SWISS-MODEL Repository - Model Details

Model Overview
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1
423

Sequence
UniProt P34223
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P34223: 4932.YBL058W

Domain
Link to: [ InterPro ]
UBX
SEP

Model 3D Structure
Model information:
Modelled residue range: 306 to 421
Based on template: [ 1s3s ]  
Sequence Identity [%]: 36%
Model date: 2013-02-19
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1s3s): HETERO OCTAMER
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       FSGQGQRL GSPIPGE--- SSPAEVPKNE TPAAQEQPMP DNEPKQGDTS
1s3sG     253     ftgegqkl gstapqvlnt sspaqqaene akasssilin eaept---tn
                                                                      
TARGET                                  hhhhhhhh hhhhh                
1s3sG                                   hhhhhhhh hhhhh                


TARGET    46    IQIRYANGKR EVLHCNSTDT VKFLYEHVTS NANTDPSRNF TLNYAFPIKP
1s3sG     298   iqirladggr lvqkfnhshr isdirlfivd arpamaatsf vlmttfpnke
                                                                      
TARGET          sssss    s ssss       hhhhhhhhhh    hhh     ssss    ss
1s3sG           sssss    s ssss       hhhhhhhhhh    hhh  ss ssss    ss


TARGET    96    ISNDETTLKD ADLLNSVVVQ R -                             
1s3sG     348   ladenqtlke anllnavivq rlt                             
                                                                      
TARGET          s      hhh h      sss s                               
1s3sG           s      hhh h      sss sss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1s3s is annotated as HETERO OCTAMER 
 PISA was used to annotate the quaternary structure, because the author assignment was 
  The template was built based on the following PISA annotation file: 1s3s_assembly.xml.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 1s3s_1

Template Selection 
 - Start SMR-Pipeline for:51cff1ece9504485c3897f0c5310d613 on BC2-cluster at Mon Feb 18 23:59:02
2013 


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

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with A found
 - No template with C found
 - No template with B found
 - No template with E found
 - No template with D found
 - No template with F found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                           **********************
 - building model based on 1s3sG (306-421) was successful 
 -                                           ******************
 - building model based on 1ss6A (223-318) was successful 
 -  ********
 - building model based on 4gewA (3-46) 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:51cff1ece9504485c3897f0c5310d613 on BC2-cluster at Tue Feb 19 00:00:29
2013


Template Description
Match Chain SeqId

4gew: CRYSTAL STRUCTURE OF TDP2 FROM C. ELEGANS
Solved by: X-RAY, Resolution: 2.35A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-46 4gewA 26%
[Model]

4f1i: CRYSTAL STRUCTURE OF SEMET TDP2 FROM CAENORHABDITIS ELEGAN
Solved by: X-RAY, Resolution: 2.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-46 4f1iA 26%
[Model]

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.