SWISS-MODEL Repository - Model Details

Model Overview
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1
1274

Sequence
UniProt P34389
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P34389: 6239.F09G8.4

Domain
Link to: [ InterPro ]
Patched

Model 3D Structure
Model information:
Modelled residue range: 82 to 240
Based on template: [ 3gkj ]  
Sequence Identity [%]: 28%
Model date: 2013-02-20
Revision date: 2013-01-30

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

Ligand information: [details]
Ligands in the template: HC3: 1, NAG: 1.
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                                                          K
3gkjA     23    qscvwygecg iaygdkrync eysgppkplp kdgydlvqel cpgfffg--q
                                                                      
TARGET                                                                
3gkjA             ssssssss ss   sssss ssss  sss      hhhhhh           


TARGET    2     AQVCCTELQL KGMTDRISNA ATILGSCPSC FDNFAKLWCQ FTCSPDQSKF
3gkjA     71    vslccdvrql qtlkdnlqlp lqflsrcpsc fynllnlfce ltcsprqsqf
                                                                      
TARGET                hhhh hhhh   hhh h      hhh hhhhhhhhhh hh       s
3gkjA           sss   hhhh hhhh   hhh hhh    hhh hhhhhhhhhh hh       s


TARGET    52    MKVMETTGP- -------KNV VVKMEFKVNR DFVEGLYESC RHTWFANGLA
3gkjA     121   lqvtatedyv dpvtnqtktn vkelqyyvgq sfanamynac rdveapssnd
                                                                      
TARGET          sssssss             s ssssssssss hhhhhhhh             
3gkjA           ssssssssss s    sssss ssssssssss hhhhhhhhhh h         


TARGET    94    LRLMSLGGK- ---VSFENFY GFMGTKNLAQ ----SIPINT EFQFSRMKNA
3gkjA     171   kalgllcgkd adacqatnwi eymfnkdngq apftitpvfs dfpvhgme-p
                                                                      
TARGET            hh            hhhhh hhhh            sssss           
3gkjA             hh            hhhhh hhhh            sssss           


TARGET    136   MNIPTTPCHK SAGPKVPACG AIDC ---                        
3gkjA     220   mnnatkgcde svdevtapcs cqdcsivc                        
                                                                      
TARGET                                                                
3gkjA

Quality 


Template's ligands section 
Ligands in the template: HC3: 1, NAG: 1. 
Ligands in the template that will be assessed: NAG3. 
Model's ligands section 
NAG3 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand A.NAG3 will not be included in the model. 
NAG3: conservation:False, RMSD:False, included: False 
 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3gkj 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: 3gkj.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 28.000) 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:970852ff0801adc4bf2b0890450ef91f on BC2-cluster at Wed Feb 20 08:25:46
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
 - 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 3gkjA (82-240) was successful 
 -     ************
 - building model based on 3qntA (56-240) 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:970852ff0801adc4bf2b0890450ef91f on BC2-cluster at Wed Feb 20 08:27:59
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.
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