Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	G	S	L	R	K	M	P	V	W	L	P	I	V	I	L	L	V	A	M	A	S	I	Q	G	G	A	S	L	A	K	S	L	F	P	L	V	G	A	P	G	V	T	A	L	R	L	A	L	G	T	L	I	L	I	A	F	F	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																									?																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	W	R	L	R	F	A	K	E	Q	R	L	P	L	L	F	Y	G	V	S	L	G	G	M	N	Y	L	F	Y	L	S	I	Q	T	V	P	L	G	I	A	V	A	L	E	F	T	G	P	L	A	V	A	L	F	S	S	R	R	P	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	F	V	W	V	V	L	A	V	L	G	L	W	F	L	L	P	L	G	Q	D	V	S	H	V	D	L	T	G	C	A	L	A	L	G	A	G	A	C	W	A	I	Y	I	L	S	G	Q	R	A	G	A	E	H	G	P	A	T	V	A
Secondary structure
SS confidence
Disorder																					?		?	?																												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	G	S	L	I	A	A	L	I	F	V	P	I	G	A	L	Q	A	G	E	A	L	W	H	W	S	V	I	P	L	G	L	A	V	A	I	L	S	T	A	L	P	Y	S	L	E	M	I	A	L	T	R	L	P	T	R	T	F	G	T
Secondary structure
SS confidence
Disorder																			?	?	?	?	?	?																													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.
Sequence		L	M	S	M	E	P	A	L	A	A	V	S	G	M	I	F	L	G	E	T	L	T	P	I	Q	L	L	A	L	G	A	I	I	A	A	S	M	G	S	T	L	T	V	R	K	E	S	K	I	K	E	L	D	I	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: 214 - 288 Aligned: 75 Modelled: 75 Confidence: 97.5% Identity: 17% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 2i68 chain B Region: 218 - 281 Aligned: 58 Modelled: 64 Confidence: 72.0% Identity: 16% 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 1pw4 chain A Region: 124 - 295 Aligned: 172 Modelled: 172 Confidence: 37.9% Identity: 15% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2jwa chain A Region: 269 - 291 Aligned: 23 Modelled: 23 Confidence: 31.2% Identity: 22% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 3lrc chain C Region: 171 - 290 Aligned: 120 Modelled: 120 Confidence: 20.0% Identity: 8% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2xq2 chain A Region: 149 - 293 Aligned: 144 Modelled: 145 Confidence: 17.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 3rko chain F Region: 252 - 289 Aligned: 38 Modelled: 38 Confidence: 13.8% Identity: 8% 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 Phyre2 PDB 3aqp chain B Region: 205 - 293 Aligned: 89 Modelled: 89 Confidence: 11.3% Identity: 12% 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 1iwg chain A domain 8 Region: 211 - 293 Aligned: 83 Modelled: 83 Confidence: 11.1% Identity: 13% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1waz chain A Region: 246 - 290 Aligned: 45 Modelled: 45 Confidence: 8.6% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles Phyre2 PDB 1iwg chain A domain 7 Region: 211 - 293 Aligned: 83 Modelled: 83 Confidence: 7.9% Identity: 10% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2rdd chain B Region: 262 - 293 Aligned: 32 Modelled: 32 Confidence: 7.6% Identity: 13% 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 1s5l chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 1s5l chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3bz1 chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3kzi chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 PDB 2axt chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3a0b chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0b chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 2axt chain L Region: 7 - 28 Aligned: 22 Modelled: 22 Confidence: 7.4% Identity: 14% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 1 d1s7ba_ 2 c2i68B_ 3 d1pw4a_ 4 c2jwaA_ 5 c3lrcC_ 6 c2xq2A_ 7 c3rkoF_ 8 c3aqpB_ 9 d1iwga8 10 c1wazA_ 11 d1iwga7 12 c2rddB_ 13 c1s5ll_ 14 c1s5lL_ 15 c3bz1L_ 16 c3kziL_ 17 c2axtl_ 18 c3a0bl_ 19 c3a0bL_ 20 c2axtL_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d1s7ba_ 97.5 17 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 2 c2i68B_ 72.0 16 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 d1pw4a_ 37.9 15 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 4 c2jwaA_ 31.2 22 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 5 c3lrcC_ 20.0 8 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 6 c2xq2A_ 17.0 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 7 c3rkoF_ 13.8 8 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 8 c3aqpB_ 11.3 12 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 9 d1iwga8 11.1 13 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 10 c1wazA_ 8.6 13 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles 11 d1iwga7 7.9 10 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 12 c2rddB_ 7.6 13 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. 13 c1s5ll_ 7.4 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 14 c1s5lL_ 7.4 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 15 c3bz1L_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 16 c3kziL_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 17 c2axtl_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 18 c3a0bl_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 19 c3a0bL_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 20 c2axtL_ 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 21 c3prrL_ not modelled 7.4 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 22 c3arcL_ not modelled 7.4 14 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 23 c3bz2L_ not modelled 7.4 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 24 c3prqL_ not modelled 7.4 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 25 d2axtl1 not modelled 7.4 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 26 c3a0hl_ not modelled 7.3 16 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 27 c3a0hL_ not modelled 7.3 16 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 28 d1l7va_ not modelled 7.1 17 Fold:ABC transporter involved in vitamin B12 uptake, BtuC Superfamily:ABC transporter involved in vitamin B12 uptake, BtuC Family:ABC transporter involved in vitamin B12 uptake, BtuC 29 c2kncA_ not modelled 6.7 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 30 c2akhZ_ not modelled 6.0 24 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 31 c1yfnG_ not modelled 5.4 50 PDB header:protein binding Chain: G: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: versatile modes of peptide recognition by the aaa+ adaptor2 protein sspb- the crystal structure of a sspb-rsea complex

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