Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	T	F	S	G	K	R	S	T	L	A	L	A	I	A	G	V	T	A	M	S	G	F	M	A	M	P	E	A	R	A	E	G	F	I	D	D	S	T	L	T	G	G	I	Y	Y	W	Q	R	E	R	D	R	K	D	V	T	D	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?														?	?	?	?	?	?	?	?						?			?																?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	K	Y	K	T	N	L	S	H	S	T	W	N	A	N	L	D	F	Q	S	G	Y	A	A	D	M	F	G	L	D	I	A	A	F	T	A	I	E	M	A	E	N	G	D	S	S	H	P	N	E	I	A	F	S	K	S	N	K	A	Y
Secondary structure
SS confidence
Disorder		?	?	?	?		?		?		?																													?	?	?	?	?	?	?	?	?	?						?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	E	D	W	S	G	D	K	S	G	I	S	L	Y	K	A	A	A	K	F	K	Y	G	P	V	W	A	R	A	G	Y	I	Q	P	T	G	Q	T	L	L	A	P	H	W	S	F	M	P	G	T	Y	Q	G	A	E	A	G	A	N	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																	?	?	?	?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		D	Y	G	D	A	G	A	L	S	F	S	Y	M	W	T	N	E	Y	K	A	P	W	H	L	E	M	D	E	F	Y	Q	N	D	K	T	T	K	V	D	Y	L	H	S	F	G	A	K	Y	D	F	K	N	N	F	V	L	E	A	A	F
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?		?		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	Q	A	E	G	Y	I	D	Q	Y	F	A	K	A	S	Y	K	F	D	I	A	G	S	P	L	T	T	S	Y	Q	F	Y	G	T	R	D	K	V	D	D	R	S	V	N	D	L	Y	D	G	T	A	W	L	Q	A	L	T	F	G	Y
Secondary structure
SS confidence
Disorder																							?	?											?		?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		R	A	A	D	V	V	D	L	R	L	E	G	T	W	V	K	A	D	G	Q	Q	G	Y	F	L	Q	R	M	T	P	T	Y	A	S	S	N	G	R	L	D	I	W	W	D	N	R	S	D	F	N	A	N	G	E	K	A	V	F	F	G
Secondary structure
SS confidence
Disorder																		?			?										?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	M	Y	D	L	K	N	W	N	L	P	G	F	A	I	G	A	S	Y	V	Y	A	W	D	A	K	P	A	T	W	Q	S	N	P	D	A	Y	Y	D	K	N	R	T	I	E	E	S	A	Y	S	L	D	A	V	Y	T	I	Q	D	G
Secondary structure
SS confidence
Disorder																												?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.
Sequence		R	A	K	G	T	M	F	K	L	H	F	T	E	Y	D	N	H	S	D	I	P	S	W	G	G	G	Y	G	N	I	F	Q	D	E	R	D	V	K	F	M	V	I	A	P	F	T	I	F
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 2y0h chain A Region: 36 - 468 Aligned: 360 Modelled: 388 Confidence: 100.0% Identity: 18% PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl Phyre2 PDB 2odj chain A Region: 23 - 468 Aligned: 373 Modelled: 408 Confidence: 100.0% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:porin d; PDBTitle: crystal structure of the outer membrane protein oprd from pseudomonas2 aeruginosa Phyre2 PDB 2y0l chain A Region: 33 - 468 Aligned: 361 Modelled: 391 Confidence: 100.0% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo Phyre2 PDB 2qtk chain B Region: 35 - 466 Aligned: 365 Modelled: 396 Confidence: 100.0% Identity: 18% PDB header:membrane protein Chain: B: PDB Molecule:probable porin; PDBTitle: crystal structure of the outer membrane protein opdk from2 pseudomonas aeruginosa Phyre2 PDB 3jty chain B Region: 34 - 467 Aligned: 381 Modelled: 423 Confidence: 100.0% Identity: 14% 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 2y0k chain A Region: 32 - 468 Aligned: 362 Modelled: 391 Confidence: 100.0% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:pyroglutatmate porin opdo; PDBTitle: crystal structure of pseudomonas aeruginosa opdo Phyre2 PDB 3rbh chain C Region: 43 - 467 Aligned: 373 Modelled: 422 Confidence: 99.1% Identity: 11% PDB header:transport protein Chain: C: PDB Molecule:alginate production protein alge; PDBTitle: structure of alginate export protein alge from pseudomonas aeruginosa Phyre2 PDB 2o4v chain A Region: 40 - 465 Aligned: 352 Modelled: 374 Confidence: 95.4% Identity: 11% 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 2fgq chain X domain 1 Region: 40 - 465 Aligned: 299 Modelled: 330 Confidence: 94.9% Identity: 16% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3nsg chain A Region: 40 - 465 Aligned: 312 Modelled: 359 Confidence: 93.1% Identity: 15% 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 3qra chain A Region: 222 - 365 Aligned: 112 Modelled: 112 Confidence: 91.8% Identity: 18% 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 1osm chain A Region: 40 - 465 Aligned: 316 Modelled: 335 Confidence: 91.8% Identity: 16% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1pho chain A Region: 40 - 465 Aligned: 303 Modelled: 342 Confidence: 90.4% Identity: 17% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2k0l chain A Region: 195 - 367 Aligned: 149 Modelled: 149 Confidence: 83.5% Identity: 15% 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. Phyre2 PDB 1g90 chain A Region: 202 - 367 Aligned: 142 Modelled: 142 Confidence: 81.3% Identity: 15% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 2iwv chain D Region: 224 - 314 Aligned: 91 Modelled: 91 Confidence: 