SWISS-MODEL Repository - Model Details

Model Overview
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1
1170

Sequence
UniProt Q12200
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q12200: 4932.YPL006W

Domain
Link to: [ InterPro ]
Patched

Model 3D Structure
Model information:
Modelled residue range: 23 to 240
Based on template: [ 3qnt ]  
Sequence Identity [%]: 28%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3qnt): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: NAG: 2.
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                   CAMYGNC GKKSVFGNEL PCPVPRSFEP PVLSDETSKL
3qntA     22    epyttihqpg y--cafydec gknp----el sgslmtlsnv sclsntpark
                                                                      
TARGET                         ssssss                     s ssss    ss
3qntA                    s s  sssssss                     s ssss sssss


TARGET    38    L--------V EVCGEEWKE- VRYACCTKDQ VVALRDNLQK AQPLISSCPA
3qntA     66    itgdhlillq kicprlytgp ntqaccsakq lvsleaslsi tkalltrcpa
                                                                      
TARGET          s                      sss   hhh hhhhhhhhhh hhh     hh
3qntA           s   hhhhhh hh          sss    hh hhhhhhhhhh hhh     hh


TARGET    79    CLKNFNNLFC HFTCAADQGR FVNITKVEKS KEDKD-IVAE LDVFMNSSWA
3qntA     116   csdnfvnlhc hntcspnqsl finvtrvaql gagqlpavva yeafyqhsfa
                                                                      
TARGET          hhhhhhhhhh hh         ssssssssss    ss ssss ssssssshhh
3qntA           hhhhhhhhhh hhh        ssssssss        sssss ssssssshhh


TARGET    128   SEFYDSCKNI KFSATNGYAM DLIG----GG AKNYSQFLKF LGDAKPMLGG
3qntA     166   eqsydscsrv rvpaaatlav gtmcgvygsa lcnaqrwlnf qgdtgn--gl
                                                                      
TARGET          hhhhh               h h             hhhhhhh h         
3qntA           hhhhhhh             h h             hhhhhhh h         


TARGET    174   SPFQINYKYD LANEE--KEW QEFNDEVYAC DDA----QYK CACSDCQESC
3qntA     214   aplditfhll epgqavgsgi qplnegvarc nesqgddvat cscqdcaasc
                                                                      
TARGET             sssssss                                            
3qntA              sssssss   hh                                       


TARGET    218   P                                                     
3qntA     264   pa                                                    
                                                                      
TARGET                                                                
3qntA

Quality 


Template's ligands section 
Ligands in the template: NAG: 2. 
Ligands in the template that will be assessed: NAG1, NAG2. 
Model's ligands section 
NAG1 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.NAG1 will not be included in the model. 
NAG1: conservation:False, RMSD:False, included: False 
 
NAG2 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.NAG2 will not be included in the model. 
NAG2: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3qnt 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: 3qnt.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 28.992) to infer a conservation of the oligomeric state 
 Please use the advancend features of the SwissModel Project Mode 
       
 The target structure was calculated as SINGLE CHAIN

Template Selection 
 - Start SMR-Pipeline for:1e045e3d25a8fa813d2e92171304192d on BC2-cluster at Mon Feb 18 15:18:53
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 D found
 - No template with E found
 - No template with D found
 - No template with E found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with D found
 - No template with E found
 - No template with D found
 - No template with E found
 - No template with D found
 - No template with E found
 - Warning: Oligomer Prediction was not successfull!

 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -   ***************
 - building model based on 3qntA (23-240) was successful 
 -                                                                      **********
 - building model based on 2v50E (1002-1152) 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:1e045e3d25a8fa813d2e92171304192d on BC2-cluster at Mon Feb 18 15:21:11
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.