Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	V	S	R	R	V	I	H	H	G	L	Y	F	A	V	L	G	P	L	I	G	V	L	F	L	V	L	Y	I	F	F	A	K	E	P	L	V	L	W	V	I	I	H	P	I	F	L	L	L	S	I	T	T	G	A	I	P	A	L
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	T	G	V	M	V	A	C	L	P	E	K	I	G	S	Q	K	R	Y	R	C	L	A	G	G	I	G	G	V	V	I	T	E	I	Y	C	A	V	I	V	H	I	K	G	M	A	S	S	E	L	F	E	N	I	L	S	G	D	S	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.
Sequence		V	V	R	I	I	P	A	L	L	A	G	V	V	M	S	R	I	I	T	R	L	P	G	L	D	I	S	C	P	E	T	D	S	L	S
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 1jb0 chain M Region: 120 - 130 Aligned: 11 Modelled: 11 Confidence: 22.1% Identity: 55% Fold: Single transmembrane helix Superfamily: Subunit XII of photosystem I reaction centre, PsaM Family: Subunit XII of photosystem I reaction centre, PsaM Phyre2 PDB 1jb0 chain M Region: 120 - 130 Aligned: 11 Modelled: 11 Confidence: 22.1% Identity: 55% PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 PDB 1jss chain A Region: 55 - 81 Aligned: 27 Modelled: 27 Confidence: 11.0% Identity: 22% Fold: TBP-like Superfamily: Bet v1-like Family: STAR domain Phyre2 PDB 1jss chain B Region: 55 - 81 Aligned: 27 Modelled: 27 Confidence: 11.0% Identity: 22% PDB header:lipid binding protein Chain: B: PDB Molecule:cholesterol-regulated start protein 4; PDBTitle: crystal structure of the mus musculus cholesterol-regulated2 start protein 4 (stard4). Phyre2 PDB 1p0l chain A Region: 71 - 79 Aligned: 9 Modelled: 9 Confidence: 9.9% Identity: 33% PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution gln to trp modification in sds-d252 micelles Phyre2 PDB 2l35 chain B Region: 125 - 138 Aligned: 14 Modelled: 14 Confidence: 8.5% Identity: 36% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 1p0o chain A Region: 71 - 79 Aligned: 9 Modelled: 9 Confidence: 8.5% Identity: 33% PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution of trp for gln and asp at position2 17 and 19 modification in sds-d25 micelles Phyre2 PDB 2jd3 chain B Region: 127 - 142 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 31% PDB header:dna binding protein Chain: B: PDB Molecule:stbb protein; PDBTitle: parr from plasmid pb171 Phyre2 PDB 2l34 chain B Region: 126 - 138 Aligned: 13 Modelled: 13 Confidence: 7.9% Identity: 38% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 2l34 chain A Region: 126 - 138 Aligned: 13 Modelled: 13 Confidence: 7.9% Identity: 38% PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 1ln1 chain A Region: 55 - 82 Aligned: 28 Modelled: 28 Confidence: 6.3% Identity: 18% Fold: TBP-like Superfamily: Bet v1-like Family: STAR domain Phyre2 PDB 2zt9 chain E Region: 59 - 69 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 45% PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 Phyre2 PDB 1t0a chain A Region: 117 - 153 Aligned: 37 Modelled: 37 Confidence: 5.5% Identity: 27% Fold: Bacillus chorismate mutase-like Superfamily: IpsF-like Family: IpsF-like Phyre2 PDB 3dby chain N Region: 124 - 154 Aligned: 31 Modelled: 31 Confidence: 5.4% Identity: 19% PDB header:structural genomics, unknown function Chain: N: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein from bacillus cereus2 g9241 (csap target) Phyre2 1 d1jb0m_ 2 c1jb0M_ 3 d1jssa_ 4 c1jssB_ 5 c1p0lA_ 6 c2l35B_ 7 c1p0oA_ 8 c2jd3B_ 9 c2l34B_ 10 c2l34A_ 11 d1ln1a_ 12 c2zt9E_ 13 d1t0aa_ 14 c3dbyN_

Detailed template information

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

1 d1jb0m_ 22.1 55 Fold:Single transmembrane helix Superfamily:Subunit XII of photosystem I reaction centre, PsaM Family:Subunit XII of photosystem I reaction centre, PsaM 2 c1jb0M_ 22.1 55 PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 3 d1jssa_ 11.0 22 Fold:TBP-like Superfamily:Bet v1-like Family:STAR domain 4 c1jssB_ 11.0 22 PDB header:lipid binding protein Chain: B: PDB Molecule:cholesterol-regulated start protein 4; PDBTitle: crystal structure of the mus musculus cholesterol-regulated2 start protein 4 (stard4). 5 c1p0lA_ 9.9 33 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution gln to trp modification in sds-d252 micelles 6 c2l35B_ 8.5 36 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 7 c1p0oA_ 8.5 33 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution of trp for gln and asp at position2 17 and 19 modification in sds-d25 micelles 8 c2jd3B_ 8.3 31 PDB header:dna binding protein Chain: B: PDB Molecule:stbb protein; PDBTitle: parr from plasmid pb171 9 c2l34B_ 7.9 38 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 10 c2l34A_ 7.9 38 PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 11 d1ln1a_ 6.3 18 Fold:TBP-like Superfamily:Bet v1-like Family:STAR domain 12 c2zt9E_ 5.5 45 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 13 d1t0aa_ 5.5 27 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 14 c3dbyN_ 5.4 19 PDB header:structural genomics, unknown function Chain: N: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein from bacillus cereus2 g9241 (csap target)

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

---

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