Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionA5A630
DateThu Jan 5 10:55:32 GMT 2012
Unique Job IDb11f8cc451fde165

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3kdpD_
Top template information
PDB header:hydrolase
Chain: D: PDB Molecule:sodium/potassium-transporting atpase subunit beta-1;
PDBTitle: crystal structure of the sodium-potassium pump
Confidence and coverage
Confidence: 35.5% Coverage: 35%
32 residues ( 35% of your sequence) have been modelled with 35.5% 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.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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








SS confidence 



























































Disorder  ??




















??
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Disorder confidence 



























































 
   .........70.........80.........90.
Sequence  IQRANINLAFVGIIYTALFALYAMLFWLAFF
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 3kdp chain D

3D model

Region: 60 - 91
Aligned: 32
Modelled: 32
Confidence: 35.5%
Identity: 19%
PDB header:hydrolase
Chain: D: PDB Molecule:sodium/potassium-transporting atpase subunit beta-1;
PDBTitle: crystal structure of the sodium-potassium pump

Phyre2

PDB 2z8t chain X

3D model

Region: 23 - 32
Aligned: 10
Modelled: 10
Confidence: 21.5%
Identity: 70%
PDB header:hydrolase
Chain: X: PDB Molecule:protein-glutaminase;
PDBTitle: crystal structure of protein-glutaminase of c.proteolyticum2 strain 9670

Phyre2

PDB 8i1b chain A

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 20.0%
Identity: 33%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2

PDB 1ilr chain 1

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 19.9%
Identity: 56%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2

PDB 3a56 chain B

3D model

Region: 23 - 32
Aligned: 10
Modelled: 10
Confidence: 19.6%
Identity: 70%
PDB header:hydrolase
Chain: B: PDB Molecule:protein-glutaminase;
PDBTitle: crystal structure of pro- protein-glutaminase

Phyre2

PDB 2wry chain A

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 19.5%
Identity: 56%
PDB header:immune system
Chain: A: PDB Molecule:interleukin-1beta;
PDBTitle: crystal structure of chicken cytokine interleukin 1 beta

Phyre2

PDB 2ila chain A

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 19.0%
Identity: 22%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2

PDB 1l2h chain A

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 18.2%
Identity: 22%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2

PDB 1cn3 chain F

3D model

Region: 41 - 53
Aligned: 13
Modelled: 13
Confidence: 17.1%
Identity: 31%
PDB header:viral protein
Chain: F: PDB Molecule:fragment of coat protein vp2;
PDBTitle: interaction of polyomavirus internal protein vp2 with major2 capsid protein vp1 and implications for participation of3 vp2 in viral entry

Phyre2

PDB 1md6 chain A

3D model

Region: 38 - 46
Aligned: 9
Modelled: 9
Confidence: 16.5%
Identity: 67%
Fold: beta-Trefoil
Superfamily: Cytokine
Family: Interleukin-1 (IL-1)

Phyre2

PDB 1afo chain B

3D model

Region: 45 - 57
Aligned: 13
Modelled: 13
Confidence: 13.0%
Identity: 31%
PDB header:integral membrane protein
Chain: B: PDB Molecule:glycophorin a;
PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures

Phyre2

PDB 1kve chain A

3D model

Region: 24 - 55
Aligned: 29
Modelled: 32
Confidence: 12.1%
Identity: 24%
PDB header:toxin
Chain: A: PDB Molecule:smk toxin;
PDBTitle: killer toxin from halotolerant yeast

Phyre2

PDB 3bz1 chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.7%
Identity: 16%
PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii protein y;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer

Phyre2

PDB 3a0b chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.7%
Identity: 16%
PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex

Phyre2

PDB 3a0h chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.7%
Identity: 16%
PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex

Phyre2

PDB 3a0h chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.7%
Identity: 16%
PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex

Phyre2

PDB 3dee chain A

3D model

Region: 18 - 44
Aligned: 27
Modelled: 27
Confidence: 7.5%
Identity: 11%
PDB header:transcription
Chain: A: PDB Molecule:putative regulatory protein;
PDBTitle: crystal structure of a putative regulatory protein involved in2 transcription (ngo1945) from neisseria gonorrhoeae fa 1090 at 2.25 a3 resolution

