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Model Overview
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1
172

Sequence
UniProt Q12184
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q12184: 4932.YPL252C

Domain
Link to: [ InterPro ]
Fer2

Model 3D Structure
Model information:
Modelled residue range: 61 to 160
Based on template: [ 2wlb ]  
Sequence Identity [%]: 59%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (2wlb): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: FES: 1.
Ligands in the model: FES: 1
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        LKITFIL KDGSQKTYEV CEGETILDIA QGHNLDMEGA CGGSCACSTC
2wlbB     518   g--ikvffvt pegreimieg negdsildla hannidlega cegsvacstc
                                                                      
TARGET             sssssss    sssssss    ssshhhh hh                  s
2wlbB              sssssss    sssssss    ssshhhh hh                  s


TARGET    48    HVIVDPDYYD ALPEPEDDEN DMLDLAYGLT ETSRLGCQIK MSKDIDGIRV
2wlbB     566   hvivdpehye lldppeedee dmldlafgle etsrlgcqvl lrkdldgirv
                                                                      
TARGET          ssssshhhhh h     hhhh hhhhh       sssss  ss s      sss
2wlbB           ssssshhhhh       hhhh hhhhh       sssss  ss s      sss


TARGET    98    ALP                                                   
2wlbB     616   rip-                                                  
                                                                      
TARGET          s                                                     
2wlbB           s

Quality 


Template's ligands section 
Ligands in the template: FES: 1. 
Ligands in the template that will be assessed: FES619. 
Model's ligands section 
FES619 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.060 
Given the properties calculated previously, the ligand B.FES619 will be included in the model. 
FES619: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 2wlb 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: 2wlb.pdb2.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 0.442 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:f71029af371e1dd5cebf383035b15740 on BC2-cluster at Mon Feb 18 18:39:44
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 A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with A found
 - No template with B found
 - No template with A 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 2wlbB (61-160) 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:f71029af371e1dd5cebf383035b15740 on BC2-cluster at Mon Feb 18 18:41:10
2013

no data available!
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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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