Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AA70
DateThu Jan 5 11:12:04 GMT 2012
Unique Job ID233c2c776ceaaaf2

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1s7ba_
Top template information
Fold:Multidrug resistance efflux transporter EmrE
Superfamily:Multidrug resistance efflux transporter EmrE
Family:Multidrug resistance efflux transporter EmrE
Confidence and coverage
Confidence: 97.4% Coverage: 25%
75 residues ( 25% of your sequence) have been modelled with 97.4% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MRFRQLLPLFGALFALYIIWGSTYFVIRIGVESWPPLMMAGVRFLAAGILLLAFLLLRGH
Secondary structure 












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???
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   .........70.........80.........90.........100.........110.........120
Sequence  KLPPLRPLLNAALIGLLLLAVGNGMVTVAEHQNVPSGIAAVVVATVPLFTLCFSRLFGIK
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??

























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   .........130.........140.........150.........160.........170.........180
Sequence  TRKLEWVGIAIGLAGIIMLNSGGNLSGNPWGAILILIGSISWAFGSVYGSRITLPVGMMA
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?

???



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   .........190.........200.........210.........220.........230.........240
Sequence  GAIEMLAAGVVLMIASMIAGEKLTALPSLSGFLAVGYLALFGSIIAINAYMYLIRNVSPA
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??????

































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   .........250.........260.........270.........280.........290.........300
Sequence  LATSYAYVNPVVAVLLGTGLGGETLSKIEWLALGVIVFAVVLVTLGKYLFPAKPVVAPVI
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???????????????
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   ......
Sequence  QDASSE
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

RankAligned region

PDB 1s7b chain A

3D model

Region: 218 - 292
Aligned: 75
Modelled: 75
Confidence: 97.4%
Identity: 16%
Fold: Multidrug resistance efflux transporter EmrE
Superfamily: Multidrug resistance efflux transporter EmrE
Family: Multidrug resistance efflux transporter EmrE

Phyre2

PDB 2i68 chain B

3D model

Region: 222 - 285
Aligned: 58
Modelled: 64
Confidence: 91.1%
Identity: 24%
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 2xq2 chain A

3D model

Region: 155 - 302
Aligned: 148
Modelled: 148
Confidence: 74.0%
Identity: 12%
PDB header:transport protein
Chain: A: PDB Molecule:sodium/glucose cotransporter;
PDBTitle: structure of the k294a mutant of vsglt

Phyre2

PDB 1u7g chain A

3D model

Region: 6 - 238
Aligned: 230
Modelled: 233
Confidence: 68.1%
Identity: 15%
Fold: Ammonium transporter
Superfamily: Ammonium transporter
Family: Ammonium transporter

Phyre2

PDB 3dh4 chain A

3D model

Region: 155 - 305
Aligned: 151
Modelled: 151
Confidence: 60.4%
Identity: 12%
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

3D model

Region: 270 - 303
Aligned: 34
Modelled: 34
Confidence: 57.3%
Identity: 9%
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 3rko chain F

3D model

Region: 8 - 149
Aligned: 142
Modelled: 142
Confidence: 38.9%
Identity: 10%
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 3lrc chain C

3D model

Region: 183 - 294
Aligned: 112
Modelled: 112
Confidence: 36.4%
Identity: 12%
PDB header:transport protein
Chain: C: PDB Molecule:arginine/agmatine antiporter;
PDBTitle: structure of e. coli adic (p1)

Phyre2

PDB 1iwg chain A domain 8

3D model

Region: 215 - 306
Aligned: 92
Modelled: 92
Confidence: 32.1%
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 2jln chain A

3D model

Region: 248 - 306
Aligned: 59
Modelled: 59
Confidence: 17.6%
Identity: 5%
PDB header:membrane protein
Chain: A: PDB Molecule:mhp1;
PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter

Phyre2

PDB 1iwg chain A domain 7

3D model

Region: 215 - 306
Aligned: 92
Modelled: 92
Confidence: 17.0%
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 1oy8 chain A

3D model

Region: 215 - 306
Aligned: 92
Modelled: 92
Confidence: 16.9%
Identity: 9%
PDB header:membrane protein
Chain: A: PDB Molecule:acriflavine resistance protein b;
PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump

Phyre2

PDB 2knc chain A

3D model

Region: 273 - 306
Aligned: 34
Modelled: 34
Confidence: 16.2%
Identity: 15%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

PDB 3aqp chain B

3D model

Region: 210 - 301
Aligned: 92
Modelled: 92
Confidence: 16.2%
Identity: 16%
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 2jo1 chain A

