Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	I	T	L	R	K	L	P	L	A	V	A	V	A	A	G	V	M	S	A	Q	A	M	A	V	D	F	H	G	Y	A	R	S	G	I	G	W	T	G	S	G	G	E	Q	Q	C	F	Q	T	T	G	A	Q	S	K	Y	R	L	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?									?	?	?	?	?	?	?	?	?															?	?				?	?	?	?	?		?		?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	E	C	E	T	Y	A	E	L	K	L	G	Q	E	V	W	K	E	G	D	K	S	F	Y	F	D	T	N	V	A	Y	S	V	A	Q	Q	N	D	W	E	A	T	D	P	A	F	R	E	A	N	V	Q	G	K	N	L	I	E	W	L
Secondary structure
SS confidence
Disorder																																					?		?	?	?	?																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	G	S	T	I	W	A	G	K	R	F	Y	Q	R	H	D	V	H	M	I	D	F	Y	Y	W	D	I	S	G	P	G	A	G	L	E	N	I	D	V	G	F	G	K	L	S	L	A	A	T	R	S	S	E	A	G	G	S	S	S	F
Secondary structure
SS confidence
Disorder		?																																																					?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	S	N	N	I	Y	D	Y	T	N	E	T	A	N	D	V	F	D	V	R	L	A	Q	M	E	I	N	P	G	G	T	L	E	L	G	V	D	Y	G	R	A	N	L	R	D	N	Y	R	L	V	D	G	A	S	K	D	G	W	L	F
Secondary structure
SS confidence
Disorder								?																																				?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		T	A	E	H	T	Q	S	V	L	K	G	F	N	K	F	V	V	Q	Y	A	T	D	S	M	T	S	Q	G	K	G	L	S	Q	G	S	G	V	A	F	D	N	E	K	F	A	Y	N	I	N	N	N	G	H	M	L	R	I	L	D	H
Secondary structure
SS confidence
Disorder																							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	A	I	S	M	G	D	N	W	D	M	M	Y	V	G	M	Y	Q	D	I	N	W	D	N	D	N	G	T	K	W	W	T	V	G	I	R	P	M	Y	K	W	T	P	I	M	S	T	V	M	E	I	G	Y	D	N	V	E	S	Q	R
Secondary structure
SS confidence
Disorder																					?	?	?	?	?	?	?	?																														?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		T	G	D	K	N	N	Q	Y	K	I	T	L	A	Q	Q	W	Q	A	G	D	S	I	W	S	R	P	A	I	R	V	F	A	T	Y	A	K	W	D	E	K	W	G	Y	D	Y	T	G	N	A	D	N	N	A	N	F	G	K	A	V	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?											?	?	?	?	?	?																						?				?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.
Sequence		A	D	F	N	G	G	S	F	G	R	G	D	S	D	E	W	T	F	G	A	Q	M	E	I	W	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 1af6 chain A Region: 26 - 446 Aligned: 421 Modelled: 421 Confidence: 100.0% Identity: 100% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Maltoporin-like Phyre2 PDB 2mpr chain A Region: 26 - 446 Aligned: 417 Modelled: 421 Confidence: 100.0% Identity: 80% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Maltoporin-like Phyre2 PDB 1a0t chain P Region: 25 - 446 Aligned: 381 Modelled: 387 Confidence: 100.0% Identity: 29% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Maltoporin-like Phyre2 PDB 3qra chain A Region: 287 - 441 Aligned: 126 Modelled: 126 Confidence: 96.9% Identity: 11% 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 2vda chain B Region: 1 - 25 Aligned: 25 Modelled: 25 Confidence: 95.8% Identity: 100% PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex Phyre2 PDB 3nsg chain A Region: 26 - 364 Aligned: 304 Modelled: 307 Confidence: 93.7% Identity: 12% 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: 26 - 377 Aligned: 316 Modelled: 334 Confidence: 93.1% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1qj8 chain A Region: 297 - 442 Aligned: 117 Modelled: 117 Confidence: 92.7% Identity: 13% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 1pho chain A Region: 26 - 377 Aligned: 312 Modelled: 314 Confidence: 91.9% Identity: 9% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 1osm chain A Region: 26 - 359 Aligned: 290 Modelled: 301 Confidence: 88.8% Identity: 12% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Porin Phyre2 PDB 2wjq chain A Region: 285 - 376 Aligned: 91 Modelled: 92 Confidence: 82.8% 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 3nb3 chain C Region: 290 - 441 Aligned: 116 Modelled: 117 Confidence: 79.4% Identity: 10% 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 1qjp chain A Region: 290 - 394 Aligned: 104 Modelled: 105 Confidence: 79.1% Identity: 10% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 1g90 chain A Region: 269 - 442 Aligned: 153 Modelled: 153 Confidence: 73.7% Identity: 12% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 2x4m chain D Region: 293 - 380 Aligned: 87 Modelled: 88 Confidence: 60.4% Identity: 21% PDB header:hydrolase Chain: D: PDB Molecule:coagulase/fibrinolysin; PDBTitle: yersinia pestis plasminogen activator pla Phyre2 PDB 1i78 chain A Region: 293 - 356 Aligned: 63 Modelled: 64 Confidence: 59.4% Identity: 17% Fold: Transmembrane beta-barrels Superfamily: OMPT-like Family: Outer membrane protease OMPT Phyre2 PDB 2f1t chain B Region: 308 - 392 Aligned: 85 Modelled: 85 Confidence: 59.1% Identity: 8% PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw Phyre2 PDB 2k0l chain A Region: 278 - 394 Aligned: 117 Modelled: 117 Confidence: 57.5% Identity: 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. Phyre2 PDB 2jmm chain A Region: 290 - 442 Aligned: 120 Modelled: 121 Confidence: 38.2% Identity: 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 Phyre2 PDB 2vdf chain A domain 1 Region: 332 - 359 Aligned: 28 Modelled: 28 Confidence: 37.3% Identity: 14% Fold: Transmembrane beta-barrels Superfamily: OMPT-like Family: Outer membrane adhesin/invasin OpcA Phyre2 1 d1af6a_ 2 d2mpra_ 3 d1a0tp_ 4 c3qraA_ 5 c2vdaB_ 6 c3nsgA_ 7 d2zfga1 8 d1qj8a_ 9 d1phoa_ 10 d1osma_ 11 c2wjqA_ 12 c3nb3C_ 13 d1qjpa_ 14 d1g90a_ 15 c2x4mD_ 16 d1i78a_ 17 c2f1tB_ 18 c2k0lA_ 19 c2jmmA_ 20 d2vdfa1 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 48 49 50 51 52

