Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	L	I	T	A	P	C	R	A	L	L	A	L	P	F	C	Y	A	F	S	A	A	G	E	E	A	R	P	A	E	H	D	D	T	K	T	P	A	I	T	S	T	S	S	P	S	F	R	F	Y	G	E	L	G	V	G	G	Y	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																	?	?	?	?	?	?	?	?	?	?	?	?				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	L	E	G	E	N	K	H	K	Y	S	D	G	T	Y	I	E	G	G	L	E	M	K	Y	G	S	W	F	G	L	I	Y	G	E	G	W	T	V	Q	A	D	H	D	G	N	A	W	V	P	D	H	S	W	G	G	F	E	G	G	I
Secondary structure
SS confidence
Disorder			?			?	?			?																																			?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	R	F	Y	G	G	Y	R	T	N	D	G	T	E	I	M	L	S	L	R	Q	D	S	S	L	D	D	L	Q	W	W	G	D	F	T	P	D	L	G	Y	V	I	P	N	T	R	D	I	M	T	A	L	K	V	Q	N	L	S	G	N
Secondary structure
SS confidence
Disorder																																											?		?			?								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	R	Y	S	V	T	A	T	P	A	G	H	H	D	E	S	K	A	W	L	H	F	G	K	Y	D	R	Y	D	D	K	Y	T	Y	P	A	M	M	N	G	Y	I	Q	Y	D	L	A	E	G	I	T	W	M	N	G	L	E	I	T	D
Secondary structure
SS confidence
Disorder											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	T	G	Q	L	Y	L	T	G	L	L	T	P	N	F	A	A	R	A	W	H	H	T	G	R	A	D	G	L	D	V	P	G	S	E	S	G	M	M	V	S	A	M	Y	E	A	L	K	G	V	Y	L	S	T	A	Y	T	Y	A	K
Secondary structure
SS confidence
Disorder																								?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.
Sequence		H	R	P	D	H	A	D	D	E	T	T	S	F	M	Q	F	G	I	W	Y	E	Y	G	G	G	R	F	A	T	A	F	D	S	R	F	Y	M	K	N	A	S	H	D	P	S	D	Q	I	F	L	M	Q	Y	F	Y	W
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 2fgq chain X domain 1 Region: 47 - 325 Aligned: 261 Modelled: 279 Confidence: 99.3% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1pho chain A Region: 40 - 355 Aligned: 297 Modelled: 313 Confidence: 99.3% Identity: 15% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3prn chain A Region: 49 - 331 Aligned: 249 Modelled: 282 Confidence: 99.1% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2zfg chain A domain 1 Region: 40 - 355 Aligned: 305 Modelled: 316 Confidence: 99.0% Identity: 15% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3nsg chain A Region: 53 - 325 Aligned: 256 Modelled: 273 Confidence: 98.8% Identity: 14% 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 3a2r chain X Region: 50 - 352 Aligned: 290 Modelled: 303 Confidence: 98.6% Identity: 12% 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 1osm chain A Region: 47 - 355 Aligned: 290 Modelled: 309 Confidence: 98.6% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2por chain A Region: 53 - 331 Aligned: 253 Modelled: 277 Confidence: 98.3% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 3brz chain A Region: 122 - 323 Aligned: 195 Modelled: 202 Confidence: 92.3% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx Phyre2 PDB 3qra chain A Region: 239 - 322 Aligned: 79 Modelled: 84 Confidence: 74.4% Identity: 13% 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 2o4v chain A Region: 26 - 355 Aligned: 313 Modelled: 330 Confidence: 63.1% Identity: 16% 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 1g90 chain A Region: 176 - 328 Aligned: 150 Modelled: 153 Confidence: 60.0% Identity: 11% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 1t16 chain A Region: 127 - 323 Aligned: 197 Modelled: 197 Confidence: 57.6% Identity: 9% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Outer membrane protein transport protein Phyre2 PDB 3dwo chain X Region: 88 - 331 Aligned: 240 Modelled: 244 Confidence: 55.8% Identity: 10% PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue Phyre2 PDB 3mxn chain B Region: 82 - 137 Aligned: 54 Modelled: 56 Confidence: 45.4% Identity: 22% PDB header:replication Chain: B: PDB Molecule:recq-mediated genome instability protein 2; PDBTitle: crystal structure of the rmi core complex Phyre2 PDB 2iwv chain D Region: 236 - 322 Aligned: 86 Modelled: 87 Confidence: 34.0% Identity: 14% 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 2f1t chain B Region: 278 - 322 Aligned: 45 Modelled: 45 Confidence: 20.1% Identity: 11% PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw Phyre2 PDB 2k0l chain A Region: 239 - 330 Aligned: 92 Modelled: 92 Confidence: 14.1% Identity: 13% 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 3nb3 chain C Region: 254 - 323 Aligned: 59 