Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	V	E	D	T	Q	P	L	I	T	H	L	I	E	L	R	K	R	L	L	N	C	I	I	A	V	I	V	I	F	L	C	L	V	Y	F	A	N	D	I	Y	H	L	V	S	A	P	L	I	K	Q	L	P	Q	G	S	T	M	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	T	D	V	A	S	P	F	F	T	P	I	K	L	T	F	M	V	S	L	I	L	S	A	P	V	I	L	Y	Q	V	W	A	F	I	A	P	A	L	Y	K	H	E	R	R	L	V	V	P	L	L	V	S	S	S	L	L	F	Y	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	M	A	F	A	Y	F	V	V	F	P	L	A	F	G	F	L	A	N	T	A	P	E	G	V	Q	V	S	T	D	I	A	S	Y	L	S	F	V	M	A	L	F	M	A	F	G	V	S	F	E	V	P	V	A	I	V	L	L	C	W
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		M	G	I	T	S	P	E	D	L	R	K	K	R	P	Y	V	L	V	G	A	F	V	V	G	M	L	L	T	P	P	D	V	F	S	Q	T	L	L	A	I	P	M	Y	C	L	F	E	I	G	V	F	F	S	R	F	Y	V	G	K	G
Secondary structure
SS confidence
Disorder																												?	?																															?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.
Sequence		R	N	R	E	E	E	N	D	A	E	A	E	S	E	K	T	E	E
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 3qod chain B Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 42.0% Identity: 35% PDB header:dna binding protein Chain: B: PDB Molecule:heterocyst differentiation protein; PDBTitle: crystal structure of heterocyst differentiation protein, hetr from2 fischerella mv11 Phyre2 PDB 3qnq chain D Region: 202 - 252 Aligned: 51 Modelled: 51 Confidence: 24.4% Identity: 20% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1v54 chain L Region: 139 - 176 Aligned: 38 Modelled: 38 Confidence: 23.9% Identity: 18% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Phyre2 PDB 2klu chain A Region: 207 - 258 Aligned: 52 Modelled: 52 Confidence: 19.8% Identity: 19% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 2y69 chain Y Region: 139 - 176 Aligned: 38 Modelled: 38 Confidence: 19.3% Identity: 18% PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 2oar chain A domain 1 Region: 203 - 254 Aligned: 44 Modelled: 52 Confidence: 13.1% Identity: 23% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2knc chain A Region: 212 - 251 Aligned: 40 Modelled: 40 Confidence: 10.8% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2k21 chain A Region: 216 - 258 Aligned: 43 Modelled: 43 Confidence: 10.2% Identity: 19% 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 3h3p chain T Region: 9 - 19 Aligned: 11 Modelled: 11 Confidence: 10.0% Identity: 45% PDB header:immune system Chain: T: PDB Molecule:4e10_s0_1tjlc_004_n; PDBTitle: crystal structure of hiv epitope-scaffold 4e10 fv complex Phyre2 PDB 2aff chain B Region: 241 - 258 Aligned: 18 Modelled: 18 Confidence: 8.9% Identity: 17% PDB header:cell cycle Chain: B: PDB Molecule:mki67 fha domain interacting nucleolar phosphoprotein; PDBTitle: the solution structure of the ki67fha/hnifk(226-269)3p complex Phyre2 PDB 3j01 chain A Region: 15 - 35 Aligned: 21 Modelled: 21 Confidence: 8.9% Identity: 43% 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 2iub chain A domain 2 Region: 199 - 241 Aligned: 43 Modelled: 43 Confidence: 7.8% Identity: 7% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 2rdd chain B Region: 214 - 247 Aligned: 34 Modelled: 34 Confidence: 7.7% Identity: 15% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 3iz6 chain C Region: 236 - 257 Aligned: 22 Modelled: 22 Confidence: 7.5% Identity: 18% PDB header:ribosome Chain: C: PDB Molecule:40s ribosomal protein s9 (s4p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2voy chain G Region: 3 - 31 Aligned: 29 Modelled: 29 Confidence: 7.3% Identity: 28% PDB header:hydrolase Chain: G: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 2jln chain A Region: 151 - 257 Aligned: 103 Modelled: 107 Confidence: 6.6% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2l0e chain A Region: 201 - 219 Aligned: 19 Modelled: 19 Confidence: 5.2% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm vi of the nhe1 isoform of the2 na+/h+ exchanger Phyre2 PDB 2oar chain A Region: 203 - 254 Aligned: 44 Modelled: 52 Confidence: 5.1% Identity: 23% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 1 c3qodB_ 2 c3qnqD_ 3 d1v54l_ 4 c2kluA_ 5 c2y69Y_ 6 d2oara1 7 c2kncA_ 8 c2k21A_ 9 c3h3pT_ 10 c2affB_ 11 c3j01A_ 12 d2iuba2 13 c2rddB_ 14 c3iz6C_ 15 c2voyG_ 16 c2jlnA_ 17 c2l0eA_ 18 c2oarA_

Detailed template information

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

1 c3qodB_ 42.0 35 PDB header:dna binding protein Chain: B: PDB Molecule:heterocyst differentiation protein; PDBTitle: crystal structure of heterocyst differentiation protein, hetr from2 fischerella mv11 2 c3qnqD_ 24.4 20 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 3 d1v54l_ 23.9 18 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) 4 c2kluA_ 19.8 19 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 5 c2y69Y_ 19.3 18 PDB header:electron transport Chain: Y: PDB Molecule:cytochrome c oxidase subunit 7c; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 6 d2oara1 13.1 23 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 7 c2kncA_ 10.8 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 8 c2k21A_ 10.2 19 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 9 c3h3pT_ 10.0 45 PDB header:immune system Chain: T: PDB Molecule:4e10_s0_1tjlc_004_n; PDBTitle: crystal structure of hiv epitope-scaffold 4e10 fv complex 10 c2affB_ 8.9 17 PDB header:cell cycle Chain: B: PDB Molecule:mki67 fha domain interacting nucleolar phosphoprotein; PDBTitle: the solution structure of the ki67fha/hnifk(226-269)3p complex 11 c3j01A_ 8.9 43 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 12 d2iuba2 7.8 7 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 13 c2rddB_ 7.7 15 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 14 c3iz6C_ 7.5 18 PDB header:ribosome Chain: C: PDB Molecule:40s ribosomal protein s9 (s4p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 15 c2voyG_ 7.3 28 PDB header:hydrolase Chain: G: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 16 c2jlnA_ 6.6 16 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 17 c2l0eA_ 5.2 11 PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm vi of the nhe1 isoform of the2 na+/h+ exchanger 18 c2oarA_ 5.1 23 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl)

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