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: 2014-04-11
Revision date: 2014-04-08

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 Fri Apr 11 00:57:44
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 D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with A 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 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 B found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with D 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 A found
 - No template with A found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with C found
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with C found
 - No template with D found
 - No template with D found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with C found
 - No template with C found
 - No template with C found
 - No template with C found
 - 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:10): model based on new templates
 - Send 10 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 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 4c0pA (836-891) was successful 
 -                               *
 - building model based on 4c0oA (1020-1045) was successful 
 -                        **
 - building model based on 4c0qA (792-858) was successful 
 -                      ******
 - building model based on 4c0pA (694-889) was successful 
 -                                *
 - building model based on 4c0pD (1059-1086) was successful 
 -                         *****
 - building model based on 4c0qA (819-997) was successful 
 -                       *********
 - building model based on 4c0oA (747-1065) was successful 
 -                     **
 - building model based on 4c0oB (664-725) 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 Fri Apr 11 01:06:22
2014 




Template Description
Match Chain SeqId

4c0o: TRANSPORTIN 3 IN COMPLEX WITH PHOSPHORYLATED ASF/SF2
Solved by: X-RAY, Resolution: 2.56A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

693-828 4c0oA 15%
[Model]
801-847 4c0oA 15%
[Model]
797-850 4c0oA 11%
[Model]
819-891 4c0oA 16%
[Model]
816-889 4c0oA 12%
[Model]
1013-1046 4c0oB 18%
[Model]
694-828 4c0oB 14%
[Model]
706-851 4c0oB 10%
[Model]
748-891 4c0oB 14%
[Model]
836-890 4c0oB 18%
[Model]
747-1065 4c0oA 11%
[Model]
666-676 4c0oA 27%
[Model]
664-679 4c0oB 19%
[Model]
835-846 4c0oB 17%
[Model]
876-892 4c0oB 0%
[Model]
1020-1045 4c0oA 19%
[Model]
836-849 4c0oA 21%
[Model]
664-725 4c0oB 8%
[Model]
706-721 4c0oA 6%
[Model]
731-742 4c0oB 33%
[Model]
877-892 4c0oA 0%
[Model]

4hnw: THE NATA ACETYLTRANSFERASE COMPLEX BOUND TO INOSITOL HEXAK
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1446-1541 4hnwA 12%
[Model]
1804-1823 4hnwA 15%
[Model]
1519-1540 4hnwA 14%
[Model]

4hny: APO N-TERMINAL ACETYLTRANSFERASE COMPLEX A
Solved by: X-RAY, Resolution: 2.25A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1519-1590 4hnyA 13%
[Model]
1751-1825 4hnyA 9%
[Model]
1519-1588 4hnyC 13%
[Model]
1754-1781 4hnyC 14%
[Model]
1520-1535 4hnyC 25%
[Model]

4hnx: THE NATA ACETYLTRANSFERASE COMPLEX BOUND TO PPGPP
Solved by: X-RAY, Resolution: 2.34A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1445-1592 4hnxA 8%
[Model]

4c0p: UNLIGANDED TRANSPORTIN 3
Solved by: X-RAY, Resolution: 2.95A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

746-1067 4c0pA 11%
[Model]
794-849 4c0pA 11%
[Model]
814-847 4c0pA 12%
[Model]
816-890 4c0pA 12%
[Model]
971-1003 4c0pA 9%
[Model]
694-889 4c0pB 15%
[Model]
746-1067 4c0pB 11%
[Model]
794-849 4c0pB 11%
[Model]
814-847 4c0pB 12%
[Model]
816-890 4c0pB 12%
[Model]
836-891 4c0pB 21%
[Model]
971-1003 4c0pB 9%
[Model]
694-889 4c0pC 15%
[Model]
746-1067 4c0pC 11%
[Model]
794-849 4c0pC 11%
[Model]
814-847 4c0pC 12%
[Model]
816-890 4c0pC 12%
[Model]
836-891 4c0pC 21%
[Model]
971-1003 4c0pC 9%
[Model]
1016-1046 4c0pD 16%
[Model]
799-849 4c0pD 12%
[Model]
819-891 4c0pD 18%
[Model]
836-891 4c0pA 21%
[Model]
730-741 4c0pD 33%
[Model]
730-741 4c0pA 33%
[Model]
730-741 4c0pC 33%
[Model]
730-741 4c0pB 33%
[Model]
694-889 4c0pA 15%
[Model]
1020-1043 4c0pA 21%
[Model]
1020-1043 4c0pC 21%
[Model]
1020-1043 4c0pB 21%
[Model]
666-675 4c0pA 30%
[Model]
666-675 4c0pC 30%
[Model]
666-675 4c0pB 30%
[Model]
1059-1086 4c0pD 14%
[Model]
876-892 4c0pA 0%
[Model]
876-892 4c0pC 0%
[Model]
876-892 4c0pB 0%
[Model]
305-312 4c0pD 25%
[Model]
755-779 4c0pD 20%
[Model]
1021-1044 4c0pD 21%
[Model]
666-676 4c0pD 27%
[Model]
706-717 4c0pA 8%
[Model]
706-717 4c0pC 8%
[Model]
706-717 4c0pB 8%
[Model]

4c0q: TRANSPORTIN 3 IN COMPLEX WITH RAN(Q69L)GTP
Solved by: X-RAY, Resolution: 3.42A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

694-829 4c0qA 15%
[Model]
794-849 4c0qA 11%
[Model]
799-848 4c0qA 16%
[Model]
865-892 4c0qA 10%
[Model]
157-173 4c0qA 29%
[Model]
792-858 4c0qA 18%
[Model]
819-997 4c0qA 12%
[Model]
1027-1041 4c0qA 27%
[Model]
732-740 4c0qA 44%
[Model]
665-678 4c0qA 21%
[Model]
705-720 4c0qA 6%
[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.