Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	S	V	Q	T	G	K	A	K	Q	L	T	L	L	G	F	F	A	I	T	A	S	M	V	M	A	V	Y	E	Y	P	T	F	A	T	S	G	F	S	L	V	F	F	L	L	L	G	G	I	L	W	F	I	P	V	G	L	C
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																			?							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	E	M	A	T	V	D	G	W	E	E	G	G	V	F	A	W	V	S	N	T	L	G	P	R	W	G	F	A	A	I	S	F	G	Y	L	Q	I	A	I	G	F	I	P	M	L	Y	F	V	L	G	A	L	S	Y	I	L	K	W
Secondary structure
SS confidence
Disorder							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	A	L	N	E	D	P	I	T	K	T	I	A	A	L	I	I	L	W	A	L	A	L	T	Q	F	G	G	T	K	Y	T	A	R	I	A	K	V	G	F	F	A	G	I	L	L	P	A	F	I	L	I	A	L	A	A	I	Y	L	H
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	G	A	P	V	A	I	E	M	D	S	K	T	F	F	P	D	F	S	K	V	G	T	L	V	V	F	V	A	F	I	L	S	Y	M	G	V	E	A	S	A	T	H	V	N	E	M	S	N	P	G	R	D	Y	P	L	A	M	L	L
Secondary structure
SS confidence
Disorder					?		?			?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	M	V	A	A	I	C	L	S	S	V	G	G	L	S	I	A	M	V	I	P	G	N	E	I	N	L	S	A	G	V	M	Q	T	F	T	V	L	M	S	H	V	A	P	E	I	E	W	T	V	R	V	I	S	A	L	L	L	L	G
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?	?									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	L	A	E	I	A	S	W	I	V	G	P	S	R	G	M	Y	V	T	A	Q	K	N	L	L	P	A	A	F	A	K	M	N	K	N	G	V	P	V	T	L	V	I	S	Q	L	V	I	T	S	I	A	L	I	I	L	T	N	T	G
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		G	G	N	N	M	S	F	L	I	A	L	A	L	T	V	V	I	Y	L	C	A	Y	F	M	L	F	I	G	Y	I	V	L	V	L	K	H	P	D	L	K	R	T	F	N	I	P	G	G	K	G	V	K	L	V	V	A	I	V	G	L
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		L	T	S	I	M	A	F	I	V	S	F	L	P	P	D	N	I	Q	G	D	S	T	D	M	Y	V	E	L	L	V	V	S	F	L	V	V	L	A	L	P	F	I	L	Y	A	V	H	D	R	K	G	K	A	N	T	G	V	T	L	E
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?	?	?	?																										?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.
Sequence		P	I	N	S	Q	N	A	P	K	G	H	F	F	L	H	P	R	A	R	S	P	H	Y	I	V	M	N	D	K	K	H
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: 9 - 478 Aligned: 426 Modelled: 426 Confidence: 100.0% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 9 - 473 Aligned: 406 Modelled: 406 Confidence: 100.0% Identity: 21% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 7 - 488 Aligned: 445 Modelled: 445 Confidence: 100.0% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2xq2 chain A Region: 11 - 483 Aligned: 436 Modelled: 436 Confidence: 99.2% Identity: 12% 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: 5 - 490 Aligned: 447 Modelled: 443 Confidence: 99.0% Identity: 12% 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: 6 - 397 Aligned: 379 Modelled: 362 Confidence: 97.4% 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 2a65 chain A domain 1 Region: 16 - 475 Aligned: 445 Modelled: 455 Confidence: 97.1% Identity: 11% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 3hfx chain A Region: 83 - 399 Aligned: 303 Modelled: 309 Confidence: 92.9% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 1fft chain B domain 2 Region: 364 - 431 Aligned: 68 Modelled: 68 Confidence: 74.5% Identity: 21% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3qnq chain D Region: 406 - 483 Aligned: 78 Modelled: 78 Confidence: 61.3% Identity: 19% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 3rko chain F Region: 336 - 472 Aligned: 130 Modelled: 137 Confidence: 56.2% Identity: 11% 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 1fft chain G Region: 364 - 431 Aligned: 68 Modelled: 68 Confidence: 44.9% Identity: 21% PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 PDB 2knc chain A Region: 435 - 482 Aligned: 48 Modelled: 48 Confidence: 21.3% Identity: 8% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1iwg chain A domain 8 Region: 334 - 473 Aligned: 140 Modelled: 140 Confidence: 15.6% Identity: 9% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2bbj chain B Region: 412 - 469 Aligned: 52 Modelled: 58 Confidence: 15.4% Identity: 15% 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 2i5n chain H Region: 440 - 496 Aligned: 57 Modelled: 57 Confidence: 12.0% Identity: 16% PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique Phyre2 PDB 1w8x chain P Region: 447 - 500 Aligned: 52 Modelled: 54 Confidence: 10.2% Identity: 19% PDB header:virus Chain: P: PDB Molecule:protein p16; PDBTitle: structural analysis of prd1 Phyre2 PDB 1qle chain B Region: 364 - 432 Aligned: 69 Modelled: 69 Confidence: 9.9% Identity: 16% 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 1ar1 chain B Region: 364 - 432 Aligned: 69 Modelled: 69 Confidence: 9.9% Identity: 16% 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 1m57 chain H Region: 363 - 432 Aligned: 70 Modelled: 70 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 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c2xq2A_ 5 c3dh4A_ 6 c2w8aC_ 7 d2a65a1 8 c3hfxA_ 9 d1fftb2 10 c3qnqD_ 11 c3rkoF_ 12 c1fftG_ 13 c2kncA_ 14 d1iwga8 15 c2bbjB_ 16 c2i5nH_ 17 c1w8xP_ 18 c1qleB_ 19 c1ar1B_ 20 c1m57H_ 21 22 23 24 25 26

Detailed template information

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

1 c3giaA_ 100.0 16 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 21 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 100.0 13 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c2xq2A_ 99.2 12 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 5 c3dh4A_ 99.0 12 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 6 c2w8aC_ 97.4 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 7 d2a65a1 97.1 11 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 8 c3hfxA_ 92.9 12 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1fftb2 74.5 21 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 10 c3qnqD_ 61.3 19 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 11 c3rkoF_ 56.2 11 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 12 c1fftG_ 44.9 21 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 13 c2kncA_ 21.3 8 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 14 d1iwga8 15.6 9 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 15 c2bbjB_ 15.4 15 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 16 c2i5nH_ 12.0 16 PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique 17 c1w8xP_ 10.2 19 PDB header:virus Chain: P: PDB Molecule:protein p16; PDBTitle: structural analysis of prd1 18 c1qleB_ 9.9 16 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 19 c1ar1B_ 9.9 16 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 20 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)) 21 c2rddB_ not modelled 8.2 13 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. 22 d3ehbb2 not modelled 7.7 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 23 c1oy8A_ not modelled 7.6 9 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 24 d3dtub2 not modelled 7.3 13 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 25 c2jp3A_ not modelled 5.8 10 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 26 c3mk7F_ not modelled 5.7 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