SWISS-MODEL Repository - Model Details

Model Overview
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1
433

Sequence
UniProt P39786
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Terminase_3

Model 3D Structure
Model information:
Modelled residue range: 238 to 412
Based on template: [ 2wbn ]  
Sequence Identity [%]: 27%
Model date: 2011-04-15
Revision date: 2011-04-14

Quaternary structure information: [details]
NA

Ligand information: [details]
NA
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

This model has not been updated since 2011-04-14. 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    238      RVLPQFE VLPHDQVKKC IAAISKPIFR TGMDFGFEES YNAVVRLAVD
2wbnA     237   v--vpfenlq ieegiitdae varfdn--ir qgldfgygpd plafvrwhyd
                                                                      
TARGET                 sss ss     hhh hhhh     s ssss        sssssssss
2wbnA                  sss ss     hhh hhh  s  ss ssss        sssssssss


TARGET    285   PEKKYLYIYW EYYQNKMTDD RTAEELREFI ETQELIKADS AEPKSIQYFR
2wbnA     283   krknriyaid elvdhkvslk rtadfvrknk yesariiads seprsidalk
                                                                      
TARGET          s  sssssss ssss    hh hhhhhhhhh       ssss    hhhhhhhh
2wbnA           s  sssssss ssss    hh hhhhhhhhh       ssss    hhhhhhhh


TARGET    335   -QQGFR-MVG ARKFPGSRLQ YTKKVKRFKK IFCS-DRCEN VIYELETLTY
2wbnA     333   lehginrieg akkgpdsveh gerwldelda ividplrtpn iarefenidy
                                                                      
TARGET                  ss s      hhh hhhhhh   s sss     hh hhhhhhh ss
2wbnA           h     ssss s       hh hhhhhh   s sss     hh hhhhhhh ss


TARGET    382   AKDKNGALIE DEFTIDPHTL SAIWYALDDY E                    
2wbnA     383   qtdkngdpip rledkdnhti datryaferd xk                   
                                                                      
TARGET          sss   sss  sss    hhh hhhhhh                          
2wbnA           sss   sss  sss    hhh hhhhh   h

Quality


no data available!

no data available!
Template Selection 
 - Start SMR-Pipeline for:a1ad0a69c7cb31caf0624ff806194a37 on BC2-cluster at Thu Apr 14 22:18:56
2011 


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

 - Run HHSearch to detect more templates...
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old4 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                             ********************************
 - building model based on 2wbnA (238-412) was successful 
 -  ****************************
 - building model based on 3b85A (3-153) was successful 
 -  **************************************************************************
 - building model based on 3cpeA (5-405) 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:a1ad0a69c7cb31caf0624ff806194a37 on BC2-cluster at Thu Apr 14 22:20:40
2011


Template Description
Match Chain SeqId

2wbn:
Not available
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

238-412 2wbnA 28%
[Model]

3b85:
Not available
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

3-153 3b85B 14%
[Model]
3-153 3b85A 15%
[Model]
3-153 3b85B 14%
[Model]
3-153 3b85A 15%
[Model]
3-153 3b85B 14%
[Model]

3cpe:
Not available
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

5-405 3cpeA 9%
[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.