Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	F	E	Q	T	P	P	N	R	R	R	Y	G	L	A	A	F	I	G	L	I	A	G	V	V	S	A	F	V	K	W	G	A	E	V	P	L	P	P	R	S	P	V	D	M	F	N	A	A	C	G	P	E	S	L	I	R	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?		?		?	?	?																							?					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	G	Q	I	D	C	S	R	N	F	L	N	P	P	Y	I	F	L	R	D	W	L	G	L	T	D	P	N	A	A	V	Y	T	F	A	G	H	V	F	N	W	V	G	V	T	H	I	I	F	S	I	V	F	A	V	G	Y	C	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?							?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	E	V	F	P	K	I	K	L	W	Q	G	L	L	A	G	A	L	A	Q	L	F	V	H	M	I	S	F	P	L	M	G	L	T	P	P	L	F	D	L	P	W	Y	E	N	V	S	E	I	F	G	H	L	V	W	F	W	S	I	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.
Sequence		I	I	R	R	D	L	R	N	R	I	T	H	E	P	D	P	E	I	P	L	G	S	N	R
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 2oar chain A domain 1 Region: 132 - 197 Aligned: 66 Modelled: 66 Confidence: 41.3% Identity: 15% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2in1 chain A domain 1 Region: 119 - 148 Aligned: 30 Modelled: 30 Confidence: 35.8% Identity: 23% Fold: UBC-like Superfamily: UBC-like Family: UFC1-like Phyre2 PDB 2ht2 chain B Region: 3 - 134 Aligned: 86 Modelled: 86 Confidence: 26.3% Identity: 13% PDB header:membrane protein Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca; PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex Phyre2 PDB 3kpa chain B Region: 119 - 156 Aligned: 38 Modelled: 38 Confidence: 26.1% Identity: 18% PDB header:ligase Chain: B: PDB Molecule:probable ubiquitin fold modifier conjugating enzyme; PDBTitle: ubiquitin fold modifier conjugating enzyme from leishmania major2 (probable) Phyre2 PDB 3nke chain A Region: 127 - 184 Aligned: 58 Modelled: 58 Confidence: 23.3% Identity: 21% PDB header:immune system Chain: A: PDB Molecule:protein ygbt; PDBTitle: high resolution structure of the c-terminal domain crisp-associated2 protein cas1 from escherichia coli str. k-12 Phyre2 PDB 1xoo chain A Region: 25 - 39 Aligned: 15 Modelled: 15 Confidence: 19.5% Identity: 27% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 Phyre2 PDB 1xop chain A Region: 22 - 39 Aligned: 18 Modelled: 18 Confidence: 18.7% Identity: 22% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1v mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 Phyre2 PDB 1ibo chain A Region: 25 - 39 Aligned: 15 Modelled: 15 Confidence: 18.1% Identity: 27% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 7.4 Phyre2 PDB 1ibn chain A Region: 25 - 39 Aligned: 15 Modelled: 15 Confidence: 18.1% Identity: 27% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 5 Phyre2 PDB 2oar chain A Region: 132 - 199 Aligned: 68 Modelled: 68 Confidence: 14.3% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 1ots chain A Region: 2 - 134 Aligned: 87 Modelled: 87 Confidence: 12.7% Identity: 13% Fold: Clc chloride channel Superfamily: Clc chloride channel Family: Clc chloride channel Phyre2 PDB 3b9y chain A Region: 13 - 30 Aligned: 18 Modelled: 18 Confidence: 11.0% Identity: 33% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 3god chain A Region: 127 - 154 Aligned: 28 Modelled: 28 Confidence: 10.1% Identity: 11% PDB header:immune system Chain: A: PDB Molecule:cas1; PDBTitle: structural basis for dnase activity of a conserved protein2 implicated in crispr-mediated antiviral defense Phyre2 PDB 2jrd chain A Region: 25 - 39 Aligned: 15 Modelled: 15 Confidence: 10.0% Identity: 20% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a Phyre2 PDB 2kpe chain B Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 9.9% Identity: 28% PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 PDB 2kpe chain A Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 9.9% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 PDB 1kpl chain A Region: 16 - 134 Aligned: 73 Modelled: 73 Confidence: 8.7% Identity: 15% Fold: Clc chloride channel Superfamily: Clc chloride channel Family: Clc chloride channel Phyre2 PDB 2zt9 chain E Region: 16 - 30 Aligned: 15 Modelled: 15 Confidence: 7.2% Identity: 40% 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 3nkd chain B Region: 127 - 170 Aligned: 44 Modelled: 44 Confidence: 6.3% Identity: 16% PDB header:immune system Chain: B: PDB Molecule:crispr-associated protein cas1; PDBTitle: structure of crisp-associated protein cas1 from escherichia coli str.2 k-12 Phyre2 PDB 1jeg chain B Region: 38 - 53 Aligned: 16 Modelled: 15 Confidence: 5.8% Identity: 31% PDB header:transferase/hydrolase Chain: B: PDB Molecule:hematopoietic cell protein-tyrosine phosphatase PDBTitle: solution structure of the sh3 domain from c-terminal src2 kinase complexed with a peptide from the tyrosine3 phosphatase pep Phyre2 1 d2oara1 2 d2in1a1 3 c2ht2B_ 4 c3kpaB_ 5 c3nkeA_ 6 c1xooA_ 7 c1xopA_ 8 c1iboA_ 9 c1ibnA_ 10 c2oarA_ 11 d1otsa_ 12 c3b9yA_ 13 c3godA_ 14 c2jrdA_ 15 c2kpeB_ 16 c2kpeA_ 17 d1kpla_ 18 c2zt9E_ 19 c3nkdB_ 20 c1jegB_

