Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	V	I	E	F	L	L	A	L	A	Q	D	M	I	L	A	A	I	P	A	V	G	F	A	M	V	F	N	V	P	V	R	A	L	R	W	C	A	L	L	G	S	I	G	H	G	S	R	M	I	L	M	T	S	G	L	N	I	E
Secondary structure
SS confidence
Disorder		?	?	?																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	S	T	F	M	A	S	M	L	V	G	T	I	G	I	Q	W	S	R	W	Y	L	A	H	P	K	V	F	T	V	A	A	V	I	P	M	F	P	G	I	S	A	Y	T	A	M	I	S	A	V	K	I	S	Q	L	G	Y	S	E	P
Secondary structure
SS confidence
Disorder																																																					?	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.
Sequence		L	M	I	T	L	L	T	N	F	L	T	A	S	S	I	V	G	A	L	S	I	G	L	S	I	P	G	L	W	L	Y	R	K	R	P	R	V
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 3org chain B Region: 12 - 82 Aligned: 69 Modelled: 71 Confidence: 41.0% Identity: 26% PDB header:transport protein Chain: B: PDB Molecule:cmclc; PDBTitle: crystal structure of a eukaryotic clc transporter Phyre2 PDB 3hd6 chain A Region: 7 - 156 Aligned: 146 Modelled: 150 Confidence: 18.5% Identity: 9% 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 1cii chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 9.4% Identity: 15% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 2uwj chain F Region: 100 - 112 Aligned: 13 Modelled: 13 Confidence: 9.0% Identity: 8% PDB header:chaperone Chain: F: PDB Molecule:type iii export protein pscf; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation Phyre2 PDB 2k1a chain A Region: 135 - 155 Aligned: 21 Modelled: 21 Confidence: 8.2% Identity: 33% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 2b2h chain A Region: 8 - 157 Aligned: 126 Modelled: 126 Confidence: 7.7% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2jwa chain A Region: 125 - 156 Aligned: 32 Modelled: 32 Confidence: 6.9% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1tlq chain A Region: 35 - 80 Aligned: 46 Modelled: 46 Confidence: 6.1% Identity: 17% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ypjq; PDBTitle: crystal structure of protein ypjq from bacillus subtilis, pfam duf64 Phyre2 PDB 1tlq chain A Region: 35 - 80 Aligned: 46 Modelled: 46 Confidence: 6.1% Identity: 17% Fold: YutG-like Superfamily: YutG-like Family: YutG-like Phyre2 PDB 1jb0 chain M Region: 83 - 104 Aligned: 22 Modelled: 22 Confidence: 6.0% Identity: 27% Fold: Single transmembrane helix Superfamily: Subunit XII of photosystem I reaction centre, PsaM Family: Subunit XII of photosystem I reaction centre, PsaM Phyre2 1 c3orgB_ 2 c3hd6A_ 3 c1ciiA_ 4 c2uwjF_ 5 c2k1aA_ 6 c2b2hA_ 7 c2jwaA_ 8 c1tlqA_ 9 d1tlqa_ 10 d1jb0m_

Detailed template information

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

1 c3orgB_ 41.0 26 PDB header:transport protein Chain: B: PDB Molecule:cmclc; PDBTitle: crystal structure of a eukaryotic clc transporter 2 c3hd6A_ 18.5 9 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 3 c1ciiA_ 9.4 15 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 4 c2uwjF_ 9.0 8 PDB header:chaperone Chain: F: PDB Molecule:type iii export protein pscf; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation 5 c2k1aA_ 8.2 33 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 6 c2b2hA_ 7.7 12 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 7 c2jwaA_ 6.9 16 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 8 c1tlqA_ 6.1 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ypjq; PDBTitle: crystal structure of protein ypjq from bacillus subtilis, pfam duf64 9 d1tlqa_ 6.1 17 Fold:YutG-like Superfamily:YutG-like Family:YutG-like 10 d1jb0m_ 6.0 27 Fold:Single transmembrane helix Superfamily:Subunit XII of photosystem I reaction centre, PsaM Family:Subunit XII of photosystem I reaction centre, PsaM

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