SWISS-MODEL Repository - Model Details

Model Overview
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1
165

Sequence
UniProt Q9U616
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9U616: 7227.FBpp0078066

Domain
Link to: [ InterPro ]
GCV_H

Model 3D Structure
Model information:
Modelled residue range: 42 to 158
Based on template: [ 1hpc ]  
Sequence Identity [%]: 47%
Model date: 2013-02-22
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1hpc): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: LPA: 1.
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              R YTNKHEWVEV VSGSNAIVGI SSYAQEALGD VVFAQLPEPG
1hpcB     1     snvldgl--k yapshewvkh -egsvatigi tdhaqdhlge vvfvelpepg
                                                                      
TARGET                   s ss  sssss       sssss shhhhhhh s sssss     
1hpcB                    s ss  ssssss  s  ssssss shhhhhhh s sssss     


TARGET    42    TELKQDDECG ALESVKAASE VYSPVSGKVI EKNAEVEDTP ALVNSSCYEK
1hpcB     48    vsvtkgkgfg avesvkatsd vnspisgevi evntgltgkp glinsspyed
                                                                      
TARGET          sss   ssss sssss ssss sss  sssss sss hhh    hhhhh     
1hpcB           sss   ssss sssss ssss sss  sssss sss hhh    hhhhh     


TARGET    92    GWLFKVDLKN PKELEALMTE DQYKAF --- ----                 
1hpcB     98    gwmikikpts pdelesllga keytkfceee daah                 
                                                                      
TARGET            sssssss   hhhh    h hhhhhh                          
1hpcB             sssssss   hhhh    h hhhhhhhhhh h

Quality 


Template's ligands section 
Ligands in the template: LPA: 1. 
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 1hpc is annotated as MONOMER 
 PISA was used to annotate the quaternary structure, because the author assignment was 
 PISA annotates this structure as Monomer, therefore the corresponding PDB chain was used as template structure 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.29 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:93fa99466566319b3882264d4720d508 on BC2-cluster at Fri Feb 22 11:32:00
2013 


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

FATAL - No A3m found

 - 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 B found
 - No template with A found
 - No template with C found
 - No template with A found
 - No template with A found
 - No template with B found
 - 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 3klrA (41-161) was not successful go to next best template
 -                     ***********************************************************
 - building model based on 2edgA (41-161) was not successful go to next best template
 -                     *********************************************************
 - building model based on 1hpcB (42-158) 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:93fa99466566319b3882264d4720d508 on BC2-cluster at Fri Feb 22 11:33:12
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.