SWISS-MODEL Repository - Model Details

Model Overview
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Sequence
UniProt Q95Q95 Target of rapamycin homolog (CeTOR)
Caenorhabditis elegans.
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

Domain
Link to: [ InterPro ]
PI3_PI4_kinase
FAT
FATC
Rapamycin_bind
DUF3385

Model 3D Structure
Model information:
Modelled residue range: 2189 to 2287
Based on template: [ 1fap ]  
Sequence Identity [%]: 48%
Model date: 2014-07-16
Revision date: 2014-07-15

Quaternary structure information: [details]
Template (1fap): 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       RCAILWHE QWHDALDDAS RVYFHRRLQD NNVQAMFDAL RNMNDLMQKG
1fapB     2018    rvailwhe mwhegleeas rlyfger--- -nvkgmfevl eplhammerg
                                                                      
TARGET                 hhh hhhhhhhhhh hhhh         hhhhh    hhhhhhhh  
1fapB                  hhh hhhhhhhhhh hhhh         hhhhh    hhhhhhhhh 


TARGET    49    APTTMKEHSF QQTYSSDLKE AGRYVQAFES SGNVKDLNQA WEIYCSVFKK
1fapB     2062  -pqtlketsf nqaygrdlme aqewcrkymk sgnvkdltqa wdlyyhvfrr
                                                                      
TARGET              hhhhhh hh   hhhhh hhhhhhhhhh     hhhhhh hhhhhhhhhh
1fapB               hhhhhh hh   hhhhh hhhhhhhhhh      hhhhh hhhhhhhhhh


TARGET    99    L                                                     
1fapB     2111  is                                                    
                                                                      
TARGET                                                                
1fapB                                                                 



Quality


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


Quaternary Structure Annotation of the Template
1fap 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: 1fap.pdb1.gz

Quaternary Structure Modelling of the Target Protein
1fap_1


Template Selection
 - Start SMR-Pipeline for:3be492797e171a4bfe7a8aeb7d5c7dec on BC2-cluster at Wed Jul 16 20:23:59
2014 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with A found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with A found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with A found
 - No template with A found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with H found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with N found
 - No template with R found
 - No template with e found
 - No template with f found
 - No template with X found
 - No template with Z found
 - No template with a found
 - No template with b found
 - No template with d found
 - No template with h found
 - No template with i found
 - No template with j found
 - No template with B found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with P found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with A found
 - No template with A found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - Warning: Oligomer Prediction was not successfull!

 - 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 4jsnB (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jsnA (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jspA (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jspB (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jt5B (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jt5A (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jsvB (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jsvA (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jsxA (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jsxB (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jt6B (2042-2697) was not successful go to next best template
 -                                                              *******************
 - building model based on 4jt6A (2042-2697) was not successful go to next best template
 -                                                              ******************
 - building model based on 4d0lE (2070-2682) was not successful go to next best template
 -                                                                  ***
 - building model based on 1fapB (2189-2287) was successful 
 -                                                                           **
 - building model based on 4jpsA (2481-2558) was successful 
 -                                            ***************
 - building model based on 4jsnB (1443-1936) was successful 
 -                                                                      *******
 - building model based on 2y3aA (2322-2565) was successful 
 -                                                                       **********
 - building model based on 4d0lA (2351-2682) was successful 
 -                                                              ******************
 - building model based on 4d0lC (2070-2682) was successful 
 -       *
 - building model based on 3gq2B (212-249) 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:3be492797e171a4bfe7a8aeb7d5c7dec on BC2-cluster at Wed Jul 16 20:36:29
2014 




Template Description
Match Chain SeqId

3gq2: CRYSTAL STRUCTURE OF THE DIMER OF THE P115 TETHER GLOBULARHEAD DOMAIN
Solved by: X-RAY, Resolution: 2.18A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

212-249 3gq2B 11%
[Model]
212-234 3gq2A 17%
[Model]

3grl: CRYSTAL STRUCTURE OF THE MONOMER OF THE P115 TETHER GLOBULHEAD DOMAIN
Solved by: X-RAY, Resolution: 2.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

213-236 3grlA 17%
[Model]

4d0m: PHOSPHATIDYLINOSITOL 4-KINASE III BETA IN A COMPLEX WITH RGAMMA-S AND THE RAB-BINDING DOMAIN OF FIP3
Solved by: X-RAY, Resolution: 6.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2351-2682 4d0mC 16%
[Model]
2351-2682 4d0mA 16%
[Model]
2351-2682 4d0mS 16%
[Model]
2351-2682 4d0mO 16%
[Model]
2351-2682 4d0mG 16%
[Model]
2351-2682 4d0mQ 16%
[Model]
2351-2682 4d0mM 16%
[Model]
2351-2682 4d0mI 16%
[Model]
2351-2682 4d0mY 16%
[Model]
2351-2682 4d0mg 16%
[Model]
2351-2682 4d0mc 16%
[Model]
2351-2682 4d0mW 16%
[Model]

4d0l: PHOSPHATIDYLINOSITOL 4-KINASE III BETA-PIK93 IN A COMPLEX WITH RAB11A-GTP GAMMAS
Solved by: X-RAY, Resolution: 6.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2070-2682 4d0lE 12%
[Model]
2070-2682 4d0lC 11%
[Model]
2351-2682 4d0lA 16%
[Model]

2w3c: GLOBULAR HEAD REGION OF THE HUMAN GENERAL VESICULAR TRANSPORT FACTOR P115
Solved by: X-RAY, Resolution: 2.22A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

611-630 2w3cA 15%
[Model]

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.