Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	S	T	L	A	L	V	V	M	G	I	V	A	S	A	S	V	Q	A	A	E	I	Y	N	K	D	G	N	K	L	D	V	Y	G	K	V	K	A	M	H	Y	M	S	D	N	A	S	K	D	G	D	Q	S	Y	I	R	F	G
Secondary structure
SS confidence
Disorder		?	?	?																?					?																					?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	K	G	E	T	Q	I	N	D	Q	L	T	G	Y	G	R	W	E	A	E	F	A	G	N	K	A	E	S	D	T	A	Q	Q	K	T	R	L	A	F	A	G	L	K	Y	K	D	L	G	S	F	D	Y	G	R	N	L	G	A	L	Y
Secondary structure
SS confidence
Disorder																									?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	V	E	A	W	T	D	M	F	P	E	F	G	G	D	S	S	A	Q	T	D	N	F	M	T	K	R	A	S	G	L	A	T	Y	R	N	T	D	F	F	G	V	I	D	G	L	N	L	T	L	Q	Y	Q	G	K	N	E	N	R	D
Secondary structure
SS confidence
Disorder																								?															?															?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	K	K	Q	N	G	D	G	F	G	T	S	L	T	Y	D	F	G	G	S	D	F	A	I	S	G	A	Y	T	N	S	D	R	T	N	E	Q	N	L	Q	S	R	G	T	G	K	R	A	E	A	W	A	T	G	L	K	Y	D	A	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																									?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	I	Y	L	A	T	F	Y	S	E	T	R	K	M	T	P	I	T	G	G	F	A	N	K	T	Q	N	F	E	A	V	A	Q	Y	Q	F	D	F	G	L	R	P	S	L	G	Y	V	L	S	K	G	K	D	I	E	G	I	G	D	E
Secondary structure
SS confidence
Disorder														?	?	?	?	?		?	?																															?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.
Sequence		D	L	V	N	Y	I	D	V	G	A	T	Y	Y	F	N	K	N	M	S	A	F	V	D	Y	K	I	N	Q	L	D	S	D	N	K	L	N	I	N	N	D	D	I	V	A	V	G	M	T	Y	Q	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 1pho chain A Region: 22 - 351 Aligned: 330 Modelled: 330 Confidence: 100.0% Identity: 100% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2zfg chain A domain 1 Region: 22 - 351 Aligned: 327 Modelled: 328 Confidence: 100.0% Identity: 63% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1osm chain A Region: 22 - 351 Aligned: 329 Modelled: 330 Confidence: 100.0% Identity: 59% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3nsg chain A Region: 23 - 351 Aligned: 326 Modelled: 329 Confidence: 100.0% Identity: 52% 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 2fgq chain X domain 1 Region: 31 - 351 Aligned: 301 Modelled: 312 Confidence: 100.0% Identity: 18% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3a2r chain X Region: 31 - 351 Aligned: 315 Modelled: 321 Confidence: 100.0% Identity: 18% 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 2por chain A Region: 31 - 351 Aligned: 284 Modelled: 321 Confidence: 100.0% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3prn chain A Region: 32 - 351 Aligned: 274 Modelled: 308 Confidence: 100.0% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2o4v chain A Region: 25 - 351 Aligned: 321 Modelled: 327 Confidence: 99.9% Identity: 12% 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 3qra chain A Region: 198 - 351 Aligned: 142 Modelled: 152 Confidence: 99.1% Identity: 15% 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 2y0k chain A Region: 33 - 351 Aligned: 312 Modelled: 319 Confidence: 99.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:pyroglutatmate porin opdo; PDBTitle: crystal structure of pseudomonas aeruginosa opdo Phyre2 PDB 1p4t chain A Region: 217 - 351 Aligned: 135 Modelled: 135 Confidence: 99.0% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 1qj8 chain A Region: 201 - 351 Aligned: 135 Modelled: 150 Confidence: 98.9% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 3jty chain B Region: 33 - 351 Aligned: 311 Modelled: 315 Confidence: 98.8% Identity: 10% 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 2odj chain A Region: 13 - 351 Aligned: 308 Modelled: 315 Confidence: 98.8% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:porin d; PDBTitle: crystal structure of the outer membrane protein oprd from pseudomonas2 aeruginosa Phyre2 PDB 2y0h chain A Region: 33 - 351 Aligned: 302 Modelled: 319 Confidence: 98.7% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl Phyre2 PDB 2y0l chain A Region: 33 - 351 Aligned: 305 Modelled: 319 Confidence: 98.6% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo Phyre2 PDB 1g90 chain