Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	L	K	I	V	A	V	V	V	T	G	L	L	A	A	N	V	A	H	A	A	E	V	Y	N	K	D	G	N	K	L	D	L	Y	G	K	V	T	A	L	R	Y	F	T	D	D	K	R	D	D	G	D	K	T	Y	A	R	L	G
Secondary structure
SS confidence
Disorder		?	?	?	?											?	?	?	?	?																										?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.
Sequence		F	K	G	E	T	Q	I	N	D	Q	M	I	G	F	G	H	W	E	Y	D	F	K	G	Y	N	D	E	A	N	G	S	R	G	K	N	L
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 1osm chain A Region: 22 - 92 Aligned: 71 Modelled: 71 Confidence: 99.8% Identity: 63% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1pho chain A Region: 22 - 92 Aligned: 71 Modelled: 71 Confidence: 99.8% Identity: 58% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3nsg chain A Region: 23 - 93 Aligned: 71 Modelled: 71 Confidence: 99.8% Identity: 51% PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi Phyre2 PDB 2zfg chain A domain 1 Region: 22 - 94 Aligned: 73 Modelled: 73 Confidence: 99.8% Identity: 58% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2fgq chain X domain 1 Region: 31 - 95 Aligned: 65 Modelled: 65 Confidence: 99.6% Identity: 20% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3a2r chain X Region: 32 - 94 Aligned: 63 Modelled: 63 Confidence: 99.6% Identity: 17% PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis Phyre2 PDB 3prn chain A Region: 32 - 94 Aligned: 63 Modelled: 63 Confidence: 99.2% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2por chain A Region: 32 - 91 Aligned: 58 Modelled: 60 Confidence: 99.2% Identity: 10% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2o4v chain A Region: 26 - 88 Aligned: 61 Modelled: 63 Confidence: 90.1% Identity: 23% PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane Phyre2 PDB 2iwv chain D Region: 30 - 90 Aligned: 61 Modelled: 61 Confidence: 71.6% Identity: 11% PDB header:ion channel Chain: D: PDB Molecule:outer membrane protein g; PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation Phyre2 PDB 2jna chain A domain 1 Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 62.9% Identity: 25% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 1uyn chain X Region: 29 - 84 Aligned: 56 Modelled: 56 Confidence: 11.3% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Autotransporter Family: Autotransporter Phyre2 PDB 2wjq chain A Region: 58 - 95 Aligned: 38 Modelled: 38 Confidence: 10.1% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. Phyre2 PDB 2vda chain B Region: 2 - 21 Aligned: 20 Modelled: 20 Confidence: 9.9% Identity: 25% PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex Phyre2 PDB 2jwy chain A Region: 36 - 80 Aligned: 40 Modelled: 45 Confidence: 6.4% Identity: 23% PDB header:lipoprotein Chain: A: PDB Molecule:uncharacterized lipoprotein yaji; PDBTitle: solution nmr structure of uncharacterized lipoprotein yaji from2 escherichia coli. northeast structural genomics target er540 Phyre2 1 d1osma_ 2 d1phoa_ 3 c3nsgA_ 4 d2zfga1 5 d2fgqx1 6 c3a2rX_ 7 d3prna_ 8 d2pora_ 9 c2o4vA_ 10 c2iwvD_ 11 d2jnaa1 12 d1uynx_ 13 c2wjqA_ 14 c2vdaB_ 15 c2jwyA_

Detailed template information

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

1 d1osma_ 99.8 63 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 2 d1phoa_ 99.8 58 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 3 c3nsgA_ 99.8 51 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi 4 d2zfga1 99.8 58 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 5 d2fgqx1 99.6 20 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 6 c3a2rX_ 99.6 17 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 7 d3prna_ 99.2 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 8 d2pora_ 99.2 10 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 9 c2o4vA_ 90.1 23 PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane 10 c2iwvD_ 71.6 11 PDB header:ion channel Chain: D: PDB Molecule:outer membrane protein g; PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation 11 d2jnaa1 62.9 25 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 12 d1uynx_ 11.3 14 Fold:Transmembrane beta-barrels Superfamily:Autotransporter Family:Autotransporter 13 c2wjqA_ 10.1 13 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 14 c2vdaB_ 9.9 25 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex 15 c2jwyA_ 6.4 23 PDB header:lipoprotein Chain: A: PDB Molecule:uncharacterized lipoprotein yaji; PDBTitle: solution nmr structure of uncharacterized lipoprotein yaji from2 escherichia coli. northeast structural genomics target er540

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