SWISS-MODEL Repository - Model Details

Model Overview
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1
278

Sequence
UniProt P91353
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P91353: 6239.F59A3.3

Domain
Link to: [ InterPro ]
KOW

Model 3D Structure
Model information:
Modelled residue range: 104 to 190
Based on template: [ 3j21 ]  
Sequence Identity [%]: 19%
Model date: 2013-02-21
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3j21U): Unknown
Model: 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                                                   DTEWTFFP
3j21U     1     mkisskqprk qrkflynapl hvrqklmsap lsrelrekyk --vrnlpvrv
                                                                      
TARGET                                                                
3j21U                  hhh hhhhhh     hhhhhh  ss s hhhhhhh     sss    


TARGET    9     GDLVQVMVGK DKGRQGLVLT TSRDSSDVIV DGLHTKLGED MEGSEKLGVD
3j21U     49    gdkvrimrgd ykghegkvve vdlkryriyv egatlrktn- ----------
                                                                      
TARGET             ssss       ssssss          ss s sss            hhhh
3j21U              ssss       sssssss ss    ssss s sssss              


TARGET    59    KTLRWQEQPL SVSKKQVMLV DPNDEQPCE  --------             
3j21U     88    gt--evfypi hp--snvmii elnledekrk kiierrag             
                                                                      
TARGET          hh   sss        sss                                   
3j21U            s  ssss        sss         hhhh hhh

Quality 


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

 
Sorry, we haven't found any oligomeric annotation for this template. 
 Either the complex was too large (>60 chains) or the structures was excluded for other reasons. 
 Please contact help@swissmodel.org for more information!

Template Selection 
 - Start SMR-Pipeline for:9c38fbad69cf4ddf2bd1e4b1ca0defbd on BC2-cluster at Thu Feb 21 05:58:51
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: 
 - 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 3j21U (104-190) 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:9c38fbad69cf4ddf2bd1e4b1ca0defbd on BC2-cluster at Thu Feb 21 05:59:37
2013


Template Description
Match Chain SeqId

3j21: PROMISCUOUS BEHAVIOR OF PROTEINS IN ARCHAEAL RIBOSOMES REVCRYO-EM: IMPLICATIONS FOR EVOLUTION OF EUKARYOTIC RIBOSOMRIBOSOMAL PROTEINS)
Solved by: X-RAY, Resolution: 6.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

104-190 3j21U 20%
[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.
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