Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP08555
DateThu Jan 5 11:01:32 GMT 2012
Unique Job IDf244b65a902eb5fc

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2w8aC_
Top template information
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
Confidence and coverage
Confidence: 13.1% Coverage: 42%
186 residues ( 42% of your sequence) have been modelled with 13.1% 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.
Please note: You must be registered and logged in to use Phyrealarm.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MHSQIWVVSTLLISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIG
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   .........70.........80.........90.........100.........110.........120
Sequence  GTLGFLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSVDVIMVLVGLICGITLFVEV
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   .........130.........140.........150.........160.........170.........180
Sequence  GVVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIV
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   .........190.........200.........210.........220.........230.........240
Sequence  YGLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDEKTLPSLGATLFTILLPIA
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   .........250.........260.........270.........280.........290.........300
Sequence  LMLVKTIAELNMARESGLYILVEFIGNPITAMFIAVFVAYYVLGIRQHMSMGTMLTHTEN
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???
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   .........310.........320.........330.........340.........350.........360
Sequence  GFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLVALILHAAVGSA
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   .........370.........380.........390.........400.........410.........420
Sequence  TVAMMGATAIVAPMLPLYPDISPEIIAIAIGSGAIGCTIVTDSLFWLVKQYCGATLNETF
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   .........430.........440.....
Sequence  KYYTTATFIASVVALAGTFLLSFII
Secondary structure 

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??
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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 2w8a chain C

3D model

Region: 32 - 229
Aligned: 186
Modelled: 197
Confidence: 13.1%
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 2a65 chain A domain 1

3D model

Region: 85 - 293
Aligned: 190
Modelled: 209
Confidence: 8.4%
Identity: 7%
Fold: SNF-like
Superfamily: SNF-like
Family: SNF-like

Phyre2

PDB 3qnq chain D

3D model

Region: 23 - 216
Aligned: 194
Modelled: 194
Confidence: 8.2%
Identity: 14%
PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system

Phyre2

PDB 2knc chain A

3D model

Region: 171 - 222
Aligned: 52
Modelled: 52
Confidence: 7.9%
Identity: 15%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

PDB 2vof chain A

3D model

Region: 62 - 100
Aligned: 39
Modelled: 38
Confidence: 6.3%
Identity: 13%
PDB header:apoptosis
Chain: A: PDB Molecule:bcl-2-related protein a1;
PDBTitle: structure of mouse a1 bound to the puma bh3-domain

Phyre2
1

c2w8aC_
2

d2a65a1
3

c3qnqD_
4

c2kncA_
5

c2vofA_



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2w8aC_



13.1 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
2d2a65a1



8.4 7 Fold:SNF-like
Superfamily:SNF-like
Family:SNF-like
3c3qnqD_



8.2 14 PDB header:membrane protein, transport protein
Chain: D: PDB Molecule:pts system, cellobiose-specific iic component;
PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system
4c2kncA_



7.9 15 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
5c2vofA_



6.3 13 PDB header:apoptosis
Chain: A: PDB Molecule:bcl-2-related protein a1;
PDBTitle: structure of mouse a1 bound to the puma bh3-domain

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