Modelled: 70 Confidence: 13.5% Identity: 12% 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 Phyre2 PDB 2oqz chain A domain 1 Region: 50 - 91 Aligned: 42 Modelled: 42 Confidence: 13.1% Identity: 29% Fold: Sortase Superfamily: Sortase Family: Sortase Phyre2 1 d2fgqx1 2 d1phoa_ 3 d3prna_ 4 d2zfga1 5 c3nsgA_ 6 c3a2rX_ 7 d1osma_ 8 d2pora_ 9 c3brzA_ 10 c3qraA_ 11 c2o4vA_ 12 d1g90a_ 13 d1t16a_ 14 c3dwoX_ 15 c3mxnB_ 16 c2iwvD_ 17 c2f1tB_ 18 c2k0lA_ 19 c3nb3C_ 20 d2oqza1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 d2fgqx1 99.3 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 2 d1phoa_ 99.3 15 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 3 d3prna_ 99.1 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 4 d2zfga1 99.0 15 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 5 c3nsgA_ 98.8 14 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi 6 c3a2rX_ 98.6 12 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 7 d1osma_ 98.6 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 8 d2pora_ 98.3 14 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 9 c3brzA_ 92.3 10 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 10 c3qraA_ 74.4 13 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 c2o4vA_ 63.1 16 PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane 12 d1g90a_ 60.0 11 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 13 d1t16a_ 57.6 9 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Outer membrane protein transport protein 14 c3dwoX_ 55.8 10 PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue 15 c3mxnB_ 45.4 22 PDB header:replication Chain: B: PDB Molecule:recq-mediated genome instability protein 2; PDBTitle: crystal structure of the rmi core complex 16 c2iwvD_ 34.0 14 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 c2f1tB_ 20.1 11 PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw 18 c2k0lA_ 14.1 13 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. 19 c3nb3C_ 13.5 12 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 20 d2oqza1 13.1 29 Fold:Sortase Superfamily:Sortase Family:Sortase 21 c3h9xB_ not modelled 11.0 15 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein pspto_3016; PDBTitle: crystal structure of the pspto_3016 protein from2 pseudomonas syringae, northeast structural genomics3 consortium target psr293 22 d1vf5c2 not modelled 10.8 16 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 23 d1luza_ not modelled 10.7 50 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 24 d1i78a_ not modelled 10.4 12 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane protease OMPT 25 d1qj8a_ not modelled 9.6 12 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 26 c2l7eA_ not modelled 9.4 46 PDB header:transcription Chain: A: PDB Molecule:transcription initiation factor tfiid subunit 14; PDBTitle: the structure of a domain from yeast 27 c3bryB_ not modelled 8.9 10 PDB header:transport protein Chain: B: PDB Molecule:tbux; PDBTitle: crystal structure of the ralstonia pickettii toluene2 transporter tbux 28 c2wjqA_ not modelled 8.8 15 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 29 d1p4ta_ not modelled 7.9 8 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 30 d1mo6a2 not modelled 7.9 29 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 31 d1ubea2 not modelled 7.3 29 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 32 c3fk3B_ not modelled 7.2 31 PDB header:transcription Chain: B: PDB Molecule:protein af-9 homolog; PDBTitle: structure of the yeats domain, yaf9 33 d1xp8a2 not modelled 6.6 36 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 34 d1u94a2 not modelled 5.9 36 Fold:Anti-LPS factor/recA domain Superfamily:RecA protein, C-terminal domain Family:RecA protein, C-terminal domain 35 c2jmmA_ not modelled 5.7 13 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 36 d1a6ca3 not modelled 5.6 43 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 37 d2gria1 not modelled 5.4 38 Fold:beta-Grasp (ubiquitin-like) Superfamily:NSP3A-like Family:NSP3A-like 38 c3dpgA_ not modelled 5.3 33 PDB header:hydrolase/dna Chain: A: PDB Molecule:sgrair restriction enzyme; PDBTitle: sgrai with noncognate dna bound

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