Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	R	T	K	L	K	F	R	L	H	R	A	V	I	V	L	F	C	L	A	L	L	V	A	L	M	Q	G	A	S	W	F	S	Q	N	H	Q	R	Q	R	N	P	Q	L	E	E	L	A	R	T	L	A	R	Q	V	T	L	N	V
Secondary structure
SS confidence
Disorder		?	?	?	?																													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	P	L	M	R	T	D	S	P	D	E	K	R	I	Q	A	I	L	D	Q	L	T	D	E	S	R	I	L	D	A	G	V	Y	D	E	Q	G	D	L	I	A	R	S	G	E	S	V	E	V	R	D	R	L	A	L	D	G	K	K	A
Secondary structure
SS confidence
Disorder						?	?	?	?	?	?																																?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	G	Y	F	N	Q	Q	I	V	E	P	I	A	G	K	N	G	P	L	G	Y	L	R	L	T	L	D	T	H	T	L	A	T	E	A	Q	Q	V	D	N	T	T	N	I	L	R	L	M	L	L	L	S	L	A	I	G	V	V	L	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?							?	?			?												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.
Sequence		R	T	L	L	Q	G	K	R	T	R	W	Q	Q	S	P	F	L	L	T	A	S	K	P	V	P	E	E	E	E	S	E	K	K	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 2asx chain A domain 1 Region: 182 - 213 Aligned: 32 Modelled: 32 Confidence: 97.8% Identity: 3% Fold: HAMP domain-like Superfamily: HAMP domain-like Family: HAMP domain Phyre2 PDB 3by8 chain A domain 1 Region: 39 - 156 Aligned: 118 Modelled: 118 Confidence: 97.3% Identity: 16% Fold: Profilin-like Superfamily: Sensory domain-like Family: Sensory domain of two-component sensor kinase Phyre2 PDB 1p0z chain A Region: 43 - 152 Aligned: 110 Modelled: 110 Confidence: 97.2% Identity: 18% Fold: Profilin-like Superfamily: Sensory domain-like Family: Sensory domain of two-component sensor kinase Phyre2 PDB 3by9 chain A Region: 32 - 153 Aligned: 122 Modelled: 122 Confidence: 54.1% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the v. cholerae histidine kinase dctb2 sensor domain Phyre2 PDB 3pjv chain D Region: 35 - 157 Aligned: 119 Modelled: 123 Confidence: 48.0% Identity: 13% PDB header:lyase Chain: D: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain Phyre2 PDB 2p7j chain A domain 2 Region: 33 - 155 Aligned: 123 Modelled: 123 Confidence: 43.0% Identity: 15% Fold: Profilin-like Superfamily: Sensory domain-like Family: YkuI C-terminal domain-like Phyre2 PDB 3b42 chain B Region: 42 - 152 Aligned: 109 Modelled: 111 Confidence: 31.7% Identity: 18% PDB header:signaling protein Chain: B: PDB Molecule:methyl-accepting chemotaxis protein, putative; PDBTitle: periplasmic sensor domain of chemotaxis protein gsu0935 Phyre2 PDB 3b47 chain A Region: 43 - 149 Aligned: 104 Modelled: 107 Confidence: 28.8% Identity: 19% PDB header:signaling protein Chain: A: PDB Molecule:methyl-accepting chemotaxis protein; PDBTitle: periplasmic sensor domain of chemotaxis protein gsu0582 Phyre2 PDB 3e4p chain B Region: 41 - 156 Aligned: 116 Modelled: 116 Confidence: 25.8% Identity: 19% PDB header:transferase Chain: B: PDB Molecule:c4-dicarboxylate transport sensor protein dctb; PDBTitle: crystal structure of malonate occupied dctb Phyre2 PDB 2qhk chain A Region: 33 - 123 Aligned: 88 Modelled: 91 Confidence: 25.5% Identity: 11% PDB header:signaling protein Chain: A: PDB Molecule:methyl-accepting chemotaxis protein; PDBTitle: crystal structure of methyl-accepting chemotaxis protein from vibrio2 parahaemolyticus rimd 2210633 Phyre2 PDB 2kse chain A Region: 3 - 29 Aligned: 27 Modelled: 27 Confidence: 20.3% Identity: 22% PDB header:transferase Chain: A: PDB Molecule:sensor protein qsec; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor qsec, center for structures of3 membrane proteins (csmp) target 4311c Phyre2 PDB 1u6k chain A domain 1 Region: 180 - 214 Aligned: 35 Modelled: 35 Confidence: 19.7% Identity: 6% Fold: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) Superfamily: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) Family: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) Phyre2 PDB 3lnr chain A Region: 179 - 207 Aligned: 29 Modelled: 29 Confidence: 18.0% Identity: 7% PDB header:signaling protein Chain: A: PDB Molecule:aerotaxis transducer aer2; PDBTitle: crystal structure of poly-hamp domains from the p. aeruginosa soluble2 receptor aer2 Phyre2 PDB 3fos chain A Region: 30 - 158 Aligned: 125 Modelled: 129 Confidence: 17.0% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of two-component sensor histidine kinase domain from2 bacillus subtilis subsp. subtilis str. 168 Phyre2 PDB 3hd7 chain A Region: 3 - 33 Aligned: 31 Modelled: 31 Confidence: 10.5% Identity: 10% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 1sxj chain A domain 1 Region: 187 - 202 Aligned: 16 Modelled: 16 Confidence: 6.3% Identity: 0% Fold: post-AAA+ oligomerization domain-like Superfamily: post-AAA+ oligomerization domain-like Family: DNA polymerase III clamp loader subunits, C-terminal domain Phyre2 PDB 1hp9 chain A Region: 209 - 214 Aligned: 6 Modelled: 6 Confidence: 5.7% Identity: 33% PDB header:toxin Chain: A: PDB Molecule:kappa-hefutoxin 1; PDBTitle: kappa-hefutoxins: a novel class of potassium channel toxins2 from scorpion venom Phyre2 1 d2asxa1 2 d3by8a1 3 d1p0za_ 4 c3by9A_ 5 c3pjvD_ 6 d2p7ja2 7 c3b42B_ 8 c3b47A_ 9 c3e4pB_ 10 c2qhkA_ 11 c2kseA_ 12 d1u6ka1 13 c3lnrA_ 14 c3fosA_ 15 c3hd7A_ 16 d1sxja1 17 c1hp9A_