A Region: 198 - 351 Aligned: 153 Modelled: 153 Confidence: 98.5% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 1qjp chain A Region: 226 - 351 Aligned: 111 Modelled: 126 Confidence: 98.5% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 2k0l chain A Region: 198 - 351 Aligned: 154 Modelled: 154 Confidence: 98.4% Identity: 12% 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 2jna chain A domain 1 Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 54.1% Identity: 48% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 1 d1phoa_ 2 d2zfga1 3 d1osma_ 4 c3nsgA_ 5 d2fgqx1 6 c3a2rX_ 7 d2pora_ 8 d3prna_ 9 c2o4vA_ 10 c3qraA_ 11 c2y0kA_ 12 d1p4ta_ 13 d1qj8a_ 14 c3jtyB_ 15 c2odjA_ 16 c2y0hA_ 17 c2y0lA_ 18 d1g90a_ 19 d1qjpa_ 20 c2k0lA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 d2jnaa1 48 49 50 51 52 53 54 55 56 57 58

Detailed template information

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

1 d1phoa_ 100.0 100 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 2 d2zfga1 100.0 63 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 3 d1osma_ 100.0 59 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 4 c3nsgA_ 100.0 52 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi 5 d2fgqx1 100.0 18 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 6 c3a2rX_ 100.0 18 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 7 d2pora_ 100.0 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 8 d3prna_ 100.0 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 9 c2o4vA_ 99.9 12 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 c3qraA_ 99.1 15 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 11 c2y0kA_ 99.0 11 PDB header:transport protein Chain: A: PDB Molecule:pyroglutatmate porin opdo; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 12 d1p4ta_ 99.0 14 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 13 d1qj8a_ 98.9 14 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 14 c3jtyB_ 98.8 10 PDB header:transport protein Chain: B: PDB Molecule:benf-like porin; PDBTitle: crystal structure of a benf-like porin from pseudomonas fluorescens2 pf-5 15 c2odjA_ 98.8 13 PDB header:membrane protein Chain: A: PDB Molecule:porin d; PDBTitle: crystal structure of the outer membrane protein oprd from pseudomonas2 aeruginosa 16 c2y0hA_ 98.7 11 PDB header:transport protein Chain: A: PDB Molecule:probable porin; PDBTitle: crystal structure of pseudomonas aeruginosa opdl 17 c2y0lA_ 98.6 13 PDB header:transport protein Chain: A: PDB Molecule:cis-aconitate porin opdh; PDBTitle: crystal structure of pseudomonas aeruginosa opdo 18 d1g90a_ 98.5 13 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 19 d1qjpa_ 98.5 14 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 20 c2k0lA_ 98.4 12 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. 21 c3nb3C_ not modelled 98.3 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 d1t16a_ not modelled 98.2 12 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Outer membrane protein transport protein 23 c3brzA_ not modelled 98.2 13 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 24 c2qtkB_ not modelled 98.2 12 PDB header:membrane protein Chain: B: PDB Molecule:probable porin; PDBTitle: crystal structure of the outer membrane protein opdk from2 pseudomonas aeruginosa 25 c2f1tB_ not modelled 98.1 15 PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw 26 c2lhfA_ not modelled 98.1 13 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 27 c2x27X_ not modelled 98.0 14 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein oprg; PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa 28 c3dwoX_ not modelled 97.3 11 PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue 29 c2jmmA_ not modelled 96.7 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 c2wjqA_ not modelled 96.0 9 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 31 d2mpra_ not modelled 95.9 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 32 d1uynx_ not modelled 95.7 11 Fold:Transmembrane beta-barrels Superfamily:Autotransporter Family:Autotransporter 33 c2x4mD_ not modelled 95.5 19 PDB header:hydrolase Chain: D: PDB Molecule:coagulase/fibrinolysin; PDBTitle: yersinia pestis plasminogen activator pla 34 c3aehB_ not modelled 95.5 12 PDB header:hydrolase Chain: B: PDB Molecule:hemoglobin-binding protease hbp autotransporter; PDBTitle: integral membrane domain of autotransporter hbp 35 c3bryB_ not modelled 94.9 11 PDB header:transport protein Chain: B: PDB Molecule:tbux; PDBTitle: crystal structure of the ralstonia pickettii toluene2 transporter tbux 36 c3rbhC_ not modelled 94.6 8 PDB header:transport protein Chain: C: PDB Molecule:alginate production protein alge; PDBTitle: structure of alginate export protein alge from pseudomonas aeruginosa 37 c2iwvD_ not modelled 94.3 13 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 38 d1af6a_ not modelled 93.3 11 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 39 d1a0tp_ not modelled 93.2 12 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 40 c3qq2C_ not modelled 93.1 14 PDB header:membrane protein/protein transport Chain: C: PDB Molecule:brka autotransporter; PDBTitle: crystal structure of the beta domain of the bordetella autotransporter2 brka 41 c2qomB_ not modelled 90.7 14 PDB header:hydrolase Chain: B: PDB Molecule:serine protease espp; PDBTitle: the crystal structure of the e.coli espp autotransporter beta-domain. 42 c3sljA_ not modelled 89.2 12 PDB header:protein transport Chain: A: PDB Molecule:serine protease espp; PDBTitle: pre-cleavage structure of the autotransporter espp - n1023a mutant 43 c3kvnA_ not modelled 86.2 14 PDB header:hydrolase Chain: A: PDB Molecule:esterase esta; PDBTitle: crystal structure of the full-length autotransporter esta from2 pseudomonas aeruginosa 44 d1i78a_ not modelled 83.3 16 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane protease OMPT 45 d2gufa1 not modelled 69.4 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Ligand-gated protein channel 46 c2iahA_ not modelled 65.3 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. 47 d2jnaa1 54.1 48 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 48 c2grxB_ not modelled 43.3 11 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 49 c3fhhA_ not modelled 39.0 13 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane heme receptor shua; PDBTitle: crystal structure of the heme/hemoglobin outer membrane2 transporter shua from shigella dysenteriae 50 c3qlbA_ not modelled 35.6 12 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 51 c1xkwA_ not modelled 29.3 13 PDB header:membrane protein Chain: A: PDB Molecule:fe(iii)-pyochelin receptor; PDBTitle: pyochelin outer membrane receptor fpta from pseudomonas2 aeruginosa 52 c2hdiA_ not modelled 26.4 13 PDB header:protein transport,antimicrobial protein Chain: A: PDB Molecule:colicin i receptor; PDBTitle: crystal structure of the colicin i receptor cir from e.coli in complex2 with receptor binding domain of colicin ia. 53 c2k4tA_ not modelled 23.2 13 PDB header:membrane protein,apoptosis Chain: A: PDB Molecule:voltage-dependent anion-selective channel PDBTitle: solution structure of human vdac-1 in ldao micelles 54 c3cslB_ not modelled 12.3 16 PDB header:membrane protein/heme binding protein Chain: B: PDB Molecule:hasr protein; PDBTitle: structure of the serratia marcescens hemophore receptor hasr in2 complex with its hemophore hasa and heme 55 c1qd6C_ not modelled 10.8 12 PDB header:membrane protein Chain: C: PDB Molecule:protein (outer membrane phospholipase (ompla)); PDBTitle: outer membrane phospholipase a from escherichia coli 56 c2k3aA_ not modelled 9.7 32 PDB header:hydrolase Chain: A: PDB Molecule:chap domain protein; PDBTitle: nmr solution structure of staphylococcus saprophyticus chap2 (cysteine, histidine-dependent amidohydrolases/peptidases)3 domain protein. northeast structural genomics consortium4 target syr11 57 d1by5a_ not modelled 7.1 10 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Ligand-gated protein channel 58 c2vdaB_ not modelled 6.9 40 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex

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