SWISS-MODEL Repository - Model Details

Model Overview
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1
539

Sequence
UniProt Q03761 Transcription initiation factor TFIID subunit 12 (TAFII-61)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
Q03761: 4932.YDR145W

Domain
Link to: [ InterPro ]
TFIID_20kDa

Model 3D Structure
Model information:
Modelled residue range: 414 to 490
Based on template: [ 1h3o ]  
Sequence Identity [%]: 50%
Model date: 2014-07-16
Revision date: 2014-07-15

Quaternary structure information: [details]
Template (1h3o): HETERO 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 ]

Alignment

TARGET    1         VMSKRK LRELVKTVGI DEGDGETVID GDVEELLLDL ADDFVTNVTA
1h3oD     55    hx--vltkkk lqdlvrevdp neq-----ld edveexllqi addfiesvvt
                                                                      
TARGET                 hhh hhhhh                 hhhhhhhhhh hhhhhhhhhh
1h3oD                  hhh hhhhh                 hhhhhhhhhh hhhhhhhhhh


TARGET    47    FSCRLAKHRK SDNLEARDIQ LHLERNWNIR I                    
1h3oD     98    aacqlarhrk sstlevkdvq lhlerqwnxw i-                   
                                                                      
TARGET          hhhhhhhh         hhhh hhhhhh                          
1h3oD           hhhhhhhh         hhhh hhhhhh                          



Quality


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


Quaternary Structure Annotation of the Template
1h3o is annotated as HETERO 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: 1h3o.pdb2.gz

Quaternary Structure Modelling of the Target Protein
1h3o_2


Template Selection
 - Start SMR-Pipeline for:a259d56b4d9b672961da050cf132de85 on BC2-cluster at Wed Jul 16 15:48:12
2014 


 - 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 - make sure all DBs are sync'ed correctly
 - No template with C found
 - No template with A found
 - Warning: Oligomer Prediction was not successfull!

 - 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 1h3oD (414-490) 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:a259d56b4d9b672961da050cf132de85 on BC2-cluster at Wed Jul 16 15:48:53
2014 



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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