SWISS-MODEL Repository - Model Details

Model Overview
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1
464

Sequence
UniProt Q03557
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q03557: 4932.YMR293C

Domain
Link to: [ InterPro ]
Amidase

Model 3D Structure
Model information:
Modelled residue range: 44 to 195
Based on template: [ 1ock ]  
Sequence Identity [%]: 41%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1ock): DIMER
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 

                                                       
1ockB     1     misladlqrr ietgelspna aiaqshaaie arekevhafv rhdksaraqa
                                                                      
                                                       
1ockB              hhhhhhh hh     hhh hhhhhhhhhh        sss sss       


TARGET    1          LTGCV ASIKDNIVTK DFPTTCASHI LENFKSPFDA TVVKLLKQAG
1ockB     51    sgp--lrgia vgikdiidta nmptemgsei yrgwqprsda pvvmmlkrag
                                                                      
TARGET                  ss ssssssss                         hhhhhhhhh 
1ockB                   ss ssssssss                         hhhhhhhh  


TARGET    46    VHILGKTNLD EFGMGSGGVH SIRGPVINPL YPHEDKKIMG GSSSGAAASV
1ockB     99    atiigktttt af-------- asrdptat-l nphntghspg gsssgsaaav
                                                                      
TARGET           ssssss  s ssss  ssss s                        hhhhhhh
1ockB            sssssss                              sss      hhhhhhh


TARGET    96    ACDLVDFALG TDTGGSVRLP ACYGSVLGFK PSYGRLSRFG VIAYSQSLDT
1ockB     140   gagmiplalg tqtggsvirp aaycgtaaik psfrmlptvg vkcyswaldt
                                                                      
TARGET          h     ssss ss     hhh hhhh  sss           s ss       s
1ockB           h     ssss ss     hhh hhhh  ssss          s ss       s


TARGET    146   VGILSKK -- ---------- ---------- ---------- ----------
1ockB     190   vglfgaraed largllamtg rsefsgivpa kaprigvvrq efagavepaa
                                                                      
TARGET          sssss                                                 
1ockB           sssss  hhh hhhhhhhhh               ssssss           hh


TARGET          ---------- ---------- ---------- ---------- ----------
1ockB     240   eqglqaaika aeragasvqa idlpeavhea wrihpiiqdf eahralawef
                                                                      
TARGET                                                                
1ockB           hhhhhhhhhh hhhh  ssss s   hhhhhh h   hhhhhh hhhh   hhh


TARGET          ---------- ---------- ---------- ---------- ----------
1ockB     290   sehhdeiapm lrasldatvg ltpkeydear rigrrgrrel gevfegvdvl
                                                                      
TARGET                                                                
1ockB           hh      hh hhhhhhh      hhhhhhhh hhhhhhhhhh hhhh    ss


TARGET          ---------- ---------- ---------- ---------- ----------
1ockB     340   ltysapgtap akalastgdp rynrlwtlmg npcvnvpvlk vgglpigvqv
                                                                      
TARGET                                                                
1ockB           ss       s ss             hhhhh   sssssssss s  sssssss


TARGET          ---------- ---------- ---                             
1ockB     390   iarfgndaha latawfleda lak                             
                                                                      
TARGET                                                                
1ockB           ss    hhhh hhhhhhhhhh hh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 1ock is annotated as DIMER 
 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: 1ock.pdb1.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 (=DIMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.038 (>0.5 indicates similarity) 
 To build the complex the following chains of the complex has been additionally identified: 1ockA

Template Selection 
 - Start SMR-Pipeline for:fa642809d13b522d530cd0625956c27e on BC2-cluster at Mon Feb 18 17:40:07
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 C found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with O found
 - No template with Q found
 - No template with R found
 - No template with B found
 - No template with C found
 - No template with T found
 - No template with U found
 - No template with E found
 - No template with F found
 - No template with W found
 - No template with X found
 - No template with H found
 - No template with I found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with F found
 - No template with G found
 - No template with I found
 - No template with J found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with T found
 - No template with U found
 - No template with E found
 - No template with F found
 - No template with W found
 - No template with X found
 - No template with H found
 - No template with I found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with O found
 - No template with Q found
 - No template with R found
 - No template with H found
 - No template with I found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with O found
 - No template with Q found
 - No template with R found
 - No template with B found
 - No template with C found
 - No template with T found
 - No template with U found
 - No template with E found
 - No template with F found
 - No template with W found
 - No template with X found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -         **************************
 - building model based on 1ockB (44-195) was successful 
 -         ***********************************************************************
 - building model based on 3kfuE (44-457) was successful 
 -  ******************************************************************************
 - building model based on 3h0lA (3-457) 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:fa642809d13b522d530cd0625956c27e on BC2-cluster at Mon Feb 18 17:47:26
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.