Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	L	T	T	T	Q	T	S	P	S	L	L	G	G	V	V	I	I	G	G	T	I	I	G	A	G	M	F	S	L	P	V	V	M	S	G	A	W	F	F	W	S	M	A	A	L	I	F	T	W	F	C	M	L	H	S	G	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?																										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	I	L	E	A	N	L	N	Y	R	I	G	S	S	F	D	T	I	T	K	D	L	L	G	K	G	W	N	V	V	N	G	I	S	I	A	F	V	L	Y	I	L	T	Y	A	Y	I	S	A	S	G	S	I	L	H	H	T	F	A	E
Secondary structure
SS confidence
Disorder									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	S	L	N	V	P	A	R	A	A	G	F	G	F	A	L	L	V	A	F	V	V	W	L	S	T	K	A	V	S	R	M	T	A	I	V	L	G	A	K	V	I	T	F	F	L	T	F	G	S	L	L	G	H	V	Q	P	A	T	L
Secondary structure
SS confidence
Disorder																									?		?	?																										?					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	N	V	A	E	S	N	A	S	Y	A	P	Y	L	L	M	T	L	P	F	C	L	A	S	F	G	Y	H	G	N	V	P	S	L	M	K	Y	Y	G	K	D	P	K	T	I	V	K	C	L	V	Y	G	T	L	M	A	L	A	L	Y
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		T	I	W	L	L	A	T	M	G	N	I	P	R	P	E	F	I	G	I	A	E	K	G	G	N	I	D	V	L	V	Q	A	L	S	G	V	L	N	S	R	S	L	D	L	L	L	V	V	F	S	N	F	A	V	A	S	S	F	L	G
Secondary structure
SS confidence
Disorder																						?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	T	L	G	L	F	D	Y	L	A	D	L	F	G	F	D	D	S	A	V	G	R	L	K	T	A	L	L	T	F	A	P	P	V	V	G	G	L	L	F	P	N	G	F	L	Y	A	I	G	Y	A	G	L	A	A	T	I	W	A	A
Secondary structure
SS confidence
Disorder																?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.
Sequence		I	V	P	A	L	L	A	R	A	S	R	K	R	F	G	S	P	K	F	R	V	W	G	G	K	P	M	I	A	L	I	L	V	F	G	V	G	N	A	L	V	H	I	L	S	S	F	N	L	L	P	V	Y	Q
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: 7 - 407 Aligned: 395 Modelled: 395 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: 7 - 398 Aligned: 373 Modelled: 373 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 2 - 407 Aligned: 399 Modelled: 406 Confidence: 99.9% 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: 9 - 404 Aligned: 385 Modelled: 385 Confidence: 98.5% Identity: 9% 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: 9 - 404 Aligned: 385 Modelled: 385 Confidence: 98.5% 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: 12 - 411 Aligned: 397 Modelled: 397 Confidence: 97.9% Identity: 12% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 4 - 380 Aligned: 374 Modelled: 377 Confidence: 96.5% Identity: 10% 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: 6 - 376 Aligned: 369 Modelled: 369 Confidence: 75.3% Identity: 10% 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: 343 - 410 Aligned: 68 Modelled: 68 Confidence: 8.5% Identity: 3% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2hg5 chain D Region: 12 - 42 Aligned: 31 Modelled: 31 Confidence: 7.6% Identity: 26% PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter Phyre2 PDB 3dtu chain B domain 2 Region: 342 - 410 Aligned: 69 Modelled: 69 Confidence: 6.9% Identity: 12% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1xg8 chain A Region: 66 - 86 Aligned: 21 Modelled: 21 Confidence: 6.8% Identity: 14% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: YuzD-like Phyre2 PDB 1iwg chain A domain 8 Region: 215 - 376 Aligned: 162 Modelled: 162 Confidence: 6.8% Identity: 10% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1qle chain B Region: 342 - 410 Aligned: 69 Modelled: 69 Confidence: 6.6% Identity: 14% 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: 342 - 410 Aligned: 69 Modelled: 69 Confidence: 6.6% Identity: 14% 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 2p9x chain B Region: 64 - 96 Aligned: 31 Modelled: 33 Confidence: 6.5% Identity: 16% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 Phyre2 PDB 2knc chain B Region: 8 - 32 Aligned: 25 Modelled: 25 Confidence: 5.8% Identity: 24% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1nek chain D Region: 145 - 248 Aligned: 103 Modelled: 104 Confidence: 5.2% Identity: 12% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 3ehb chain B domain 2 Region: 342 - 410 Aligned: 69 Modelled: 69 Confidence: 5.2% Identity: 14% 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 c3dh4A_ 5 c2xq2A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 d1fftb2 10 c2hg5D_ 11 d3dtub2 12 d1xg8a_ 13 d1iwga8 14 c1qleB_ 15 c1ar1B_ 16 c2p9xB_ 17 c2kncB_ 18 d1nekd_ 19 d3ehbb2

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 12 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 99.9 10 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c3dh4A_ 98.5 9 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_ 98.5 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 6 d2a65a1 97.9 12 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 96.5 10 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_ 75.3 10 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 d1fftb2 8.5 3 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 10 c2hg5D_ 7.6 26 PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter 11 d3dtub2 6.9 12 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 d1xg8a_ 6.8 14 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:YuzD-like 13 d1iwga8 6.8 10 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 14 c1qleB_ 6.6 14 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 15 c1ar1B_ 6.6 14 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 16 c2p9xB_ 6.5 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 17 c2kncB_ 5.8 24 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 18 d1nekd_ 5.2 12 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 19 d3ehbb2 5.2 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region

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