Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	D	Q	V	K	V	V	A	D	D	Q	A	P	A	E	Q	S	L	R	R	N	L	T	N	R	H	I	Q	L	I	A	I	G	G	A	I	G	T	G	L	F	M	G	S	G	K	T	I	S	L	A	G	P	S	I	I	F	V	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	I	I	G	F	M	L	F	F	V	M	R	A	M	G	E	L	L	L	S	N	L	E	Y	K	S	F	S	D	F	A	S	D	L	L	G	P	W	A	G	Y	F	T	G	W	T	Y	W	F	C	W	V	V	T	G	M	A	D	V	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	I	T	A	Y	A	Q	F	W	F	P	D	L	S	D	W	V	A	S	L	A	V	I	V	L	L	L	T	L	N	L	A	T	V	K	M	F	G	E	M	E	F	W	F	A	M	I	K	I	V	A	I	V	S	L	I	V	V	G	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	M	V	A	M	H	F	Q	S	P	T	G	V	E	A	S	F	A	H	L	W	N	D	G	G	W	F	P	K	G	L	S	G	F	F	A	G	F	Q	I	A	V	F	A	F	V	G	I	E	L	V	G	T	T	A	A	E	T	K	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	E	K	S	L	P	R	A	I	N	S	I	P	I	R	I	I	M	F	Y	V	F	A	L	I	V	I	M	S	V	T	P	W	S	S	V	V	P	E	K	S	P	F	V	E	L	F	V	L	V	G	L	P	A	A	A	S	V	I	N
Secondary structure
SS confidence
Disorder																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		F	V	V	L	T	S	A	A	S	S	A	N	S	G	V	F	S	T	S	R	M	L	F	G	L	A	Q	E	G	V	A	P	K	A	F	A	K	L	S	K	R	A	V	P	A	K	G	L	T	F	S	C	I	C	L	L	G	G	V	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		M	L	Y	V	N	P	S	V	I	G	A	F	T	M	I	T	T	V	S	A	I	L	F	M	F	V	W	T	I	I	L	C	S	Y	L	V	Y	R	K	Q	R	P	H	L	H	E	K	S	I	Y	K	M	P	L	G	K	L	M	C	W
Secondary structure
SS confidence
Disorder				?	?		?	?		?																																	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470
Sequence		V	C	M	A	F	F	V	F	V	V	V	L	L	T	L	E	D	D	T	R	Q	A	L	L	V	T	P	L	W	F	I	A	L	G	L	G	W	L	F	I	G	K	K	R	A	A	E	L	R	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: 20 - 469 Aligned: 426 Modelled: 426 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 20 - 467 Aligned: 404 Modelled: 404 Confidence: 100.0% Identity: 17% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 6 - 470 Aligned: 447 Modelled: 451 Confidence: 100.0% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 3dh4 chain A Region: 3 - 470 Aligned: 452 Modelled: 436 Confidence: 99.6% 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 2xq2 chain A Region: 21 - 470 Aligned: 433 Modelled: 438 Confidence: 99.6% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 2a65 chain A domain 1 Region: 24 - 467 Aligned: 433 Modelled: 433 Confidence: 98.0% Identity: 14% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 15 - 411 Aligned: 384 Modelled: 384 Confidence: 97.6% Identity: 12% 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: 57 - 404 Aligned: 340 Modelled: 348 Confidence: 96.1% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 2l2t chain A Region: 442 - 470 Aligned: 29 Modelled: 29 Confidence: 32.1% Identity: 7% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 2jwa chain A Region: 436 - 470 Aligned: 35 Modelled: 35 Confidence: 29.3% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1fft chain B domain 2 Region: 369 - 434 Aligned: 66 Modelled: 66 Confidence: 27.5% Identity: 5% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1m57 chain H Region: 370 - 434 Aligned: 65 Modelled: 65 Confidence: 18.6% Identity: 17% 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 2bbj chain B Region: 412 - 463 Aligned: 52 Modelled: 52 Confidence: 12.6% Identity: 13% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 1ar1 chain B Region: 372 - 434 Aligned: 63 Modelled: 63 Confidence: 9.8% Identity: 10% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 PDB 1qle chain B Region: 372 - 434 Aligned: 63 Modelled: 63 Confidence: 9.8% Identity: 10% PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment Phyre2 PDB 2w2e chain A Region: 3 - 241 Aligned: 239 Modelled: 239 Confidence: 8.5% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 Phyre2 PDB 2rm9 chain A Region: 2 - 19 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 17% PDB header:neuropeptide Chain: A: PDB Molecule:astressin2b; PDBTitle: astressin2b Phyre2 PDB 4a19 chain X Region: 7 - 23 Aligned: 17 Modelled: 17 Confidence: 7.9% Identity: 24% PDB header:ribosome Chain: X: PDB Molecule:rpl18a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 2. Phyre2 PDB 3ehb chain B domain 2 Region: 369 - 434 Aligned: 66 Modelled: 66 Confidence: 6.4% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3rko chain A Region: 381 - 469 Aligned: 88 Modelled: 89 Confidence: 6.4% Identity: 9% 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 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c3dh4A_ 5 c2xq2A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 c2l2tA_ 10 c2jwaA_ 11 d1fftb2 12 c1m57H_ 13 c2bbjB_ 14 c1ar1B_ 15 c1qleB_ 16 c2w2eA_ 17 c2rm9A_ 18 c4a19X_ 19 d3ehbb2 20 c3rkoA_ 21 22 23

Detailed template information

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

1 c3giaA_ 100.0 12 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 17 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 100.0 10 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c3dh4A_ 99.6 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 5 c2xq2A_ 99.6 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 6 d2a65a1 98.0 14 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 97.6 12 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_ 96.1 11 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 c2l2tA_ 32.1 7 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 10 c2jwaA_ 29.3 23 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 11 d1fftb2 27.5 5 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 c1m57H_ 18.6 17 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 13 c2bbjB_ 12.6 13 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 14 c1ar1B_ 9.8 10 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment 15 c1qleB_ 9.8 10 PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment 16 c2w2eA_ 8.5 11 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 17 c2rm9A_ 8.1 17 PDB header:neuropeptide Chain: A: PDB Molecule:astressin2b; PDBTitle: astressin2b 18 c4a19X_ 7.9 24 PDB header:ribosome Chain: X: PDB Molecule:rpl18a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 2. 19 d3ehbb2 6.4 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 20 c3rkoA_ 6.4 9 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 21 c3rkoF_ not modelled 5.7 13 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 22 d3dtub2 not modelled 5.5 17 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 23 c2rddB_ not modelled 5.2 4 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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