Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	D	T	P	S	L	E	T	P	Q	A	A	R	L	R	R	R	Q	L	I	R	Q	L	L	E	R	D	K	T	P	L	A	I	L	F	M	A	A	V	V	G	T	L	V	G	L	A	A	V	A	F	D	K	G	V	A	W	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?															?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	N	Q	R	M	G	A	L	V	H	T	A	D	N	Y	P	L	L	L	T	V	A	F	L	C	S	A	V	L	A	M	F	G	Y	F	L	V	R	K	Y	A	P	E	A	G	G	S	G	I	P	E	I	E	G	A	L	E	D	Q	R
Secondary structure
SS confidence
Disorder																																														?	?	?													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	V	R	W	W	R	V	L	P	V	K	F	F	G	G	L	G	T	L	G	G	G	M	V	L	G	R	E	G	P	T	V	Q	I	G	G	N	I	G	R	M	V	L	D	I	F	R	L	K	G	D	E	A	R	H	T	L	L	A	T
Secondary structure
SS confidence
Disorder		?	?	?																																															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	A	A	A	G	L	A	A	A	F	N	A	P	L	A	G	I	L	F	I	I	E	E	M	R	P	Q	F	R	Y	T	L	I	S	I	K	A	V	F	I	G	V	I	M	S	T	I	M	Y	R	I	F	N	H	E	V	A	L	I	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	G	K	L	S	D	A	P	L	N	T	L	W	L	Y	L	I	L	G	I	I	F	G	I	F	G	P	I	F	N	K	W	V	L	G	M	Q	D	L	L	H	R	V	H	G	G	N	I	T	K	W	V	L	M	G	G	A	I	G	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	C	G	L	L	G	F	V	A	P	A	T	S	G	G	G	F	N	L	I	P	I	A	T	A	G	N	F	S	M	G	M	L	V	F	I	F	V	A	R	V	I	T	T	L	L	C	F	S	S	G	A	P	G	G	I	F	A	P	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	A	L	G	T	V	L	G	T	A	F	G	M	V	A	V	E	L	F	P	Q	Y	H	L	E	A	G	T	F	A	I	A	G	M	G	A	L	L	A	A	S	I	R	A	P	L	T	G	I	I	L	V	L	E	M	T	D	N	Y	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.
Sequence		L	I	L	P	M	I	I	T	G	L	G	A	T	L	L	A	Q	F	T	G	G	K	P	L	Y	S	A	I	L	A	R	T	L	A	K	Q	E	A	E	Q	L	A	R	S	K	A	A	S	A	S	E	N	T
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 1ots chain A Region: 17 - 460 Aligned: 444 Modelled: 444 Confidence: 100.0% Identity: 100% Fold: Clc chloride channel Superfamily: Clc chloride channel Family: Clc chloride channel Phyre2 PDB 2ht2 chain B Region: 18 - 458 Aligned: 441 Modelled: 441 Confidence: 100.0% Identity: 100% 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 1kpl chain A Region: 31 - 460 Aligned: 430 Modelled: 430 Confidence: 100.0% Identity: 81% Fold: Clc chloride channel Superfamily: Clc chloride channel Family: Clc chloride channel Phyre2 PDB 3nd0 chain A Region: 32 - 458 Aligned: 423 Modelled: 427 Confidence: 100.0% Identity: 40% PDB header:transport protein Chain: A: PDB Molecule:sll0855 protein; PDBTitle: x-ray crystal structure of a slow cyanobacterial cl-/h+ antiporter Phyre2 PDB 3org chain B Region: 33 - 467 Aligned: 403 Modelled: 421 Confidence: 100.0% Identity: 23% PDB header:transport protein Chain: B: PDB Molecule:cmclc; PDBTitle: crystal structure of a eukaryotic clc transporter Phyre2 PDB 3p5n chain A Region: 133 - 278 Aligned: 131 Modelled: 146 Confidence: 26.9% Identity: 21% PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter Phyre2 PDB 2ksf chain A Region: 217 - 267 Aligned: 50 Modelled: 51 Confidence: 21.4% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:sensor protein kdpd; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor kdpd, center for structures of3 membrane proteins (csmp) target 4312c Phyre2 PDB 1v54 chain A Region: 212 - 451 Aligned: 240 Modelled: 240 Confidence: 12.9% Identity: 13% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 3c4r chain C Region: 419 - 466 Aligned: 48 Modelled: 48 Confidence: 10.9% Identity: 19% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein encoded by2 cryptic prophage Phyre2 PDB 2dw3 chain A Region: 349 - 363 Aligned: 15 Modelled: 15 Confidence: 7.7% Identity: 40% PDB header:photosynthesis Chain: A: PDB Molecule:intrinsic membrane protein pufx; PDBTitle: solution structure of the rhodobacter sphaeroides pufx2 membrane protein Phyre2 PDB 3mk7 chain F Region: 33 - 96 Aligned: 64 Modelled: 64 Confidence: 7.5% Identity: 17% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 3din chain D Region: 11 - 64 Aligned: 53 Modelled: 54 Confidence: 5.9% Identity: 11% PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 2akh chain Z Region: 7 - 65 Aligned: 58 Modelled: 59 Confidence: 5.6% Identity: 12% PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 2kjf chain A Region: 133 - 161 Aligned: 29 Modelled: 29 Confidence: 5.3% Identity: 21% PDB header:antimicrobial protein Chain: A: PDB Molecule:carnocyclin-a; PDBTitle: the solution structure of the circular bacteriocin2 carnocyclin a (ccla) Phyre2 PDB 2yl4 chain A Region: 20 - 100 Aligned: 81 Modelled: 81 Confidence: 5.1% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:atp-binding cassette sub-family b member 10, PDBTitle: structure of the human mitochondrial abc transporter, abcb10 Phyre2 1 d1otsa_ 2 c2ht2B_ 3 d1kpla_ 4 c3nd0A_ 5 c3orgB_ 6 c3p5nA_ 7 c2ksfA_ 8 d1v54a_ 9 c3c4rC_ 10 c2dw3A_ 11 c3mk7F_ 12 c3dinD_ 13 c2akhZ_ 14 c2kjfA_ 15 c2yl4A_

