Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	E	L	L	F	V	I	G	F	F	V	M	L	M	V	T	G	V	S	L	L	G	I	I	A	A	L	V	V	A	T	A	I	M	F	L	G	G	M	L	A	L	M	I	K	L	L	P	W	L	L	L	A	I	A	V	V	W	V
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80
Sequence		I	K	A	I	K	A	P	K	V	P	K	Y	Q	R	Y	D	R	W	R	Y
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 3sok chain B Region: 10 - 30 Aligned: 21 Modelled: 21 Confidence: 28.4% Identity: 29% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 2ww9 chain B Region: 21 - 48 Aligned: 25 Modelled: 28 Confidence: 26.6% Identity: 24% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1oqw chain A Region: 10 - 30 Aligned: 21 Modelled: 21 Confidence: 26.4% Identity: 29% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2hg5 chain D Region: 10 - 34 Aligned: 25 Modelled: 25 Confidence: 15.5% Identity: 24% PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter Phyre2 PDB 2l0o chain A Region: 55 - 68 Aligned: 14 Modelled: 14 Confidence: 12.8% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb3 peptide structure in 100% tfe Phyre2 PDB 2axt chain J domain 1 Region: 25 - 41 Aligned: 17 Modelled: 17 Confidence: 8.6% Identity: 24% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 PDB 2k21 chain A Region: 4 - 27 Aligned: 18 Modelled: 24 Confidence: 8.0% Identity: 50% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 PDB 1rhz chain B Region: 21 - 48 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 16% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 3mp7 chain B Region: 35 - 53 Aligned: 19 Modelled: 19 Confidence: 5.6% Identity: 26% PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 2jag chain A Region: 15 - 42 Aligned: 27 Modelled: 28 Confidence: 5.5% Identity: 26% PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v Phyre2 PDB 3fgx chain A Region: 64 - 78 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:rbstp2171; PDBTitle: structure of uncharacterised protein rbstp2171 from bacillus2 stearothermophilus Phyre2 PDB 3a7k chain D Region: 15 - 42 Aligned: 27 Modelled: 28 Confidence: 5.3% Identity: 15% PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis Phyre2 1 c3sokB_ 2 c2ww9B_ 3 d1oqwa_ 4 c2hg5D_ 5 c2l0oA_ 6 d2axtj1 7 c2k21A_ 8 d1rhzb_ 9 c3mp7B_ 10 c2jagA_ 11 c3fgxA_ 12 c3a7kD_

Detailed template information

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

1 c3sokB_ 28.4 29 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 2 c2ww9B_ 26.6 24 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 3 d1oqwa_ 26.4 29 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 4 c2hg5D_ 15.5 24 PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter 5 c2l0oA_ 12.8 21 PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb3 peptide structure in 100% tfe 6 d2axtj1 8.6 24 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 7 c2k21A_ 8.0 50 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c 8 d1rhzb_ 6.3 16 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 9 c3mp7B_ 5.6 26 PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes 10 c2jagA_ 5.5 26 PDB header:membrane protein Chain: A: PDB Molecule:halorhodopsin; PDBTitle: l1-intermediate of halorhodopsin t203v 11 c3fgxA_ 5.3 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:rbstp2171; PDBTitle: structure of uncharacterised protein rbstp2171 from bacillus2 stearothermophilus 12 c3a7kD_ 5.3 15 PDB header:membrane protein Chain: D: PDB Molecule:halorhodopsin; PDBTitle: crystal structure of halorhodopsin from natronomonas2 pharaonis

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