Phyre2

PDB 3arc chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.3%
Identity: 16%
PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution

Phyre2

PDB 3arc chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.3%
Identity: 16%
PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution

Phyre2

PDB 3a0b chain Y

3D model

Region: 47 - 65
Aligned: 19
Modelled: 19
Confidence: 7.3%
Identity: 16%
PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex

Phyre2
1

c3kdpD_
2

c2z8tX_
3

d8i1ba_
4

d1ilr1_
5

c3a56B_
6

c2wryA_
7

d2ilaa_
8

d1l2ha_
9

c1cn3F_
10

d1md6a_
11

c1afoB_
12

c1kveA_
13

c3bz1y_
14

c3a0by_
15

c3a0hy_
16

c3a0hY_
17

c3deeA_
18

c3arcy_
19

c3arcY_
20

c3a0bY_
21






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3kdpD_



35.5 19 PDB header:hydrolase
Chain: D: PDB Molecule:sodium/potassium-transporting atpase subunit beta-1;
PDBTitle: crystal structure of the sodium-potassium pump
2c2z8tX_



21.5 70 PDB header:hydrolase
Chain: X: PDB Molecule:protein-glutaminase;
PDBTitle: crystal structure of protein-glutaminase of c.proteolyticum2 strain 9670
3d8i1ba_



20.0 33 Fold:beta-Trefoil
Superfamily:Cytokine
Family:Interleukin-1 (IL-1)
4d1ilr1_



19.9 56 Fold:beta-Trefoil
Superfamily:Cytokine
Family:Interleukin-1 (IL-1)
5c3a56B_



19.6 70 PDB header:hydrolase
Chain: B: PDB Molecule:protein-glutaminase;
PDBTitle: crystal structure of pro- protein-glutaminase
6c2wryA_



19.5 56 PDB header:immune system
Chain: A: PDB Molecule:interleukin-1beta;
PDBTitle: crystal structure of chicken cytokine interleukin 1 beta
7d2ilaa_



19.0 22 Fold:beta-Trefoil
Superfamily:Cytokine
Family:Interleukin-1 (IL-1)
8d1l2ha_



18.2 22 Fold:beta-Trefoil
Superfamily:Cytokine
Family:Interleukin-1 (IL-1)
9c1cn3F_



17.1 31 PDB header:viral protein
Chain: F: PDB Molecule:fragment of coat protein vp2;
PDBTitle: interaction of polyomavirus internal protein vp2 with major2 capsid protein vp1 and implications for participation of3 vp2 in viral entry
10d1md6a_



16.5 67 Fold:beta-Trefoil
Superfamily:Cytokine
Family:Interleukin-1 (IL-1)
11c1afoB_



13.0 31 PDB header:integral membrane protein
Chain: B: PDB Molecule:glycophorin a;
PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures
12c1kveA_



12.1 24 PDB header:toxin
Chain: A: PDB Molecule:smk toxin;
PDBTitle: killer toxin from halotolerant yeast
13c3bz1y_



7.7 16 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii protein y;
PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer
14c3a0by_



7.7 16 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex
15c3a0hy_



7.7 16 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex
16c3a0hY_



7.7 16 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of i-substituted photosystem ii complex
17c3deeA_



7.5 11 PDB header:transcription
Chain: A: PDB Molecule:putative regulatory protein;
PDBTitle: crystal structure of a putative regulatory protein involved in2 transcription (ngo1945) from neisseria gonorrhoeae fa 1090 at 2.25 a3 resolution
18c3arcy_



7.3 16 PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution
19c3arcY_



7.3 16 PDB header:electron transport, photosynthesis
Chain: Y: PDB Molecule:protein ycf12;
PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution
20c3a0bY_



7.3 16 PDB header:electron transport
Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12;
PDBTitle: crystal structure of br-substituted photosystem ii complex
21c1w2wA_



not modelled 7.3 36 PDB header:isomerase
Chain: A: PDB Molecule:5-methylthioribose-1-phosphate isomerase;
PDBTitle: crystal structure of yeast ypr118w, a methylthioribose-1-2 phosphate isomerase related to regulatory eif2b subunits

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
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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