Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	W	Q	Q	F	K	H	A	W	L	I	K	F	W	A	P	I	P	A	V	I	A	A	G	I	L	S	T	Y	Y	F	G	I	T	G	T	F	W	A	V	T	G	E	F	T	R	W	G	G	Q	L	L	Q	L	F	G	V	H	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	E	W	G	Y	F	K	I	I	H	L	E	G	S	P	L	T	R	I	D	G	M	M	I	L	G	M	F	G	G	C	F	A	A	A	L	W	A	N	N	V	K	L	R	M	P	R	S	R	I	R	I	M	Q	A	I	I	G	G	I
Secondary structure
SS confidence
Disorder												?	?	?	?	?	?																											?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	A	G	F	G	A	R	L	A	M	G	C	N	L	A	A	F	F	T	G	I	P	Q	F	S	L	H	A	W	F	F	A	I	A	T	A	I	G	S	W	F	G	A	R	F	T	L	L	P	I	F	R	I	P	V	K	M	Q	K	V
Secondary structure
SS confidence
Disorder																						?				?	?																									?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	A	A	S	P	L	T	Q	K	P	D	Q	A	R	R	R	F	R	L	G	M	L	V	F	F	G	M	L	G	W	A	L	L	T	A	M	N	Q	P	K	L	G	L	A	M	L	F	G	V	G	F	G	L	L	I	E	R	A	Q	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		C	F	T	S	A	F	R	D	M	W	I	T	G	R	T	H	M	A	K	A	I	I	I	G	M	A	V	S	A	I	G	I	F	S	Y	V	Q	L	G	V	E	P	K	I	M	W	A	G	P	N	A	V	I	G	G	L	L	F	G	F
Secondary structure
SS confidence
Disorder																																											?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	I	V	L	A	G	G	C	E	T	G	W	M	Y	R	A	V	E	G	Q	V	H	Y	W	W	V	G	L	G	N	V	I	G	S	T	I	L	A	Y	Y	W	D	D	F	A	P	A	L	A	T	D	W	D	K	I	N	L	L	K	T
Secondary structure
SS confidence
Disorder																																																		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.
Sequence		F	G	P	M	G	G	L	L	V	T	Y	L	L	L	F	A	A	L	M	L	I	I	G	W	E	K	R	F	F	R	R	A	A	P	Q	T	A	K	E	I	A
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 1jb0 chain L Region: 214 - 299 Aligned: 81 Modelled: 86 Confidence: 31.8% Identity: 14% Fold: Photosystem I reaction center subunit XI, PsaL Superfamily: Photosystem I reaction center subunit XI, PsaL Family: Photosystem I reaction center subunit XI, PsaL Phyre2 PDB 2wvm chain A Region: 86 - 122 Aligned: 37 Modelled: 37 Confidence: 11.5% Identity: 24% PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii) Phyre2 PDB 2zu8 chain A Region: 86 - 122 Aligned: 37 Modelled: 34 Confidence: 9.1% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii Phyre2 PDB 3hfx chain A Region: 356 - 398 Aligned: 43 Modelled: 43 Confidence: 8.6% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 2y69 chain Q Region: 234 - 288 Aligned: 55 Modelled: 55 Confidence: 8.1% Identity: 9% PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 2vv5 chain A domain 3 Region: 149 - 236 Aligned: 82 Modelled: 88 Confidence: 7.3% Identity: 16% Fold: Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily: Mechanosensitive channel protein MscS (YggB), transmembrane region Family: Mechanosensitive channel protein MscS (YggB), transmembrane region Phyre2 PDB 2b5k chain A Region: 236 - 242 Aligned: 7 Modelled: 7 Confidence: 7.0% Identity: 29% PDB header:antimicrobial protein Chain: A: PDB Molecule:polyphemusin-1; PDBTitle: pv5 nmr solution structure in dpc micelles Phyre2 PDB 1v54 chain D Region: 234 - 288 Aligned: 55 Modelled: 55 Confidence: 6.7% Identity: 9% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit IV Family: Mitochondrial cytochrome c oxidase subunit IV Phyre2 PDB 3pm7 chain A Region: 2 - 17 Aligned: 16 Modelled: 16 Confidence: 6.0% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of ef_3132 protein from enterococcus faecalis at the2 resolution 2a, northeast structural genomics consortium target efr184 Phyre2 PDB 2w2e chain A Region: 221 - 347 Aligned: 122 Modelled: 127 Confidence: 5.4% Identity: 17% 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 1 d1jb0l_ 2 c2wvmA_ 3 c2zu8A_ 4 c3hfxA_ 5 c2y69Q_ 6 d2vv5a3 7 c2b5kA_ 8 d1v54d_ 9 c3pm7A_ 10 c2w2eA_

Detailed template information

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

1 d1jb0l_ 31.8 14 Fold:Photosystem I reaction center subunit XI, PsaL Superfamily:Photosystem I reaction center subunit XI, PsaL Family:Photosystem I reaction center subunit XI, PsaL 2 c2wvmA_ 11.5 24 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii) 3 c2zu8A_ 9.1 19 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii 4 c3hfxA_ 8.6 9 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 5 c2y69Q_ 8.1 9 PDB header:electron transport Chain: Q: PDB Molecule:cytochrome c oxidase subunit 4 isoform 1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 6 d2vv5a3 7.3 16 Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region 7 c2b5kA_ 7.0 29 PDB header:antimicrobial protein Chain: A: PDB Molecule:polyphemusin-1; PDBTitle: pv5 nmr solution structure in dpc micelles 8 d1v54d_ 6.7 9 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit IV Family:Mitochondrial cytochrome c oxidase subunit IV 9 c3pm7A_ 6.0 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of ef_3132 protein from enterococcus faecalis at the2 resolution 2a, northeast structural genomics consortium target efr184 10 c2w2eA_ 5.4 17 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

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