SWISS-MODEL Repository - Model Details

Model Overview
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1
547

Sequence
UniProt Q09316
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q09316: 6239.F25B5.5

Domain
Link to: [ InterPro ]
UPF0004
TRAM
Radical_SAM

Model 3D Structure
Model information:
Modelled residue range: 238 to 495
Based on template: [ 2qgq ]  
Sequence Identity [%]: 22%
Model date: 2013-02-20
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2qgq): MONOMER
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          YCVVP FTRGRERSRP IESIVEEVQR LRDQGYKQVT LLGQNVNSYR
2qgqD     136   erp--yayvk isdgslrsrs ieditreved llkegkkeii lvaqdttsy-
                                                                      
TARGET                ssss sss   sss  hhhhhhhhhh hhhh  ssss ss        
2qgqD             s  sssss sss   sss  hhhhhhhhhh hhh   ssss ss        


TARGET    46    DMTSMDFSMA PSTSQEDRVP GFKTVYKPKS GGLTFTTLLE KVADAAPDIR
2qgqD     198   ---gid---- ---------- ----lyrkqa ----lpdllr rlnslngefw
                                                                      
TARGET             sssssss sss   ssss ssssss          hhhhh hhh      s
2qgqD               hh                    hh         hhhhhh hhh      s


TARGET    96    FRFTSPHPKD FPMQLIELIA SRPNLCKQLH LPAQSGDDET LERMERGYTR
2qgqD     223   irvxylhpdh lteeiisaxl eldkvvkyfd vpvqhgsdki lklxgrtkss
                                                                      
TARGET          ssss         hhhhhhhh h     ssss s      hhh hhhh     h
2qgqD           ssss         hhhhhhhh h     ssss s      hhh hhhh     h


TARGET    146   DLYLRLVDDI RHVLPSVSLT SDFIAGFCGE TEQAHQNTLS LIRAVRYSFC
2qgqD     273   eelkkxlssi rerfpdavlr tsiivgfpge teedfeelkq fveeiqfdkl
                                                                      
TARGET          hhhhhhhhhh hhh    sss sssss       hhhhhhhhh hhhhh   ss
2qgqD           hhhhhhhhhh hhh    sss sssss       hhhhhhhhh hhhhh   ss


TARGET    196   FVFPYSMRGK TRAHHRLTDD VPEDVKARRH LDLTTVFREE ALKLNQALIG
2qgqD     323   gafvys---- --------dk vdpexakrrq eellllqaei snsrldrfvg
                                                                      
TARGET          sssss hhhh h            hhhhhhhh hhhhhhhhhh hhhhhhh   
2qgqD           sssss                   hhhhhhhh hhhhhhhhhh hhhhhhh   


TARGET    246   SEQTVLLEGK SKR ------ ---------- ---------- ----------
2qgqD     372   kklkflvegk egkflvgrtw teapevdgvv fvrgkgkigd flevvikehd
                                                                      
TARGET                                                                
2qgqD           ssssssssss s ssssssss         ss ssss     s ssssssssss


TARGET          ---------                                             
2qgqD     422   eydxwgsvi                                             
                                                                      
TARGET                                                                
2qgqD             sssssss

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2qgq is annotated as MONOMER 
 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: 2qgq.pdb4.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 (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.382 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:9284c31a2c98181dbab8e5eb857e909e on BC2-cluster at Wed Feb 20 16:25:28
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
 - 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 2qgqD (238-495) 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:9284c31a2c98181dbab8e5eb857e909e on BC2-cluster at Wed Feb 20 16:27:35
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.