Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AE74
DateThu Jan 5 11:22:42 GMT 2012
Unique Job ID119e847f2bcc5073

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1y5ic1
Top template information
Fold:Heme-binding four-helical bundle
Superfamily:Respiratory nitrate reductase 1 gamma chain
Family:Respiratory nitrate reductase 1 gamma chain
Confidence and coverage
Confidence: 48.6% Coverage: 26%
125 residues ( 26% of your sequence) have been modelled with 48.6% 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  MSLAKDNIWKLLAPLVVMGVMFLIPVPDGMPPQAWHYFAVFVAMIVGMILEPIPATAISF
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   .........70.........80.........90.........100.........110.........120
Sequence  IAVTICVIGSNYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVS
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   .........130.........140.........150.........160.........170.........180
Sequence  GLGRRIALFLVKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKS
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???
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   .........190.........200.........210.........220.........230.........240
Sequence  FPNDPSARRIGGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWFLCF
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   .........250.........260.........270.........280.........290.........300
Sequence  LPVGVILLIIAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGL
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??
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   .........310.........320.........330.........340.........350.........360
Sequence  WVFGSEVINATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSGF
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   .........370.........380.........390.........400.........410.........420
Sequence  IDWFAGTMSTHLEGFSPNATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVGKGIPGVP
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   .........430.........440.........450.........460.........470.........480
Sequence  MEQLCILLVLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLVGW
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   .......
Sequence  PILAMWN
Secondary structure 

SS confidence 






Disorder 


?

?
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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 1y5i chain C domain 1

3D model

Region: 232 - 356
Aligned: 125
Modelled: 125
Confidence: 48.6%
Identity: 10%
Fold: Heme-binding four-helical bundle
Superfamily: Respiratory nitrate reductase 1 gamma chain
Family: Respiratory nitrate reductase 1 gamma chain

Phyre2

PDB 1w8x chain P

3D model

Region: 3 - 23
Aligned: 21
Modelled: 21
Confidence: 38.8%
Identity: 14%
PDB header:virus
Chain: P: PDB Molecule:protein p16;
PDBTitle: structural analysis of prd1

Phyre2

PDB 3d9s chain B

3D model

Region: 183 - 279
Aligned: 94
Modelled: 97
Confidence: 10.0%
Identity: 14%
PDB header:membrane protein
Chain: B: PDB Molecule:aquaporin-5;
PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure

Phyre2

PDB 1ymg chain A

3D model

Region: 183 - 274
Aligned: 88
Modelled: 92
Confidence: 9.2%
Identity: 19%
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 1ymg chain A domain 1

3D model

Region: 183 - 274
Aligned: 88
Modelled: 92
Confidence: 9.2%
Identity: 19%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2

PDB 2knc chain A

3D model

Region: 236 - 276
Aligned: 41
Modelled: 41
Confidence: 6.1%
Identity: 17%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

PDB 3qnq chain D

3D model

Region: 191 - 271
Aligned: 80
Modelled: 81
Confidence: 5.5%
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
1

d1y5ic1
2

c1w8xP_
3

c3d9sB_
4

c1ymgA_
5

d1ymga1
6

c2kncA_
7

c3qnqD_



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1y5ic1



48.6 10 Fold:Heme-binding four-helical bundle
Superfamily:Respiratory nitrate reductase 1 gamma chain
Family:Respiratory nitrate reductase 1 gamma chain
2c1w8xP_



38.8 14 PDB header:virus
Chain: P: PDB Molecule:protein p16;
PDBTitle: structural analysis of prd1
3c3d9sB_



10.0 14 PDB header:membrane protein
Chain: B: PDB Molecule:aquaporin-5;
PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure
4c1ymgA_



9.2 19 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
5d1ymga1



9.2 19 Fold:Aquaporin-like
Superfamily:Aquaporin-like
Family:Aquaporin-like
6c2kncA_



6.1 17 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
7c3qnqD_



5.5 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

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