Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Q	Q	A	G	I	G	I	L	L	A	L	T	T	A	I	C	W	G	A	L	P	I	A	M	K	Q	V	L	E	V	M	E	P	P	T	I	V	F	Y	R	F	L	M	A	S	I	G	L	G	A	I	L	A	V	K	K	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																																				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	P	L	R	V	F	R	K	P	R	W	L	I	L	L	A	V	A	T	A	G	L	F	G	N	F	I	L	F	S	S	S	L	Q	Y	L	S	P	T	A	S	Q	V	I	G	Q	L	S	P	V	G	M	M	V	A	S	V	F	I	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	E	K	M	R	S	T	Q	V	V	G	A	L	M	L	L	S	G	L	V	M	F	F	N	T	S	L	V	E	I	F	T	K	L	T	D	Y	T	W	G	V	I	F	G	V	G	A	A	T	V	W	V	S	Y	G	V	A	Q	K	V
Secondary structure
SS confidence
Disorder																											?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	L	R	R	L	A	S	P	Q	I	L	F	L	L	Y	T	L	C	T	I	A	L	F	P	L	A	K	P	G	V	I	A	Q	L	S	H	W	Q	L	A	C	L	I	F	C	G	L	N	T	L	V	G	Y	G	A	L	A	E	A	M
Secondary structure
SS confidence
Disorder				?																									?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	R	W	Q	A	A	Q	V	S	A	I	I	T	L	T	P	L	F	T	L	F	F	S	D	L	L	S	L	A	W	P	D	F	F	A	R	P	M	L	N	L	L	G	Y	L	G	A	F	V	V	V	A	G	A	M	Y	S	A	I	G
Secondary structure
SS confidence
Disorder																																?	?																										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.
Sequence		H	R	I	W	G	G	L	R	K	H	T	T	V	V	S	Q	P	R	A	G	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 1s7b chain A Region: 224 - 302 Aligned: 71 Modelled: 79 Confidence: 97.5% Identity: 15% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 228 - 299 Aligned: 58 Modelled: 72 Confidence: 75.0% Identity: 17% 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 3b9y chain A Region: 44 - 321 Aligned: 221 Modelled: 221 Confidence: 63.1% Identity: 13% 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 3hd6 chain A Region: 2 - 231 Aligned: 230 Modelled: 230 Confidence: 25.9% Identity: 13% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 2knc chain A Region: 281 - 319 Aligned: 39 Modelled: 39 Confidence: 21.0% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2jo1 chain A Region: 284 - 321 Aligned: 38 Modelled: 38 Confidence: 20.4% Identity: 8% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 PDB 2akh chain Z Region: 260 - 321 Aligned: 62 Modelled: 62 Confidence: 17.2% Identity: 19% 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 3dh4 chain A Region: 160 - 321 Aligned: 154 Modelled: 162 Confidence: 15.1% Identity: 7% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 2jp3 chain A Region: 284 - 317 Aligned: 34 Modelled: 34 Confidence: 14.4% Identity: 12% PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles Phyre2 PDB 1zrt chain D Region: 258 - 312 Aligned: 50 Modelled: 55 Confidence: 12.6% Identity: 12% PDB header:oxidoreductase/metal transport Chain: D: PDB Molecule:cytochrome c1; PDBTitle: rhodobacter capsulatus cytochrome bc1 complex with2 stigmatellin bound Phyre2 PDB 3cwb chain Q Region: 258 - 318 Aligned: 56 Modelled: 61 Confidence: 8.1% Identity: 9% PDB header:oxidoreductase Chain: Q: PDB Molecule:mitochondrial cytochrome c1, heme protein; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d Phyre2 PDB 1p84 chain D Region: 258 - 311 Aligned: 49 Modelled: 54 Confidence: 7.8% Identity: 10% PDB header:oxidoreductase Chain: D: PDB Molecule:cytochrome c1, heme protein; PDBTitle: hdbt inhibited yeast cytochrome bc1 complex Phyre2 PDB 2rdd chain B Region: 280 - 316 Aligned: 37 Modelled: 37 Confidence: 7.2% Identity: 14% 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 1iwg chain A domain 7 Region: 221 - 321 Aligned: 93 Modelled: 101 Confidence: 6.7% Identity: 11% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2gfp chain A Region: 151 - 321 Aligned: 166 Modelled: 171 Confidence: 6.6% Identity: 7% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3aqp chain B Region: 216 - 314 Aligned: 91 Modelled: 99 Confidence: 6.5% Identity: 10% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 2fyn chain H Region: 258 - 308 Aligned: 46 Modelled: 51 Confidence: 6.2% Identity: 15% PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c1; PDBTitle: crystal structure analysis of the double mutant rhodobacter2 sphaeroides bc1 complex Phyre2 PDB 1y5i chain C domain 1 Region: 285 - 315 Aligned: 31 Modelled: 31 Confidence: 6.1% Identity: 13% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 2yiu chain E Region: 258 - 308 Aligned: 46 Modelled: 51 Confidence: 5.6% Identity: 11% PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution Phyre2 PDB 2b2h chain A Region: 8 - 244 Aligned: 231 Modelled: 228 Confidence: 5.2% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 1 d1s7ba_ 2 c2i68B_ 3 c3b9yA_ 4 c3hd6A_ 5 c2kncA_ 6 c2jo1A_ 7 c2akhZ_ 8 c3dh4A_ 9 c2jp3A_ 10 c1zrtD_ 11 c3cwbQ_ 12 c1p84D_ 13 c2rddB_ 14 d1iwga7 15 c2gfpA_ 16 c3aqpB_ 17 c2fynH_ 18 d1y5ic1 19 c2yiuE_ 20 c2b2hA_ 21 22

Detailed template information

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

1 d1s7ba_ 97.5 15 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 75.0 17 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 3 c3b9yA_ 63.1 13 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 4 c3hd6A_ 25.9 13 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 5 c2kncA_ 21.0 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 6 c2jo1A_ 20.4 8 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 7 c2akhZ_ 17.2 19 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 8 c3dh4A_ 15.1 7 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 9 c2jp3A_ 14.4 12 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 10 c1zrtD_ 12.6 12 PDB header:oxidoreductase/metal transport Chain: D: PDB Molecule:cytochrome c1; PDBTitle: rhodobacter capsulatus cytochrome bc1 complex with2 stigmatellin bound 11 c3cwbQ_ 8.1 9 PDB header:oxidoreductase Chain: Q: PDB Molecule:mitochondrial cytochrome c1, heme protein; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 12 c1p84D_ 7.8 10 PDB header:oxidoreductase Chain: D: PDB Molecule:cytochrome c1, heme protein; PDBTitle: hdbt inhibited yeast cytochrome bc1 complex 13 c2rddB_ 7.2 14 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 d1iwga7 6.7 11 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 15 c2gfpA_ 6.6 7 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 16 c3aqpB_ 6.5 10 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 17 c2fynH_ 6.2 15 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c1; PDBTitle: crystal structure analysis of the double mutant rhodobacter2 sphaeroides bc1 complex 18 d1y5ic1 6.1 13 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 19 c2yiuE_ 5.6 11 PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution 20 c2b2hA_ 5.2 13 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 21 c3rkoF_ not modelled 5.1 6 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 22 c2jwaA_ not modelled 5.1 28 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure

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