100.0% Identity: 22% PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure Phyre2 PDB 2w8a chain C Region: 13 - 314 Aligned: 290 Modelled: 282 Confidence: 53.3% Identity: 11% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 3hfx chain A Region: 13 - 313 Aligned: 292 Modelled: 292 Confidence: 24.9% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1xme chain A domain 1 Region: 14 - 281 Aligned: 250 Modelled: 257 Confidence: 22.4% Identity: 10% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 3eh4 chain A Region: 14 - 281 Aligned: 250 Modelled: 257 Confidence: 18.3% Identity: 10% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus Phyre2 PDB 1ejx chain B Region: 5 - 12 Aligned: 8 Modelled: 8 Confidence: 7.7% Identity: 38% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 2a5y chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 7.4% Identity: 15% PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator ced-9; PDBTitle: structure of a ced-4/ced-9 complex Phyre2 PDB 1zy3 chain A domain 1 Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 7.3% Identity: 20% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1ysg chain A domain 1 Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 7.2% Identity: 15% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 2yv6 chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 15% PDB header:apoptosis Chain: A: PDB Molecule:bcl-2 homologous antagonist/killer; PDBTitle: crystal structure of human bcl-2 family protein bak Phyre2 PDB 1bxl chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 15% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 2zt9 chain E Region: 17 - 33 Aligned: 17 Modelled: 17 Confidence: 6.6% Identity: 35% PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 Phyre2 PDB 1e9y chain A domain 1 Region: 5 - 12 Aligned: 8 Modelled: 8 Confidence: 6.6% Identity: 50% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 4ubp chain B Region: 5 - 12 Aligned: 8 Modelled: 8 Confidence: 6.5% Identity: 38% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 2o2f chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.5% Identity: 15% PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: solution structure of the anti-apoptotic protein bcl-2 in2 complex with an acyl-sulfonamide-based ligand Phyre2 PDB 3rko chain A Region: 18 - 113 Aligned: 85 Modelled: 96 Confidence: 6.3% Identity: 11% PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3chx chain F Region: 286 - 308 Aligned: 23 Modelled: 23 Confidence: 6.2% Identity: 17% PDB header:membrane protein Chain: F: PDB Molecule:pmoa; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) Phyre2 PDB 2xa0 chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.1% Identity: 15% PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: crystal structure of bcl-2 in complex with a bax bh32 peptide Phyre2 PDB 1g5m chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.1% Identity: 15% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1pq1 chain A Region: 10 - 29 Aligned: 20 Modelled: 20 Confidence: 6.1% Identity: 15% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 1 c2vpzG_ 2 c2w8aC_ 3 c3hfxA_ 4 d1xmea1 5 c3eh4A_ 6 d1ejxb_ 7 c2a5yA_ 8 d1zy3a1 9 d1ysga1 10 c2yv6A_ 11 d1bxla_ 12 c2zt9E_ 13 d1e9ya1 14 d4ubpb_ 15 c2o2fA_ 16 c3rkoA_ 17 c3chxF_ 18 c2xa0A_ 19 d1g5ma_ 20 d1pq1a_ 21 22 23 24 25 26

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2vpzG_ 100.0 22 PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure 2 c2w8aC_ 53.3 11 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 3 c3hfxA_ 24.9 11 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 4 d1xmea1 22.4 10 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 5 c3eh4A_ 18.3 10 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus 6 d1ejxb_ 7.7 38 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 7 c2a5yA_ 7.4 15 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator ced-9; PDBTitle: structure of a ced-4/ced-9 complex 8 d1zy3a1 7.3 20 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 9 d1ysga1 7.2 15 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 10 c2yv6A_ 6.8 15 PDB header:apoptosis Chain: A: PDB Molecule:bcl-2 homologous antagonist/killer; PDBTitle: crystal structure of human bcl-2 family protein bak 11 d1bxla_ 6.8 15 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 12 c2zt9E_ 6.6 35 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 13 d1e9ya1 6.6 50 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 14 d4ubpb_ 6.5 38 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 15 c2o2fA_ 6.5 15 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: solution structure of the anti-apoptotic protein bcl-2 in2 complex with an acyl-sulfonamide-based ligand 16 c3rkoA_ 6.3 11 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh-quinone oxidoreductase subunit a; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 17 c3chxF_ 6.2 17 PDB header:membrane protein Chain: F: PDB Molecule:pmoa; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) 18 c2xa0A_ 6.1 15 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis regulator bcl-2; PDBTitle: crystal structure of bcl-2 in complex with a bax bh32 peptide 19 d1g5ma_ 6.1 15 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 20 d1pq1a_ 6.1 15 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 21 d1o0la_ not modelled 6.0 20 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 22 c3qbrA_ not modelled 6.0 33 PDB header:apoptosis Chain: A: PDB Molecule:sjchgc06286 protein; PDBTitle: bakbh3 in complex with sja 23 d1ohua_ not modelled 5.7 14 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 24 d1ak0a_ not modelled 5.6 16 Fold:Phospholipase C/P1 nuclease Superfamily:Phospholipase C/P1 nuclease Family:P1 nuclease 25 d2ponb1 not modelled 5.5 15 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 26 c1m56G_ not modelled 5.4 10 PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type)

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0