Detailed template information

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

1 d1otsa_ 100.0 100 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 2 c2ht2B_ 100.0 100 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 3 d1kpla_ 100.0 81 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 4 c3nd0A_ 100.0 40 PDB header:transport protein Chain: A: PDB Molecule:sll0855 protein; PDBTitle: x-ray crystal structure of a slow cyanobacterial cl-/h+ antiporter 5 c3orgB_ 100.0 23 PDB header:transport protein Chain: B: PDB Molecule:cmclc; PDBTitle: crystal structure of a eukaryotic clc transporter 6 c3p5nA_ 26.9 21 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 7 c2ksfA_ 21.4 12 PDB header:transferase Chain: A: PDB Molecule:sensor protein kdpd; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor kdpd, center for structures of3 membrane proteins (csmp) target 4312c 8 d1v54a_ 12.9 13 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 9 c3c4rC_ 10.9 19 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein encoded by2 cryptic prophage 10 c2dw3A_ 7.7 40 PDB header:photosynthesis Chain: A: PDB Molecule:intrinsic membrane protein pufx; PDBTitle: solution structure of the rhodobacter sphaeroides pufx2 membrane protein 11 c3mk7F_ 7.5 17 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 12 c3dinD_ 5.9 11 PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 13 c2akhZ_ 5.6 12 PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli 14 c2kjfA_ 5.3 21 PDB header:antimicrobial protein Chain: A: PDB Molecule:carnocyclin-a; PDBTitle: the solution structure of the circular bacteriocin2 carnocyclin a (ccla) 15 c2yl4A_ 5.1 9 PDB header:membrane protein Chain: A: PDB Molecule:atp-binding cassette sub-family b member 10, PDBTitle: structure of the human mitochondrial abc transporter, abcb10

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