Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	Q	S	L	T	L	A	F	L	I	A	A	G	I	G	L	V	V	Q	N	T	L	M	V	R	I	T	Q	T	S	S	T	I	L	I	A	M	L	L	N	S	L	V	G	I	V	L	F	V	S	I	L	W	F	K	Q	G	M	A
Secondary structure
SS confidence
Disorder		?	?																																																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	F	G	E	L	V	S	S	V	R	W	W	T	L	I	P	G	L	L	G	S	F	F	V	F	A	S	I	S	G	Y	Q	N	V	G	A	A	T	T	I	A	V	L	V	A	S	Q	L	I	G	G	L	M	L	D	I	F	R	S	H
Secondary structure
SS confidence
Disorder		?	?	?			?	?																									?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.
Sequence		G	V	P	L	R	A	L	F	G	P	I	C	G	A	I	L	L	V	V	G	A	W	L	V	A	R	R	S	F
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 2knc chain A Region: 67 - 91 Aligned: 25 Modelled: 25 Confidence: 41.5% Identity: 16% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2b2h chain A Region: 2 - 125 Aligned: 121 Modelled: 124 Confidence: 22.0% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2d68 chain A Region: 106 - 122 Aligned: 17 Modelled: 17 Confidence: 20.7% Identity: 12% PDB header:cell cycle Chain: A: PDB Molecule:fop; PDBTitle: structure of the n-terminal domain of fop (fgfr1op) protein Phyre2 PDB 2e2z chain A Region: 115 - 127 Aligned: 13 Modelled: 13 Confidence: 20.4% Identity: 8% PDB header:protein transport, chaperone regulator Chain: A: PDB Molecule:tim15; PDBTitle: solution nmr structure of yeast tim15, co-chaperone of2 mitochondrial hsp70 Phyre2 PDB 3hd6 chain A Region: 33 - 126 Aligned: 94 Modelled: 94 Confidence: 17.7% Identity: 16% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 2ptz chain A domain 2 Region: 20 - 80 Aligned: 53 Modelled: 61 Confidence: 14.6% Identity: 15% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 2jp3 chain A Region: 131 - 148 Aligned: 18 Modelled: 18 Confidence: 7.1% Identity: 28% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 2k1a chain A Region: 67 - 91 Aligned: 25 Modelled: 25 Confidence: 6.5% Identity: 16% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 1 c2kncA_ 2 c2b2hA_ 3 c2d68A_ 4 c2e2zA_ 5 c3hd6A_ 6 d2ptza2 7 c2jp3A_ 8 c2k1aA_

Detailed template information

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

1 c2kncA_ 41.5 16 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 c2b2hA_ 22.0 17 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 3 c2d68A_ 20.7 12 PDB header:cell cycle Chain: A: PDB Molecule:fop; PDBTitle: structure of the n-terminal domain of fop (fgfr1op) protein 4 c2e2zA_ 20.4 8 PDB header:protein transport, chaperone regulator Chain: A: PDB Molecule:tim15; PDBTitle: solution nmr structure of yeast tim15, co-chaperone of2 mitochondrial hsp70 5 c3hd6A_ 17.7 16 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 6 d2ptza2 14.6 15 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 7 c2jp3A_ 7.1 28 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 8 c2k1aA_ 6.5 16 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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