Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionC1P611
DateWed Jan 25 15:20:06 GMT 2012
Unique Job ID8351749dbbfae35f

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1dfwA_
Top template information
PDB header:immune system
Chain: A: PDB Molecule:lung surfactant protein b;
PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir)
Confidence and coverage
Confidence: 37.7% Coverage: 46%
12 residues ( 46% of your sequence) have been modelled with 37.7% 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......
Sequence  MTDCRYLIKRVIKIIIAVLQLILLFL
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 1dfw chain A

3D model

Region: 4 - 15
Aligned: 12
Modelled: 12
Confidence: 37.7%
Identity: 58%
PDB header:immune system
Chain: A: PDB Molecule:lung surfactant protein b;
PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir)

Phyre2

PDB 1ssz chain A

3D model

Region: 4 - 15
Aligned: 12
Modelled: 12
Confidence: 22.8%
Identity: 58%
PDB header:surface active protein
Chain: A: PDB Molecule:pulmonary surfactant-associated protein b;
PDBTitle: conformational mapping of mini-b: an n-terminal/c-terminal2 construct of surfactant protein b using 13c-enhanced3 fourier transform infrared (ftir) spectroscopy

Phyre2

PDB 3lbw chain C

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 20.6%
Identity: 56%
PDB header:transport protein
Chain: C: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2

Phyre2

PDB 3lbw chain B

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 20.6%
Identity: 56%
PDB header:transport protein
Chain: B: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2

Phyre2

PDB 3lbw chain D

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 20.6%
Identity: 56%
PDB header:transport protein
Chain: D: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2

Phyre2

PDB 3lbw chain A

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 20.6%
Identity: 56%
PDB header:transport protein
Chain: A: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2

Phyre2

PDB 3c9j chain C

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 16.3%
Identity: 56%
PDB header:membrane protein
Chain: C: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex

Phyre2

PDB 3c9j chain B

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 16.3%
Identity: 56%
PDB header:membrane protein
Chain: B: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex

Phyre2

PDB 3c9j chain A

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 15.7%
Identity: 56%
PDB header:membrane protein
Chain: A: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex

Phyre2

PDB 3c9j chain D

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 14.8%
Identity: 56%
PDB header:membrane protein
Chain: D: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex

Phyre2

PDB 1nyj chain D

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:viral protein
Chain: D: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy

Phyre2

PDB 1nyj chain B

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:viral protein
Chain: B: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy

Phyre2

PDB 2kqt chain B

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:transport protein
Chain: B: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine

Phyre2

PDB 1mp6 chain A

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:membrane protein
Chain: A: PDB Molecule:matrix protein m2;
PDBTitle: structure of the transmembrane region of the m2 protein h+2 channel by solid state nmr spectroscopy

Phyre2

PDB 1nyj chain A

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:viral protein
Chain: A: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy

Phyre2

PDB 1nyj chain C

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:viral protein
Chain: C: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy

Phyre2

PDB 2kqt chain D

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:transport protein
Chain: D: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine

Phyre2

PDB 2kqt chain C

3D model

Region: 11 - 26
Aligned: 16
Modelled: 16
Confidence: 6.3%
Identity: 50%
PDB header:transport protein
Chain: C: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine

Phyre2
1

c1dfwA_
2

c1sszA_
3

c3lbwC_
4

c3lbwB_
5

c3lbwD_
6

c3lbwA_
7

c3c9jC_
8

c3c9jB_
9

c3c9jA_
10

c3c9jD_
11

c1nyjD_
12

c1nyjB_
13

c2kqtB_
14

c1mp6A_
15

c1nyjA_
16

c1nyjC_
17

c2kqtD_
18

c2kqtC_



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1dfwA_



37.7 58 PDB header:immune system
Chain: A: PDB Molecule:lung surfactant protein b;
PDBTitle: conformational mapping of the n-terminal segment of2 surfactant protein b in lipid using 13c-enhanced fourier3 transform infrared spectroscopy (ftir)
2c1sszA_



22.8 58 PDB header:surface active protein
Chain: A: PDB Molecule:pulmonary surfactant-associated protein b;
PDBTitle: conformational mapping of mini-b: an n-terminal/c-terminal2 construct of surfactant protein b using 13c-enhanced3 fourier transform infrared (ftir) spectroscopy
3c3lbwC_



20.6 56 PDB header:transport protein
Chain: C: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2
4c3lbwB_



20.6 56 PDB header:transport protein
Chain: B: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2
5c3lbwD_



20.6 56 PDB header:transport protein
Chain: D: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2
6c3lbwA_



20.6 56 PDB header:transport protein
Chain: A: PDB Molecule:m2 protein;
PDBTitle: high resolution crystal structure of transmembrane domain of m2
7c3c9jC_



16.3 56 PDB header:membrane protein
Chain: C: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex
8c3c9jB_



16.3 56 PDB header:membrane protein
Chain: B: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex
9c3c9jA_



15.7 56 PDB header:membrane protein
Chain: A: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex
10c3c9jD_



14.8 56 PDB header:membrane protein
Chain: D: PDB Molecule:proton channel protein m2, transmembrane segment;
PDBTitle: the crystal structure of transmembrane domain of m2 protein and2 amantadine complex
11c1nyjD_



6.3 50 PDB header:viral protein
Chain: D: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy
12c1nyjB_



6.3 50 PDB header:viral protein
Chain: B: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy
13c2kqtB_



6.3 50 PDB header:transport protein
Chain: B: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine
14c1mp6A_



6.3 50 PDB header:membrane protein
Chain: A: PDB Molecule:matrix protein m2;
PDBTitle: structure of the transmembrane region of the m2 protein h+2 channel by solid state nmr spectroscopy
15c1nyjA_



6.3 50 PDB header:viral protein
Chain: A: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy
16c1nyjC_



6.3 50 PDB header:viral protein
Chain: C: PDB Molecule:matrix protein m2;
PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy
17c2kqtD_



6.3 50 PDB header:transport protein
Chain: D: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine
18c2kqtC_



6.3 50 PDB header:transport protein
Chain: C: PDB Molecule:m2 protein;
PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine

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