Detailed template information

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

1 d2asxa1 97.8 3 Fold:HAMP domain-like Superfamily:HAMP domain-like Family:HAMP domain 2 d3by8a1 97.3 16 Fold:Profilin-like Superfamily:Sensory domain-like Family:Sensory domain of two-component sensor kinase 3 d1p0za_ 97.2 18 Fold:Profilin-like Superfamily:Sensory domain-like Family:Sensory domain of two-component sensor kinase 4 c3by9A_ 54.1 16 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the v. cholerae histidine kinase dctb2 sensor domain 5 c3pjvD_ 48.0 13 PDB header:lyase Chain: D: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain 6 d2p7ja2 43.0 15 Fold:Profilin-like Superfamily:Sensory domain-like Family:YkuI C-terminal domain-like 7 c3b42B_ 31.7 18 PDB header:signaling protein Chain: B: PDB Molecule:methyl-accepting chemotaxis protein, putative; PDBTitle: periplasmic sensor domain of chemotaxis protein gsu0935 8 c3b47A_ 28.8 19 PDB header:signaling protein Chain: A: PDB Molecule:methyl-accepting chemotaxis protein; PDBTitle: periplasmic sensor domain of chemotaxis protein gsu0582 9 c3e4pB_ 25.8 19 PDB header:transferase Chain: B: PDB Molecule:c4-dicarboxylate transport sensor protein dctb; PDBTitle: crystal structure of malonate occupied dctb 10 c2qhkA_ 25.5 11 PDB header:signaling protein Chain: A: PDB Molecule:methyl-accepting chemotaxis protein; PDBTitle: crystal structure of methyl-accepting chemotaxis protein from vibrio2 parahaemolyticus rimd 2210633 11 c2kseA_ 20.3 22 PDB header:transferase Chain: A: PDB Molecule:sensor protein qsec; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor qsec, center for structures of3 membrane proteins (csmp) target 4311c 12 d1u6ka1 19.7 6 Fold:F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) Superfamily:F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) Family:F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) 13 c3lnrA_ 18.0 7 PDB header:signaling protein Chain: A: PDB Molecule:aerotaxis transducer aer2; PDBTitle: crystal structure of poly-hamp domains from the p. aeruginosa soluble2 receptor aer2 14 c3fosA_ 17.0 18 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of two-component sensor histidine kinase domain from2 bacillus subtilis subsp. subtilis str. 168 15 c3hd7A_ 10.5 10 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 16 d1sxja1 6.3 0 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain 17 c1hp9A_ 5.7 33 PDB header:toxin Chain: A: PDB Molecule:kappa-hefutoxin 1; PDBTitle: kappa-hefutoxins: a novel class of potassium channel toxins2 from scorpion venom

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