Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	Q	I	T	K	P	H	C	G	A	R	L	D	R	L	P	D	C	R	W	H	S	S	M	F	A	I	V	A	F	G	L	L	V	C	W	S	N	A	V	G	G	L	I	L	A	Q	L	K	A	L	G	W	T	D	N	S	T	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																														?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	T	F	S	A	I	T	T	A	G	M	F	L	G	A	L	V	G	G	I	I	G	D	K	T	G	R	R	N	A	F	I	L	Y	E	A	I	H	I	A	S	M	V	V	G	A	F	S	P	N	M	D	F	L	I	A	C	R	F	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	G	V	G	L	G	A	L	L	V	T	L	F	A	G	F	T	E	Y	M	P	G	R	N	R	G	T	W	S	S	R	V	S	F	I	G	N	W	S	Y	P	L	C	S	L	I	A	M	G	L	T	P	L	I	S	A	E	W	N	W
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	V	Q	L	L	I	P	A	I	L	S	L	I	A	T	A	L	A	W	R	Y	F	P	E	S	P	R	W	L	E	S	R	G	R	Y	Q	E	A	E	K	V	M	R	S	I	E	E	G	V	I	R	Q	T	G	K	P	L	P	P	V
Secondary structure
SS confidence
Disorder																																																	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	I	A	D	D	G	K	A	P	Q	A	V	P	Y	S	A	L	L	T	G	V	L	L	K	R	V	I	L	G	S	C	V	L	I	A	M	N	V	V	Q	Y	T	L	I	N	W	L	P	T	I	F	M	T	Q	G	I	N	L	K	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?																																									?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		S	I	V	L	N	T	M	S	M	F	G	A	P	F	G	I	F	I	A	M	L	V	M	D	K	I	P	R	K	T	M	G	V	G	L	L	I	L	I	A	V	L	G	Y	I	Y	S	L	Q	T	S	M	L	L	I	T	L	I	G	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		F	L	I	T	F	V	Y	M	Y	V	C	Y	A	S	A	V	Y	V	P	E	I	W	P	T	E	A	K	L	R	G	S	G	L	A	N	A	V	G	R	I	S	G	I	A	A	P	Y	A	V	A	V	L	L	S	S	Y	G	V	T	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.
Sequence		V	F	I	L	L	G	A	V	S	I	I	V	A	I	A	I	A	T	I	G	I	E	T	K	G	V	S	V	E	S	L	S	I	D	A	V	A	N	K
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 1pw4 chain A Region: 4 - 453 Aligned: 422 Modelled: 422 Confidence: 100.0% Identity: 13% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 21 - 457 Aligned: 411 Modelled: 411 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3o7p chain A Region: 26 - 443 Aligned: 404 Modelled: 406 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 2gfp chain A Region: 25 - 432 Aligned: 368 Modelled: 373 Confidence: 100.0% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 2xut chain C Region: 27 - 439 Aligned: 412 Modelled: 413 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 3qnq chain D Region: 406 - 458 Aligned: 53 Modelled: 53 Confidence: 43.6% Identity: 15% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1mv4 chain B Region: 445 - 459 Aligned: 15 Modelled: 15 Confidence: 25.6% Identity: 33% PDB header:de novo protein Chain: B: PDB Molecule:tropomyosin 1 alpha chain; PDBTitle: tm9a251-284: a peptide model of the c-terminus of a rat2 striated alpha tropomyosin Phyre2 PDB 2g9p chain A Region: 77 - 90 Aligned: 14 Modelled: 14 Confidence: 13.6% Identity: 29% PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom Phyre2 PDB 1cwp chain A Region: 439 - 456 Aligned: 18 Modelled: 18 Confidence: 12.7% Identity: 33% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Bromoviridae-like VP Phyre2 PDB 1cwp chain B Region: 439 - 456 Aligned: 18 Modelled: 18 Confidence: 11.3% Identity: 33% PDB header:virus/rna Chain: B: PDB Molecule:coat protein; PDBTitle: structures of the native and swollen forms of cowpea2 chlorotic mottle virus determined by x-ray crystallography3 and cryo-electron microscopy Phyre2 PDB 1yew chain C Region: 418 - 456 Aligned: 39 Modelled: 39 Confidence: 8.3% Identity: 10% PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 2qfa chain C Region: 448 - 457 Aligned: 10 Modelled: 10 Confidence: 8.0% Identity: 20% PDB header:cell cycle/cell cycle/cell cycle Chain: C: PDB Molecule:inner centromere protein; PDBTitle: crystal structure of a survivin-borealin-incenp core complex Phyre2 PDB 1by0 chain A Region: 445 - 455 Aligned: 11 Modelled: 11 Confidence: 7.9% Identity: 27% PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen Phyre2 PDB 1ofc chain X domain 1 Region: 442 - 453 Aligned: 12 Modelled: 12 Confidence: 7.6% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 3mmy chain F Region: 439 - 454 Aligned: 16 Modelled: 16 Confidence: 6.6% Identity: 25% PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 Phyre2 PDB 3chx chain G Region: 427 - 456 Aligned: 30 Modelled: 30 Confidence: 6.0% Identity: 13% PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) Phyre2 PDB 1ymg chain A Region: 401 - 450 Aligned: 47 Modelled: 50 Confidence: 5.3% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution Phyre2 PDB 1ymg chain A domain 1 Region: 401 - 450 Aligned: 47 Modelled: 50 Confidence: 5.3% Identity: 11% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 1 d1pw4a_ 2 d1pv7a_ 3 c3o7pA_ 4 c2gfpA_ 5 c2xutC_ 6 c3qnqD_ 7 c1mv4B_ 8 c2g9pA_ 9 d1cwpa_ 10 c1cwpB_ 11 c1yewC_ 12 c2qfaC_ 13 c1by0A_ 14 d1ofcx1 15 c3mmyF_ 16 c3chxG_ 17 c1ymgA_ 18 d1ymga1

Detailed template information

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

1 d1pw4a_ 100.0 13 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 c3o7pA_ 100.0 11 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 4 c2gfpA_ 100.0 14 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 5 c2xutC_ 100.0 12 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 6 c3qnqD_ 43.6 15 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 7 c1mv4B_ 25.6 33 PDB header:de novo protein Chain: B: PDB Molecule:tropomyosin 1 alpha chain; PDBTitle: tm9a251-284: a peptide model of the c-terminus of a rat2 striated alpha tropomyosin 8 c2g9pA_ 13.6 29 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 9 d1cwpa_ 12.7 33 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Bromoviridae-like VP 10 c1cwpB_ 11.3 33 PDB header:virus/rna Chain: B: PDB Molecule:coat protein; PDBTitle: structures of the native and swollen forms of cowpea2 chlorotic mottle virus determined by x-ray crystallography3 and cryo-electron microscopy 11 c1yewC_ 8.3 10 PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase 12 c2qfaC_ 8.0 20 PDB header:cell cycle/cell cycle/cell cycle Chain: C: PDB Molecule:inner centromere protein; PDBTitle: crystal structure of a survivin-borealin-incenp core complex 13 c1by0A_ 7.9 27 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 14 d1ofcx1 7.6 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 15 c3mmyF_ 6.6 25 PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 16 c3chxG_ 6.0 13 PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) 17 c1ymgA_ 5.3 11 PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution 18 d1ymga1 5.3 11 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like

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