SWISS-MODEL Repository - Model Details

Model Overview
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1
244

Sequence
UniProt Q9TYK1
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9TYK1: 6239.Y66H1A.4.2

Domain
Link to: [ InterPro ]
Gar1

Model 3D Structure
Model information:
Modelled residue range: 56 to 147
Based on template: [ 3u28 ]  
Sequence Identity [%]: 52%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3u28): HETERO TRIMER
Model built :SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1     PPEEVVLVGV FSHQCQDDIV CNNTSGKIPY FNAPIYFKNK EQVGKIDEIF
3u28C     33    ppdtvlemga flhpcegdiv crsintkipy fnapiylenk tqvgkvdeil
                                                                      
TARGET               sssss sssss  sss ssss   sss   sssss    ssssssssss
3u28C                sssss sssss  sss ssss   sss   sssss    ssssssssss


TARGET    51    GSPGENGFSV TLSQGVKASS FEPESQLYID PGKLLPVDRF LP        
3u28C     83    gplnevffti kcgdgvqats fkegdkfyia adkllpierf lp-       
                                                                      
TARGET          ss  ssssss sss            sssss    sss                
3u28C           ss  ssssss sss            sssss    sss  hh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3u28 is annotated as HETERO TRIMER 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 3u28.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3u28_1

Template Selection 
 - Start SMR-Pipeline for:5896085084cba7d6352edd4ba6cf1630 on BC2-cluster at Wed Feb 20 22:42:04
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with D found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                   ******************************
 - building model based on 3u28C (56-147) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:5896085084cba7d6352edd4ba6cf1630 on BC2-cluster at Wed Feb 20 22:42:48
2013

no data available!
Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.