Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	K	L	Q	L	K	I	L	S	F	L	Q	F	C	L	W	G	S	W	L	T	T	L	G	S	Y	M	F	V	T	L	K	F	D	G	A	S	I	G	A	V	Y	S	S	L	G	I	A	A	V	F	M	P	A	L	L	G	I
Secondary structure
SS confidence
Disorder		?	?	?	?																														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	A	D	K	W	L	S	A	K	W	V	Y	A	I	C	H	T	I	G	A	I	T	L	F	M	A	A	Q	V	T	T	P	E	A	M	F	L	V	I	L	I	N	S	F	A	Y	M	P	T	L	G	L	I	N	T	I	S	Y	Y	R
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	Q	N	A	G	M	D	I	V	T	D	F	P	P	I	R	I	W	G	T	I	G	F	I	M	A	M	W	V	V	S	L	S	G	F	E	L	S	H	M	Q	L	Y	I	G	A	A	L	S	A	I	L	V	L	F	T	L	T	L	P
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		H	I	P	V	A	K	Q	Q	A	N	Q	S	W	T	T	L	L	G	L	D	A	F	A	L	F	K	N	K	R	M	A	I	F	F	I	F	S	M	L	L	G	A	E	L	Q	I	T	N	M	F	G	N	T	F	L	H	S	F	D	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?																																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		D	P	M	F	A	S	S	F	I	V	Q	H	A	S	I	I	M	S	I	S	Q	I	S	E	T	L	F	I	L	T	I	P	F	F	L	S	R	Y	G	I	K	N	V	M	M	I	S	I	V	A	W	I	L	R	F	A	L	F	A	Y
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	D	P	T	P	F	G	T	V	L	L	V	L	S	M	I	V	Y	G	C	A	F	D	F	F	N	I	S	G	S	V	F	V	E	K	E	V	S	P	A	I	R	A	S	A	Q	G	M	F	L	M	M	T	N	G	F	G	C	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.
Sequence		G	G	I	V	S	G	K	V	V	E	M	Y	T	Q	N	G	I	T	D	W	Q	T	V	W	L	I	F	A	G	Y	S	V	V	L	A	F	A	F	M	A	M	F	K	Y	K	H	V	R	V	P	T	G	T	Q	T	V	S	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 1pv7 chain A Region: 2 - 417 Aligned: 406 Modelled: 410 Confidence: 100.0% Identity: 10% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 1pw4 chain A Region: 2 - 416 Aligned: 406 Modelled: 409 Confidence: 100.0% Identity: 11% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2xut chain C Region: 7 - 398 Aligned: 391 Modelled: 392 Confidence: 100.0% Identity: 14% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 2gfp chain A Region: 7 - 396 Aligned: 366 Modelled: 388 Confidence: 100.0% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3o7p chain A Region: 8 - 405 Aligned: 388 Modelled: 398 Confidence: 100.0% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 1fft chain B domain 2 Region: 380 - 418 Aligned: 39 Modelled: 39 Confidence: 50.9% Identity: 15% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2knc chain A Region: 380 - 417 Aligned: 38 Modelled: 38 Confidence: 42.1% Identity: 11% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2rdd chain B Region: 390 - 417 Aligned: 28 Modelled: 28 Confidence: 29.3% Identity: 7% 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. Phyre2 PDB 3dtu chain B domain 2 Region: 382 - 418 Aligned: 36 Modelled: 37 Confidence: 22.2% Identity: 17% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2bbj chain B Region: 373 - 406 Aligned: 34 Modelled: 34 Confidence: 19.5% Identity: 21% 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 3qnq chain D Region: 366 - 418 Aligned: 53 Modelled: 53 Confidence: 18.2% Identity: 9% 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 3ehb chain B domain 2 Region: 382 - 418 Aligned: 36 Modelled: 37 Confidence: 17.3% 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 PDB 1j4n chain A Region: 375 - 416 Aligned: 42 Modelled: 42 Confidence: 11.3% Identity: 10% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 3a0b chain T Region: 381 - 407 Aligned: 27 Modelled: 27 Confidence: 9.7% Identity: 19% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3arc chain T Region: 381 - 407 Aligned: 27 Modelled: 27 Confidence: 9.7% Identity: 19% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 2fno chain A domain 1 Region: 49 - 72 Aligned: 24 Modelled: 24 Confidence: 8.7% Identity: 25% Fold: GST C-terminal domain-like Superfamily: GST C-terminal domain-like Family: Glutathione S-transferase (GST), C-terminal domain Phyre2 PDB 1m57 chain H Region: 380 - 418 Aligned: 38 Modelled: 39 Confidence: 7.8% Identity: 16% 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 1ar1 chain B Region: 380 - 418 Aligned: 39 Modelled: 39 Confidence: 7.6% 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: 380 - 418 Aligned: 39 Modelled: 39 Confidence: 7.6% 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 1v54 chain B domain 2 Region: 382 - 417 Aligned: 36 Modelled: 36 Confidence: 6.5% Identity: 19% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 1 d1pv7a_ 2 d1pw4a_ 3 c2xutC_ 4 c2gfpA_ 5 c3o7pA_ 6 d1fftb2 7 c2kncA_ 8 c2rddB_ 9 d3dtub2 10 c2bbjB_ 11 c3qnqD_ 12 d3ehbb2 13 d1j4na_ 14 c3a0bT_ 15 c3arct_ 16 d2fnoa1 17 c1m57H_ 18 c1ar1B_ 19 c1qleB_ 20 d1v54b2 21 22

Detailed template information

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

1 d1pv7a_ 100.0 10 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 2 d1pw4a_ 100.0 11 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 3 c2xutC_ 100.0 14 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 4 c2gfpA_ 100.0 10 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 5 c3o7pA_ 100.0 9 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 6 d1fftb2 50.9 15 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 7 c2kncA_ 42.1 11 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 8 c2rddB_ 29.3 7 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. 9 d3dtub2 22.2 17 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 10 c2bbjB_ 19.5 21 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 11 c3qnqD_ 18.2 9 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 12 d3ehbb2 17.3 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 13 d1j4na_ 11.3 10 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 14 c3a0bT_ 9.7 19 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 15 c3arct_ 9.7 19 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 16 d2fnoa1 8.7 25 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain 17 c1m57H_ 7.8 16 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 18 c1ar1B_ 7.6 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 19 c1qleB_ 7.6 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 20 d1v54b2 6.5 19 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 21 c1v55B_ not modelled 6.2 18 PDB header:oxidoreductase Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: bovine heart cytochrome c oxidase at the fully reduced state 22 c2g9pA_ not modelled 5.8 25 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom

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