Detailed template information

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

1 d1af6a_ 100.0 100 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 2 d2mpra_ 100.0 80 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 3 d1a0tp_ 100.0 29 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Maltoporin-like 4 c3qraA_ 96.9 11 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 5 c2vdaB_ 95.8 100 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex 6 c3nsgA_ 93.7 12 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein f; PDBTitle: crystal structure of ompf, an outer membrane protein from salmonella2 typhi 7 d2zfga1 93.1 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 8 d1qj8a_ 92.7 13 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 9 d1phoa_ 91.9 9 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 10 d1osma_ 88.8 12 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 11 c2wjqA_ 82.8 14 PDB header:transport protein Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel PDBTitle: nanc porin structure in hexagonal crystal form. 12 c3nb3C_ 79.4 10 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 13 d1qjpa_ 79.1 10 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 14 d1g90a_ 73.7 12 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 15 c2x4mD_ 60.4 21 PDB header:hydrolase Chain: D: PDB Molecule:coagulase/fibrinolysin; PDBTitle: yersinia pestis plasminogen activator pla 16 d1i78a_ 59.4 17 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane protease OMPT 17 c2f1tB_ 59.1 8 PDB header:membrane protein Chain: B: PDB Molecule:outer membrane protein w; PDBTitle: outer membrane protein ompw 18 c2k0lA_ 57.5 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. 19 c2jmmA_ 38.2 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 20 d2vdfa1 37.3 14 Fold:Transmembrane beta-barrels Superfamily:OMPT-like Family:Outer membrane adhesin/invasin OpcA 21 c3dzmB_ not modelled 35.6 19 PDB header:unknown function Chain: B: PDB Molecule:hypothetical conserved protein; PDBTitle: crystal structure of a major outer membrane protein from thermus2 thermophilus hb27 22 c2iwvD_ not modelled 25.0 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 23 c2o4vA_ not modelled 25.0 17 PDB header:membrane protein Chain: A: PDB Molecule:porin p; PDBTitle: an arginine ladder in oprp mediates phosphate specific transfer across2 the outer membrane 24 d2fgqx1 not modelled 23.6 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 25 c2l8aA_ not modelled 20.7 14 PDB header:hydrolase Chain: A: PDB Molecule:endoglucanase; PDBTitle: structure of a novel cbm3 lacking the calcium-binding site 26 d2jnaa1 not modelled 18.6 33 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 27 c2bs5A_ not modelled 12.7 35 PDB header:sugar binding protein Chain: A: PDB Molecule:fucose-binding lectin protein; PDBTitle: lectin from ralstonia solanacearum complexed with 2-2 fucosyllactose 28 d1cz5a2 not modelled 9.3 50 Fold:Cdc48 domain 2-like Superfamily:Cdc48 domain 2-like Family:Cdc48 domain 2-like 29 c2wo4A_ not modelled 9.3 16 PDB header:hydrolase Chain: A: PDB Molecule:glycoside hydrolase, family 9; PDBTitle: 3b' carbohydrate-binding module from the cel9v glycoside2 hydrolase from clostridium thermocellum, in-house data 30 c3aehB_ not modelled 8.8 9 PDB header:hydrolase Chain: B: PDB Molecule:hemoglobin-binding protease hbp autotransporter; PDBTitle: integral membrane domain of autotransporter hbp 31 c2rfyB_ not modelled 8.1 20 PDB header:hydrolase Chain: B: PDB Molecule:cellulose 1,4-beta-cellobiosidase; PDBTitle: crystal structure of cellobiohydrolase from melanocarpus2 albomyces complexed with cellobiose 32 d2jb0b1 not modelled 8.0 29 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif 33 c3sf5D_ not modelled 7.7 9 PDB header:chaperone Chain: D: PDB Molecule:urease accessory protein ureh; PDBTitle: crystal structure of helicobacter pylori urease accessory protein2 uref/h complex 34 d1p4ta_ not modelled 7.4 8 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 35 c2x27X_ not modelled 7.0 12 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein oprg; PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa 36 d3prna_ not modelled 6.7 13 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Porin 37 c3lywA_ not modelled 6.3 39 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ybbr family protein; PDBTitle: crystal structure of ybbr family protein dhaf_0833 from2 desulfitobacterium hafniense dcb-2. northeast structural3 genomics consortium target id dhr29b 38 d2q07a3 not modelled 6.2 14 Fold:Cystatin-like Superfamily:Pre-PUA domain Family:AF0587 pre C-terminal domain-like 39 d2v3ia1 not modelled 6.0 24 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Glycosyl hydrolase family 7 catalytic core 40 c3dwoX_ not modelled 5.8 15 PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue 41 c3qq2C_ not modelled 5.8 11 PDB header:membrane protein/protein transport Chain: C: PDB Molecule:brka autotransporter; PDBTitle: crystal structure of the beta domain of the bordetella autotransporter2 brka 42 c2outA_ not modelled 5.7 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mu-like prophage flumu protein gp35, protein PDBTitle: solution structure of hi1506, a novel two domain protein2 from haemophilus influenzae 43 c3a2rX_ not modelled 5.7 11 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein ii; PDBTitle: crystal structure of outer membrane protein porb from neisseria2 meningitidis 44 c3kvnA_ not modelled 5.7 12 PDB header:hydrolase Chain: A: PDB Molecule:esterase esta; PDBTitle: crystal structure of the full-length autotransporter esta from2 pseudomonas aeruginosa 45 d1g43a_ not modelled 5.6 12 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 46 d1tpna_ not modelled 5.6 57 Fold:FnI-like domain Superfamily:FnI-like domain Family:Fibronectin type I module 47 d1nbca_ not modelled 5.4 14 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 48 c3kihC_ not modelled 5.3 21 PDB header:sugar binding protein Chain: C: PDB Molecule:5-bladed -propeller lectin; PDBTitle: the crystal structures of two fragments truncated from 5-bladed -2 propeller lectin, tachylectin-2 (lib2-d2-15) 49 d1ojja_ not modelled 5.1 22 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Glycosyl hydrolase family 7 catalytic core 50 c2ei5B_ not modelled 5.1 29 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ttha0061; PDBTitle: crystal structure of hypothetical protein(ttha0061) from thermus2 thermophilus 51 d2outa2 not modelled 5.1 31 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:YqbF N-terminal domain-like 52 d3ovwa_ not modelled 5.1 13 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Glycosyl hydrolase family 7 catalytic core

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

---

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