Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		D	G	D	Q	T	Y	M	R	L	G	F	K	G	E	T	Q	V	T	D	Q	L	T	G	Y	G	Q	W	E	Y	Q	I	Q	G	N	S	A	E	N	E	N	N	S	W	T	R	V	A	F	A	G	L	K	F	Q	D	V	G	S	F	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																											?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	G	R	N	Y	G	V	V	Y	D	V	T	S	W	T	D	V	L	P	E	F	G	G	D	T	Y	G	S	D	N	F	M	Q	Q	R	G	N	G	F	A	T	Y	R	N	T	D	F	F	G	L	V	D	G	L	N	F	A	V	Q	Y
Secondary structure
SS confidence
Disorder																													?		?	?															?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Q	G	K	N	G	N	P	S	G	E	G	V	T	N	N	G	R	D	A	L	R	Q	N	G	D	G	V	G	G	S	I	T	Y	D	Y	E	G	F	G	I	G	G	A	I	S	S	S	K	R	T	D	A	Q	N	T	A	A	Y	I	G
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?	?	?	?	?	?		?	?	?	?	?		?	?																											?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		N	G	D	R	A	E	T	Y	T	G	G	L	K	Y	D	A	N	N	I	Y	L	A	A	Q	Y	T	Q	T	Y	N	A	T	R	V	G	S	L	G	W	A	N	K	A	Q	N	F	E	A	V	A	Q	Y	Q	F	D	F	G	L	R	P
Secondary structure
SS confidence
Disorder		?	?																													?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.
Sequence		S	L	A	Y	L	Q	S	K	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: 1 - 251 Aligned: 251 Modelled: 251 Confidence: 100.0% Identity: 75% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2fgq chain X domain 1 Region: 1 - 251 Aligned: 227 Modelled: 242 Confidence: 100.0% Identity: 19% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3nsg chain A Region: 1 - 252 Aligned: 241 Modelled: 241 Confidence: 100.0% Identity: 56% 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: 1 - 251 Aligned: 240 Modelled: 241 Confidence: 100.0% Identity: 63% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3a2r chain X Region: 1 - 251 Aligned: 239 Modelled: 251 Confidence: 100.0% Identity: 15% 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 1pho chain A Region: 1 - 251 Aligned: 240 Modelled: 241 Confidence: 100.0% Identity: 58% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3prn chain A Region: 4 - 251 Aligned: 221 Modelled: 233 Confidence: 100.0% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2por chain A Region: 2 - 251 Aligned: 236 Modelled: 250 Confidence: 100.0% Identity: 8% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2o4v chain A Region: 6 - 251 Aligned: 241 Modelled: 246 Confidence: 99.2% Identity: 15% 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 1t16 chain A Region: 100 - 252 Aligned: 153 Modelled: 153 Confidence: 96.9% Identity: 11% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Outer membrane protein transport protein Phyre2 PDB 3brz chain A Region: 100 - 252 Aligned: 147 Modelled: 153 Confidence: 96.8% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx Phyre2 PDB 2wjq chain A Region: 113 - 252 Aligned: 140 Modelled: 140 Confidence: 95.5% Identity: 14% 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 2y0l chain A Region: 17 - 252 Aligned: 214 Modelled: 222 Confidence: 95.2% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo Phyre2 PDB 2y0h chain A Region: 46 - 251 Aligned: 170 Modelled: 172 Confidence: 94.8% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl Phyre2 PDB 1qj8 chain A Region: 146 - 252 Aligned: 107 Modelled: 107 Confidence: 94.6% Identity: 16% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 3qra chain A Region: 138 - 252 Aligned: 111 Modelled: 115 Confidence: 92.9% Identity: 16% PDB header:cell invasion Chain: A: PDB Molecule:attachment invasion locus protein; PDBTitle: the crystal structure of ail, the attachment invasion locus protein of2 yersinia pestis Phyre2 PDB 3jty chain B Region: 20 - 251 Aligned: 204 Modelled: 206 Confidence: 92.2% Identity: 8% PDB header:transport protein Chain: B: PDB Molecule:benf-like porin; PDBTitle: crystal structure of a benf-like porin from pseudomonas fluorescens2 pf-5 Phyre2 PDB 3bry chain B Region: 49 - 252 Aligned: 191 Modelled: 204 Confidence: 89.3% Identity: 11% PDB header:transport protein Chain: B: PDB Molecule:tbux; PDBTitle: crystal structure of the ralstonia pickettii toluene2 transporter tbux Phyre2 PDB 2qtk chain B Region: 5 - 251 Aligned: 219 Modelled: 221 Confidence: 89.1% Identity: 11% PDB header:membrane protein Chain: B: PDB Molecule:probable porin; PDBTitle: crystal structure of the outer membrane protein opdk from2 pseudomonas aeruginosa Phyre2 PDB 1p4t chain A Region: 138 - 252 Aligned: 109 Modelled: 115 Confidence: 86.7% Identity: 7% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 1 d1osma_ 2 d2fgqx1 3 c3nsgA_ 4 d2zfga1 5 c3a2rX_ 6 d1phoa_ 7 d3prna_ 8 d2pora_ 9 c2o4vA_ 10 d1t16a_ 11 c3brzA_ 12 c2wjqA_ 13 c2y0lA_ 14 c2y0hA_ 15 d1qj8a_ 16 c3qraA_ 17 c3jtyB_ 18 c3bryB_ 19 c2qtkB_ 20 d1p4ta_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

