Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	A	I	T	M	G	I	F	W	H	L	I	G	A	A	S	A	A	C	F	Y	A	P	F	K	K	V	K	K	W	S	W	E	T	M	W	S	V	G	G	I	V	S	W	I	I	L	P	W	A	I	S	A	L	L	L	P	N
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	W	A	Y	Y	S	S	F	S	L	S	T	R	L	P	V	F	L	F	G	A	M	W	G	I	G	N	I	N	Y	G	L	T	M	R	Y	L	G	M	S	M	G	I	G	I	A	I	G	I	T	L	I	V	G	T	L	M	T	P	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	N	G	N	F	D	V	L	I	S	T	E	G	G	R	M	T	L	L	G	V	L	V	A	L	I	G	V	G	I	V	T	R	A	G	Q	L	K	E	R	K	M	G	I	K	A	E	E	F	N	L	K	K	G	L	V	L	A	V	M
Secondary structure
SS confidence
Disorder					?	?	?	?	?		?		?		?																					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		C	G	I	F	S	A	G	M	S	F	A	M	N	A	A	K	P	M	H	E	A	A	A	A	L	G	V	D	P	L	Y	V	A	L	P	S	Y	V	V	I	M	G	G	G	A	I	I	N	L	G	F	C	F	I	R	L	A	K	V	K
Secondary structure
SS confidence
Disorder																										?																																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		D	L	S	L	K	A	D	F	S	L	A	K	S	L	I	I	H	N	V	L	L	S	T	L	G	G	L	M	W	Y	L	Q	F	F	F	Y	A	W	G	H	A	R	I	P	A	Q	Y	D	Y	I	S	W	M	L	H	M	S	F	Y	V
Secondary structure
SS confidence
Disorder			?			?		?	?	?	?	?	?	?																												?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.
Sequence		L	C	G	G	I	V	G	L	V	L	K	E	W	N	N	A	G	R	R	P	V	T	V	L	S	L	G	C	V	V	I	I	V	A	A	N	I	V	G	I	G	M	A	N
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 1s7b chain A Region: 81 - 150 Aligned: 63 Modelled: 70 Confidence: 94.4% Identity: 16% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2w8a chain C Region: 88 - 337 Aligned: 234 Modelled: 250 Confidence: 34.2% Identity: 11% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 2ht2 chain B Region: 157 - 330 Aligned: 162 Modelled: 170 Confidence: 26.0% Identity: 11% 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 3gia chain A Region: 4 - 338 Aligned: 324 Modelled: 335 Confidence: 21.4% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 2i68 chain B Region: 99 - 150 Aligned: 39 Modelled: 52 Confidence: 18.8% Identity: 26% PDB header:transport protein Chain: B: PDB Molecule:protein emre; PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre Phyre2 PDB 1ots chain A Region: 153 - 335 Aligned: 172 Modelled: 179 Confidence: 16.3% Identity: 10% Fold: Clc chloride channel Superfamily: Clc chloride channel Family: Clc chloride channel Phyre2 PDB 1jb0 chain L Region: 115 - 174 Aligned: 60 Modelled: 60 Confidence: 11.6% Identity: 13% Fold: Photosystem I reaction center subunit XI, PsaL Superfamily: Photosystem I reaction center subunit XI, PsaL Family: Photosystem I reaction center subunit XI, PsaL Phyre2 PDB 1kf6 chain D Region: 26 - 58 Aligned: 33 Modelled: 33 Confidence: 7.7% Identity: 30% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 1q90 chain B Region: 307 - 340 Aligned: 33 Modelled: 34 Confidence: 6.8% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1ymg chain A domain 1 Region: 103 - 247 Aligned: 136 Modelled: 145 Confidence: 5.7% Identity: 13% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 1ymg chain A Region: 103 - 247 Aligned: 136 Modelled: 145 Confidence: 5.7% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution Phyre2 PDB 1ycy chain A domain 1 Region: 310 - 319 Aligned: 8 Modelled: 10 Confidence: 5.4% Identity: 63% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: PF1955-like Phyre2 PDB 2e74 chain A domain 1 Region: 307 - 340 Aligned: 33 Modelled: 34 Confidence: 5.3% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3gbg chain A Region: 309 - 327 Aligned: 19 Modelled: 19 Confidence: 5.1% Identity: 21% PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395 Phyre2 1 d1s7ba_ 2 c2w8aC_ 3 c2ht2B_ 4 c3giaA_ 5 c2i68B_ 6 d1otsa_ 7 d1jb0l_ 8 d1kf6d_ 9 d1q90b_ 10 d1ymga1 11 c1ymgA_ 12 d1ycya1 13 d2e74a1 14 c3gbgA_

Detailed template information

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

1 d1s7ba_ 94.4 16 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2w8aC_ 34.2 11 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 3 c2ht2B_ 26.0 11 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 c3giaA_ 21.4 11 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 5 c2i68B_ 18.8 26 PDB header:transport protein Chain: B: PDB Molecule:protein emre; PDBTitle: cryo-em based theoretical model structure of transmembrane2 domain of the multidrug-resistance antiporter from e. coli3 emre 6 d1otsa_ 16.3 10 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 7 d1jb0l_ 11.6 13 Fold:Photosystem I reaction center subunit XI, PsaL Superfamily:Photosystem I reaction center subunit XI, PsaL Family:Photosystem I reaction center subunit XI, PsaL 8 d1kf6d_ 7.7 30 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 9 d1q90b_ 6.8 15 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 10 d1ymga1 5.7 13 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 11 c1ymgA_ 5.7 13 PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution 12 d1ycya1 5.4 63 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:PF1955-like 13 d2e74a1 5.3 15 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 c3gbgA_ 5.1 21 PDB header:transcription regulator Chain: A: PDB Molecule:tcp pilus virulence regulatory protein; PDBTitle: crystal structure of toxt from vibrio cholerae o395

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