SWISS-MODEL Repository - Model Details

Model Overview
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1
181

Sequence
UniProt P34605
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P34605: 6239.ZK1098.5

Domain
Link to: [ InterPro ]
TRAPP

Model 3D Structure
Model information:
Modelled residue range: 14 to 167
Based on template: [ 1sz7 ]  
Sequence Identity [%]: 50%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1sz7): DIMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: PLM: 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       KMSAELFC LTYGAMVTEM LKDYEDPKDV TIQLDKMGFN MGTRLADDFL
1sz7A     13      kmsselft ltygalvtql ckdyendedv nkqldkmgfn igvrliedfl
                                                                      
TARGET                hhhh hhhhhhhhhh hhh   hhhh hhhhhhhhhh hhhhhhhhhh
1sz7A                 hhhh hhhhhhhhhh hhh   hhhh hhhhhhhhhh hhhhhhhhhh


TARGET    49    AKNANVPRCV DTRQIADVLC RNAIPCYLGI SATASSWTSG DREFTITLEA
1sz7A     61    ar-snvgrch dfretadvia kvafkmylgi tpsitnwspa gdefslilen
                                                                      
TARGET          h           hhhhhhhhh    hhhh      sss       sssssss  
1sz7A           hh          hhhhhhhhh hhhhhhh      sss       sssssss  


TARGET    99    NPLTELVQVP AHLVSAGLSY SQLIAGAIRG ALEAVHFKVY ASA-TDT---
1sz7A     110   nplvdfvelp dn--hssliy snllcgvlrg alemvqmave akfvqdtlkg
                                                                      
TARGET                                  hhhhhhhh hhh    sss ss        
1sz7A                                   hhhhhhhh hhh  sssss ssss      


TARGET    145   GANTEIRIRF  ---                                       
1sz7A     158   dgvteirmrf irri                                       
                                                                      
TARGET             sssssss                                            
1sz7A              sssssss ssss

Quality 


Template's ligands section 
Ligands in the template: PLM: 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 
 1sz7 is annotated as DIMER 
 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: 1sz7.pdb1.gz 
      
 
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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.194 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:e0f358bda2ffc4050beff0a24c3bc0b8 on BC2-cluster at Wed Feb 20 10:44:40
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 M found
 - No template with N found
 - No template with O found
 - No template with R found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with F found
 - No template with S found
 - No template with T found
 - No template with U found
 - No template with X found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with L found
 - No template with D found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with F found
 - No template with C found
 - No template with C found
 - No template with B found
 - No template with D 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 1sz7A (14-167) 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:e0f358bda2ffc4050beff0a24c3bc0b8 on BC2-cluster at Wed Feb 20 10:45:53
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.