Detailed template information

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

1 d1osma_ 100.0 75 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 2 d2fgqx1 100.0 19 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 3 c3nsgA_ 100.0 56 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 100.0 63 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 5 c3a2rX_ 100.0 15 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 6 d1phoa_ 100.0 58 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 7 d3prna_ 100.0 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 8 d2pora_ 100.0 8 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 9 c2o4vA_ 99.2 15 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 d1t16a_ 96.9 11 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Outer membrane protein transport protein 11 c3brzA_ 96.8 16 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 12 c2wjqA_ 95.5 14 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 13 c2y0lA_ 95.2 15 PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 14 c2y0hA_ 94.8 16 PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl 15 d1qj8a_ 94.6 16 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 16 c3qraA_ 92.9 16 PDB header:cell invasion Chain: A: PDB Molecule:attachment invasion locus protein; PDBTitle: the crystal structure of ail, the attachment invasion locus protein of2 yersinia pestis 17 c3jtyB_ 92.2 8 PDB header:transport protein Chain: B: PDB Molecule:benf-like porin; PDBTitle: crystal structure of a benf-like porin from pseudomonas fluorescens2 pf-5 18 c3bryB_ 89.3 11 PDB header:transport protein Chain: B: PDB Molecule:tbux; PDBTitle: crystal structure of the ralstonia pickettii toluene2 transporter tbux 19 c2qtkB_ 89.1 11 PDB header:membrane protein Chain: B: PDB Molecule:probable porin; PDBTitle: crystal structure of the outer membrane protein opdk from2 pseudomonas aeruginosa 20 d1p4ta_ 86.7 7 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 21 c3dwoX_ not modelled 84.8 16 PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue 22 c2f1tB_ not modelled 84.0 12 PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw 23 c2y0kA_ not modelled 81.6 13 PDB header:transport protein Chain: A: PDB Molecule:pyroglutatmate porin opdo; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 24 d1g90a_ not modelled 65.4 15 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 25 c3nb3C_ not modelled 62.1 18 PDB header:virus Chain: C: PDB Molecule:outer membrane protein a; PDBTitle: the host outer membrane proteins ompa and ompc are packed at specific2 sites in the shigella phage sf6 virion as structural components 26 c2x4mD_ not modelled 55.1 13 PDB header:hydrolase Chain: D: PDB Molecule:coagulase/fibrinolysin; PDBTitle: yersinia pestis plasminogen activator pla 27 c2k0lA_ not modelled 50.1 11 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein a; PDBTitle: nmr structure of the transmembrane domain of the outer2 membrane protein a from klebsiella pneumoniae in dhpc3 micelles. 28 d1qjpa_ not modelled 48.3 18 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 29 c2jmmA_ not modelled 41.4 14 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein a; PDBTitle: nmr solution structure of a minimal transmembrane beta-2 barrel platform protein 30 c3rbhC_ not modelled 34.8 11 PDB header:transport protein Chain: C: PDB Molecule:alginate production protein alge; PDBTitle: structure of alginate export protein alge from pseudomonas aeruginosa 31 c2x27X_ not modelled 32.4 13 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein oprg; PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa 32 c2iwvD_ not modelled 25.1 10 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 33 c3kvnA_ not modelled 24.7 12 PDB header:hydrolase Chain: A: PDB Molecule:esterase esta; PDBTitle: crystal structure of the full-length autotransporter esta from2 pseudomonas aeruginosa 34 c2odjA_ not modelled 19.5 11 PDB header:membrane protein Chain: A: PDB Molecule:porin d; PDBTitle: crystal structure of the outer membrane protein oprd from pseudomonas2 aeruginosa 35 d1i78a_ not modelled 15.7 11 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane protease OMPT 36 c2lhfA_ not modelled 10.0 14 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein h1; PDBTitle: solution structure of outer membrane protein h (oprh) from p.2 aeruginosa in dhpc micelles 37 c2iahA_ not modelled 9.7 16 PDB header:membrane protein Chain: A: PDB Molecule:ferripyoverdine receptor; PDBTitle: crystal structure of the ferripyoverdine receptor of the outer2 membrane of pseudomonas aeruginosa bound to ferripyoverdine. 38 d2gufa1 not modelled 8.8 8 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Ligand-gated protein channel 39 d1uynx_ not modelled 5.9 18 Fold:Transmembrane beta-barrels Superfamily:Autotransporter Family:Autotransporter

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