Detailed template information

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

1 d2oara1 41.3 15 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 2 d2in1a1 35.8 23 Fold:UBC-like Superfamily:UBC-like Family:UFC1-like 3 c2ht2B_ 26.3 13 PDB header:membrane protein Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca; PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex 4 c3kpaB_ 26.1 18 PDB header:ligase Chain: B: PDB Molecule:probable ubiquitin fold modifier conjugating enzyme; PDBTitle: ubiquitin fold modifier conjugating enzyme from leishmania major2 (probable) 5 c3nkeA_ 23.3 21 PDB header:immune system Chain: A: PDB Molecule:protein ygbt; PDBTitle: high resolution structure of the c-terminal domain crisp-associated2 protein cas1 from escherichia coli str. k-12 6 c1xooA_ 19.5 27 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 7 c1xopA_ 18.7 22 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1v mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 8 c1iboA_ 18.1 27 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 7.4 9 c1ibnA_ 18.1 27 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 5 10 c2oarA_ 14.3 16 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 11 d1otsa_ 12.7 13 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 12 c3b9yA_ 11.0 33 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 13 c3godA_ 10.1 11 PDB header:immune system Chain: A: PDB Molecule:cas1; PDBTitle: structural basis for dnase activity of a conserved protein2 implicated in crispr-mediated antiviral defense 14 c2jrdA_ 10.0 20 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a 15 c2kpeB_ 9.9 28 PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles 16 c2kpeA_ 9.9 28 PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles 17 d1kpla_ 8.7 15 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 18 c2zt9E_ 7.2 40 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 19 c3nkdB_ 6.3 16 PDB header:immune system Chain: B: PDB Molecule:crispr-associated protein cas1; PDBTitle: structure of crisp-associated protein cas1 from escherichia coli str.2 k-12 20 c1jegB_ 5.8 31 PDB header:transferase/hydrolase Chain: B: PDB Molecule:hematopoietic cell protein-tyrosine phosphatase PDBTitle: solution structure of the sh3 domain from c-terminal src2 kinase complexed with a peptide from the tyrosine3 phosphatase pep

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