76.0% Identity: 15% 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 2zfg chain A domain 1 Region: 40 - 465 Aligned: 313 Modelled: 328 Confidence: 74.9% Identity: 15% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3prn chain A Region: 40 - 417 Aligned: 256 Modelled: 292 Confidence: 69.6% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1qjp chain A Region: 217 - 316 Aligned: 100 Modelled: 100 Confidence: 68.6% Identity: 15% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 3a2r chain X Region: 39 - 417 Aligned: 300 Modelled: 321 Confidence: 63.0% 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 1 c2y0hA_ 2 c2odjA_ 3 c2y0lA_ 4 c2qtkB_ 5 c3jtyB_ 6 c2y0kA_ 7 c3rbhC_ 8 c2o4vA_ 9 d2fgqx1 10 c3nsgA_ 11 c3qraA_ 12 d1osma_ 13 d1phoa_ 14 c2k0lA_ 15 d1g90a_ 16 c2iwvD_ 17 d2zfga1 18 d3prna_ 19 d1qjpa_ 20 c3a2rX_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 c2y0hA_ 100.0 18 PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl 2 c2odjA_ 100.0 21 PDB header:membrane protein Chain: A: PDB Molecule:porin d; PDBTitle: crystal structure of the outer membrane protein oprd from pseudomonas2 aeruginosa 3 c2y0lA_ 100.0 17 PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 4 c2qtkB_ 100.0 18 PDB header:membrane protein Chain: B: PDB Molecule:probable porin; PDBTitle: crystal structure of the outer membrane protein opdk from2 pseudomonas aeruginosa 5 c3jtyB_ 100.0 14 PDB header:transport protein Chain: B: PDB Molecule:benf-like porin; PDBTitle: crystal structure of a benf-like porin from pseudomonas fluorescens2 pf-5 6 c2y0kA_ 100.0 15 PDB header:transport protein Chain: A: PDB Molecule:pyroglutatmate porin opdo; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 7 c3rbhC_ 99.1 11 PDB header:transport protein Chain: C: PDB Molecule:alginate production protein alge; PDBTitle: structure of alginate export protein alge from pseudomonas aeruginosa 8 c2o4vA_ 95.4 11 PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane 9 d2fgqx1 94.9 16 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 10 c3nsgA_ 93.1 15 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi 11 c3qraA_ 91.8 18 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 12 d1osma_ 91.8 16 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 13 d1phoa_ 90.4 17 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 14 c2k0lA_ 83.5 15 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. 15 d1g90a_ 81.3 15 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 16 c2iwvD_ 76.0 15 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 17 d2zfga1 74.9 15 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 18 d3prna_ 69.6 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 19 d1qjpa_ 68.6 15 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 20 c3a2rX_ 63.0 15 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 21 c3nb3C_ not modelled 48.7 15 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 22 c2jmmA_ not modelled 43.6 17 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 23 c2grxB_ not modelled 38.7 15 PDB header:metal transport Chain: B: PDB Molecule:ferrichrome-iron receptor; PDBTitle: crystal structure of tonb in complex with fhua, e. coli2 outer membrane receptor for ferrichrome 24 c2wjqA_ not modelled 29.7 11 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 25 d2pora_ not modelled 28.0 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 26 d1by5a_ not modelled 26.5 15 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Ligand-gated protein channel 27 c2vdaB_ not modelled 16.9 32 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex 28 c3kvnA_ not modelled 16.4 9 PDB header:hydrolase Chain: A: PDB Molecule:esterase esta; PDBTitle: crystal structure of the full-length autotransporter esta from2 pseudomonas aeruginosa 29 c3brzA_ not modelled 15.5 13 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 30 c2f1tB_ not modelled 14.6 14 PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw 31 d1qj8a_ not modelled 10.8 13 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 32 d1t16a_ not modelled 10.1 12 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Outer membrane protein transport protein 33 c1xkhC_ not modelled 7.9 13 PDB header:membrane protein Chain: C: PDB Molecule:ferripyoverdine receptor; PDBTitle: pyoverdine outer membrane receptor fpva from pseudomonas aeruginosa2 pao1 bound to pyoverdine 34 c3qlbA_ not modelled 6.2 15 PDB header:metal transport Chain: A: PDB Molecule:enantio-pyochelin receptor; PDBTitle: enantiopyochelin outer membrane tonb-dependent transporter from2 pseudomonas fluorescens bound to the ferri-enantiopyochelin

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