3D model

Region: 270 - 305
Aligned: 36
Modelled: 36
Confidence: 13.7%
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 3dtu chain B domain 2

3D model

Region: 270 - 306
Aligned: 37
Modelled: 37
Confidence: 11.5%
Identity: 16%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2

PDB 3ehb chain B domain 2

3D model

Region: 270 - 306
Aligned: 37
Modelled: 37
Confidence: 10.5%
Identity: 22%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2

PDB 1fft chain B domain 2

3D model

Region: 275 - 305
Aligned: 31
Modelled: 31
Confidence: 9.0%
Identity: 13%
Fold: Transmembrane helix hairpin
Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region
Family: Cytochrome c oxidase subunit II-like, transmembrane region

Phyre2

PDB 3gia chain A

3D model

Region: 59 - 303
Aligned: 224
Modelled: 245
Confidence: 6.3%
Identity: 12%
PDB header:transport protein
Chain: A: PDB Molecule:uncharacterized protein mj0609;
PDBTitle: crystal structure of apct transporter

Phyre2

PDB 2b2h chain A

3D model

Region: 6 - 238
Aligned: 232
Modelled: 233
Confidence: 6.0%
Identity: 14%
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

c2xq2A_
4

d1u7ga_
5

c3dh4A_
6

c2jp3A_
7

c3rkoF_
8

c3lrcC_
9

d1iwga8
10

c2jlnA_
11

d1iwga7
12

c1oy8A_
13

c2kncA_
14

c3aqpB_
15

c2jo1A_
16

d3dtub2
17

d3ehbb2
18

d1fftb2
19

c3giaA_
20

c2b2hA_
21



22






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1s7ba_



97.4 16 Fold:Multidrug resistance efflux transporter EmrE
Superfamily:Multidrug resistance efflux transporter EmrE
Family:Multidrug resistance efflux transporter EmrE
2c2i68B_



91.1 24 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
3c2xq2A_



74.0 12 PDB header:transport protein
Chain: A: PDB Molecule:sodium/glucose cotransporter;
PDBTitle: structure of the k294a mutant of vsglt
4d1u7ga_



68.1 15 Fold:Ammonium transporter
Superfamily:Ammonium transporter
Family:Ammonium transporter
5c3dh4A_



60.4 12 PDB header:transport protein
Chain: A: PDB Molecule:sodium/glucose cotransporter;
PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus
6c2jp3A_



57.3 9 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
7c3rkoF_



38.9 10 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
8c3lrcC_



36.4 12 PDB header:transport protein
Chain: C: PDB Molecule:arginine/agmatine antiporter;
PDBTitle: structure of e. coli adic (p1)
9d1iwga8



32.1 13 Fold:Multidrug efflux transporter AcrB transmembrane domain
Superfamily:Multidrug efflux transporter AcrB transmembrane domain
Family:Multidrug efflux transporter AcrB transmembrane domain
10c2jlnA_



17.6 5 PDB header:membrane protein
Chain: A: PDB Molecule:mhp1;
PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter
11d1iwga7



17.0 10 Fold:Multidrug efflux transporter AcrB transmembrane domain
Superfamily:Multidrug efflux transporter AcrB transmembrane domain
Family:Multidrug efflux transporter AcrB transmembrane domain
12c1oy8A_



16.9 9 PDB header:membrane protein
Chain: A: PDB Molecule:acriflavine resistance protein b;
PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump
13c2kncA_



16.2 15 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
14c3aqpB_



16.2 16 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
15c2jo1A_



13.7 8 PDB header:hydrolase regulator
Chain: A: PDB Molecule:phospholemman;
PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles
16d3dtub2



11.5 16 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
17d3ehbb2



10.5 22 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
18d1fftb2



9.0 13 Fold:Transmembrane helix hairpin
Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region
Family:Cytochrome c oxidase subunit II-like, transmembrane region
19c3giaA_



6.3 12 PDB header:transport protein
Chain: A: PDB Molecule:uncharacterized protein mj0609;
PDBTitle: crystal structure of apct transporter
20c2b2hA_



6.0 14 PDB header:transport protein
Chain: A: PDB Molecule:ammonium transporter;
PDBTitle: ammonium transporter amt-1 from a. fulgidus (as)
21c2mltB_



not modelled 5.2 12 PDB header:toxin (hemolytic polypeptide)
Chain: B: PDB Molecule:melittin;
PDBTitle: melittin
22c2mltA_



not modelled 5.2 12 PDB header:toxin (hemolytic polypeptide)
Chain: A: PDB Molecule:melittin;
PDBTitle: melittin

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



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