Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	G	N	V	Q	E	K	Q	L	R	W	Y	N	I	A	L	M	S	F	I	T	V	W	G	F	G	N	V	V	N	N	Y	A	N	Q	G	L	V	V	V	F	S	W	V	F	I	F	A	L	Y	F	T	P	Y	A	L	I	V	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?																?	?	?	?	?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	L	G	S	T	F	K	D	G	K	G	G	V	S	T	W	I	K	H	T	M	G	P	G	L	A	Y	L	A	A	W	T	Y	W	V	V	H	I	P	Y	L	A	Q	K	P	Q	A	I	L	I	A	L	G	W	A	M	K	G	D	G
Secondary structure
SS confidence
Disorder					?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	L	I	K	E	Y	S	V	V	A	L	Q	G	L	T	L	V	L	F	I	F	F	M	W	V	A	S	R	G	M	K	S	L	K	I	V	G	S	V	A	G	I	A	M	F	V	M	S	L	L	Y	V	A	M	A	V	T	A	P	A
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	T	E	V	H	I	A	T	T	N	I	T	W	E	T	F	I	P	H	I	D	F	T	Y	I	T	T	I	S	M	L	V	F	A	V	G	G	A	E	K	I	S	P	Y	V	N	Q	T	R	N	P	G	K	E	F	P	K	G	M	L
Secondary structure
SS confidence
Disorder					?	?	?	?	?			?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		C	L	A	V	M	V	A	V	C	A	I	L	G	S	L	A	M	G	M	M	F	D	S	R	N	I	P	D	D	L	M	T	N	G	Q	Y	Y	A	F	Q	K	L	G	E	Y	Y	N	M	G	N	T	L	M	V	I	Y	A	I	A	N
Secondary structure
SS confidence
Disorder																											?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	L	G	Q	V	A	A	L	V	F	S	I	D	A	P	L	K	V	L	L	G	D	A	D	S	K	Y	I	P	A	S	L	C	R	T	N	A	S	G	T	P	V	N	G	Y	F	L	T	L	V	L	V	A	I	L	I	M	L	P	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	G	I	G	D	M	N	N	L	Y	K	W	L	L	N	L	N	S	V	V	M	P	L	R	Y	L	W	V	F	V	A	F	I	A	V	V	R	L	A	Q	K	Y	K	P	E	Y	V	F	I	R	N	K	P	L	A	M	T	V	G	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																			?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.
Sequence		W	C	F	A	F	T	A	F	A	C	L	T	G	I	F	P	K	M	E	A	F	T	A	E	W	T	F	Q	L	A	L	N	V	A	T	P	F	V	L	V	G	L	G	L	I	F	P	L	L	A	R	K	A	N	S	K
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 3gia chain A Region: 6 - 476 Aligned: 422 Modelled: 422 Confidence: 100.0% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 6 - 476 Aligned: 407 Modelled: 407 Confidence: 100.0% Identity: 16% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 4 - 476 Aligned: 431 Modelled: 431 Confidence: 100.0% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2a65 chain A domain 1 Region: 11 - 475 Aligned: 452 Modelled: 465 Confidence: 99.2% Identity: 15% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2xq2 chain A Region: 8 - 476 Aligned: 431 Modelled: 453 Confidence: 98.9% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 3dh4 chain A Region: 3 - 476 Aligned: 434 Modelled: 431 Confidence: 98.7% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 2w8a chain C Region: 3 - 410 Aligned: 393 Modelled: 398 Confidence: 97.8% 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: 3 - 402 Aligned: 383 Modelled: 383 Confidence: 92.9% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1iwg chain A domain 8 Region: 337 - 476 Aligned: 140 Modelled: 140 Confidence: 70.3% Identity: 12% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1fft chain B domain 2 Region: 367 - 434 Aligned: 68 Modelled: 68 Confidence: 60.2% Identity: 10% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1oy8 chain A Region: 337 - 476 Aligned: 140 Modelled: 140 Confidence: 56.3% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 3rko chain F Region: 338 - 475 Aligned: 131 Modelled: 138 Confidence: 36.0% Identity: 8% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3b8e chain C Region: 380 - 476 Aligned: 97 Modelled: 97 Confidence: 21.0% Identity: 9% PDB header:hydrolase/transport protein Chain: C: PDB Molecule:sodium/potassium-transporting atpase subunit PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 1fft chain G Region: 366 - 434 Aligned: 69 Modelled: 69 Confidence: 16.8% Identity: 10% PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 PDB 3ixz chain A Region: 380 - 476 Aligned: 97 Modelled: 97 Confidence: 11.0% Identity: 8% PDB header:hydrolase Chain: A: PDB Molecule:potassium-transporting atpase alpha; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride Phyre2 PDB 3aqp chain B Region: 229 - 435 Aligned: 197 Modelled: 207 Confidence: 10.3% Identity: 9% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 1m57 chain H Region: 366 - 434 Aligned: 67 Modelled: 69 Confidence: 9.7% Identity: 13% PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) Phyre2 PDB 3ehb chain B domain 2 Region: 366 - 429 Aligned: 64 Modelled: 64 Confidence: 8.1% Identity: 13% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2jwa chain A Region: 443 - 476 Aligned: 34 Modelled: 34 Confidence: 8.0% Identity: 24% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 3dtu chain B domain 2 Region: 366 - 429 Aligned: 64 Modelled: 64 Confidence: 7.5% Identity: 13% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 d2a65a1 5 c2xq2A_ 6 c3dh4A_ 7 c2w8aC_ 8 c3hfxA_ 9 d1iwga8 10 d1fftb2 11 c1oy8A_ 12 c3rkoF_ 13 c3b8eC_ 14 c1fftG_ 15 c3ixzA_ 16 c3aqpB_ 17 c1m57H_ 18 d3ehbb2 19 c2jwaA_ 20 d3dtub2 21 22

Detailed template information

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

1 c3giaA_ 100.0 13 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 16 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 100.0 9 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 d2a65a1 99.2 15 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 5 c2xq2A_ 98.9 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 6 c3dh4A_ 98.7 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 7 c2w8aC_ 97.8 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 8 c3hfxA_ 92.9 9 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1iwga8 70.3 12 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 10 d1fftb2 60.2 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 11 c1oy8A_ 56.3 11 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 12 c3rkoF_ 36.0 8 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 13 c3b8eC_ 21.0 9 PDB header:hydrolase/transport protein Chain: C: PDB Molecule:sodium/potassium-transporting atpase subunit PDBTitle: crystal structure of the sodium-potassium pump 14 c1fftG_ 16.8 10 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 15 c3ixzA_ 11.0 8 PDB header:hydrolase Chain: A: PDB Molecule:potassium-transporting atpase alpha; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride 16 c3aqpB_ 10.3 9 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 17 c1m57H_ 9.7 13 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 18 d3ehbb2 8.1 13 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 19 c2jwaA_ 8.0 24 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 20 d3dtub2 7.5 13 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 21 d2yvxa3 not modelled 5.8 10 Fold:MgtE membrane domain-like Superfamily:MgtE membrane domain-like Family:MgtE membrane domain-like 22 c3mk7F_ not modelled 5.5 6 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase

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