Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	G	F	N	I	K	H	W	F	A	D	G	A	F	R	T	I	I	R	N	S	A	W	L	G	S	S	N	V	V	S	A	L	L	G	L	L	A	L	S	C	A	G	K	G	M	T	P	A	M	F	G	V	L	V	I	V	Q	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?				?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	A	K	S	I	S	D	F	I	K	F	Q	T	W	Q	L	V	V	Q	Y	G	T	P	A	L	T	N	N	N	P	Q	Q	F	R	N	V	V	S	F	S	F	S	L	D	I	V	S	G	A	V	A	I	V	G	G	I	A	L	L	P
Secondary structure
SS confidence
Disorder											?	?	?	?														?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	L	S	H	S	L	G	L	D	D	Q	S	F	W	L	A	A	L	Y	C	T	L	I	P	S	M	A	S	S	T	P	T	G	I	L	R	A	V	D	R	F	D	L	I	A	V	Q	Q	A	T	K	P	F	L	R	A	A	G	S	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	A	W	Y	F	D	F	G	F	A	G	F	V	I	A	W	Y	V	S	N	L	V	G	G	T	M	Y	W	W	F	A	A	R	E	L	R	R	R	N	I	H	N	A	F	K	L	N	L	F	E	S	A	R	Y	I	K	G	A	W	S
Secondary structure
SS confidence
Disorder																																						?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	V	W	S	T	N	I	A	H	S	I	W	S	A	R	N	S	C	S	T	V	L	V	G	I	V	L	G	P	A	A	A	G	L	F	K	I	A	M	T	F	F	D	A	A	G	T	P	A	G	L	L	G	K	S	F	Y	P	E	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.
Sequence		M	R	L	D	P	R	T	T	R	P	W	L	L	G	V	K	S	G	L	L	A	G	G	I	G	I	L	V	A	L	A	V	L	I	V	G	K	P	L	I	S	L	V	F	G	V	K	Y	L	E	A	Y	D	L	I
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 3mku chain A Region: 4 - 355 Aligned: 347 Modelled: 347 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter Phyre2 PDB 1mqs chain B Region: 1 - 7 Aligned: 7 Modelled: 7 Confidence: 22.6% Identity: 86% PDB header:endocytosis/exocytosis Chain: B: PDB Molecule:integral membrane protein sed5; PDBTitle: crystal structure of sly1p in complex with an n-terminal2 peptide of sed5p Phyre2 PDB 3j01 chain A Region: 284 - 336 Aligned: 53 Modelled: 53 Confidence: 8.1% Identity: 6% PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment Phyre2 PDB 1jo5 chain A Region: 305 - 339 Aligned: 35 Modelled: 35 Confidence: 7.4% Identity: 17% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1kdx chain B Region: 5 - 23 Aligned: 19 Modelled: 19 Confidence: 6.3% Identity: 11% PDB header:transcription regulation complex Chain: B: PDB Molecule:creb; PDBTitle: kix domain of mouse cbp (creb binding protein) in complex2 with phosphorylated kinase inducible domain (pkid) of rat3 creb (cyclic amp response element binding protein), nmr 174 structures Phyre2 PDB 2vck chain C Region: 336 - 352 Aligned: 17 Modelled: 17 Confidence: 6.2% Identity: 24% PDB header:oxidoreductase Chain: C: PDB Molecule:cyanobacterial phycoerythrobilin; PDBTitle: structure of phycoerythrobilin synthase pebs from the2 cyanophage p-ssm2 in complex with the bound substrate3 biliverdin ixa Phyre2 PDB 1u17 chain A domain 1 Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 6.0% Identity: 31% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 2nzz chain A Region: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 6.0% Identity: 36% PDB header:membrane protein Chain: A: PDB Molecule:penetratin conjugated gas (374-394) peptide; PDBTitle: nmr structure analysis of the penetratin conjugated gas2 (374-394) peptide Phyre2 PDB 2r6g chain F domain 2 Region: 5 - 48 Aligned: 44 Modelled: 44 Confidence: 5.9% Identity: 11% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1x8q chain A Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 5.6% Identity: 31% Fold: Lipocalins Superfamily: Lipocalins Family: Retinol binding protein-like Phyre2 PDB 1akh chain A Region: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 5.6% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Homeodomain Phyre2 1 c3mkuA_ 2 c1mqsB_ 3 c3j01A_ 4 d1jo5a_ 5 c1kdxB_ 6 c2vckC_ 7 d1u17a1 8 c2nzzA_ 9 d2r6gf2 10 d1x8qa_ 11 d1akha_

Detailed template information

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

1 c3mkuA_ 100.0 11 PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter 2 c1mqsB_ 22.6 86 PDB header:endocytosis/exocytosis Chain: B: PDB Molecule:integral membrane protein sed5; PDBTitle: crystal structure of sly1p in complex with an n-terminal2 peptide of sed5p 3 c3j01A_ 8.1 6 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 4 d1jo5a_ 7.4 17 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 5 c1kdxB_ 6.3 11 PDB header:transcription regulation complex Chain: B: PDB Molecule:creb; PDBTitle: kix domain of mouse cbp (creb binding protein) in complex2 with phosphorylated kinase inducible domain (pkid) of rat3 creb (cyclic amp response element binding protein), nmr 174 structures 6 c2vckC_ 6.2 24 PDB header:oxidoreductase Chain: C: PDB Molecule:cyanobacterial phycoerythrobilin; PDBTitle: structure of phycoerythrobilin synthase pebs from the2 cyanophage p-ssm2 in complex with the bound substrate3 biliverdin ixa 7 d1u17a1 6.0 31 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 8 c2nzzA_ 6.0 36 PDB header:membrane protein Chain: A: PDB Molecule:penetratin conjugated gas (374-394) peptide; PDBTitle: nmr structure analysis of the penetratin conjugated gas2 (374-394) peptide 9 d2r6gf2 5.9 11 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d1x8qa_ 5.6 31 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 11 d1akha_ 5.6 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain

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