SWISS-MODEL Repository - Model Details

Model Overview
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1
433

Sequence
UniProt Q12463
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q12463: 4932.YOL124C

Domain
Link to: [ InterPro ]
UPF0020

Model 3D Structure
Model information:
Modelled residue range: 193 to 365
Based on template: [ 3vse ]  
Sequence Identity [%]: 15%
Model date: 2015-06-28
Revision date: 2015-06-25

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

Ligand information: [details]
Ligands in the template: ALA: 1.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment

                                                       
3vseB     1     mkiatlnkgk etkyfngypl ieeediysqd hlkegdifqi vtdksqyvat
                                                                      
                                                       
3vseB            ssssss    hhhhh   ss sss sss         sssss ss   sssss


                                                       
3vseB     51    ayvgrqhkgl gwvltydkaq eintaffvkl fntalaerdy yfnidgtnaf
                                                                      
                                                       
3vseB           ssssss sss ssss          hhhhhhh hhhhhhhhhh      sssss


                                                       
3vseB     101   rlfnaegdgv ggltidnydg hlliqwyskg iykfkyaile avrkvfdyks
                                                                      
                                                       
3vseB           sssss       ssssssss  sssssss hh hh   hhhhh hhhh    ss


TARGET    1                                                      FEAEL
3vseB     151   iyekvrfsgg fvegdapefp ivieenftfy nvdledglmt gif--ldqke
                                                                      
TARGET                                                              hh
3vseB           ssssss sss sssss      ssssss sss ss                 hh


TARGET    6     SLVSANIAQV KPGTIMYDPF AGTGSFLVAG GHFGSLVIGS DIDGRMIRGK
3vseB     204   vrkkl-rgqy akerhvlnlf sytgafsvia aseassttsv dlanrsrsl-
                                                                      
TARGET          hhhh           ssssss     hhhhhh h    sssss s   hh    
3vseB           hhhhh hh        sssss     hhhhhh h    sssss s   hhhhh 


TARGET    56    GAQVNISANF KKYGESSQFL DVLTMDFTNN ---ALRNNLV IDTILCDPPY
3vseB     252   -----teenf glnaidpksq yiyvmdtfdf ykyaarhghs ydtividpps
                                                                      
TARGET                hhhh h          sssss                  sssss   s
3vseB                hhhhh h          sssss hhhh hhhhhhh     sssss   s


TARGET    103   GIRESIKVLG AKDPERFLGK EDMEIDGEKA YLRRDYIPTK KPYALDSLLD
3vseB     297   farn------ -kk-r----- ---------- ---------- -tfsvqkdyd
                                                                      
TARGET          ssssssss          sss ss  ssssss ss   sssss sssss    h
3vseB           ssss           s                             ssss    h


TARGET    153   DLLQYSSERL PIGGRLAFWM P -------- ---------- ----------
3vseB     313   klingalnil ssegtlllct nasvyplkqf kntikktlee sgvdyeltev
                                                                      
TARGET          hhhhhhh        sssss                                  
3vseB           hhhhhhh     sssssssss       hhhh hhhhhhhhhh    sssssss


TARGET          ---------- ---------- ---------- ---                  
3vseB     363   mglpkdfkth phykpskylk avfvnirhle hhh                  
                                                                      
TARGET                                                                
3vseB           s                   s ssssssss                        



Quality


Template's ligands section
Ligands in the template: ALA: 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
3vse 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: 3vse.pdb2.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 (=MONOMER)
The target structure was calculated as SINGLE CHAIN
The corresponding reliability score is 0.024 (>0.5 indicates similarity)


Template Selection
 - Start SMR-Pipeline for:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Sun Jun 28 02:28:50
2015 


 - 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 B found
 - No template with C found
 - No template with H found
 - No template with D found
 - No template with E found
 - No template with G found
 - No template with B found
 - No template with F found
 - No template with H found
 - No template with C found
 - No template with F found
 - No template with A found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with C found
 - No template with A found
 - No template with B found
 - 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 3vseB (193-365) was successful 
 - ***************************************************************************
 - building model based on 3tljB (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tljA (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm4B (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm4A (1-405) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm5A (1-404) was not successful go to next best template
 - ***************************************************************************
 - building model based on 3tm5B (1-404) was not successful go to next best template
 - 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:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Sun Jun 28 02:34:46
2015 




Template Description
Match Chain SeqId

3vse: CRYSTAL STRUCTURE OF METHYLTRANSFERASE
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

193-366 3vseA 15%
[Model]
193-364 3vseC 16%
[Model]
193-364 3vseD 15%
[Model]
193-365 3vseB 16%
[Model]

2igt: CRYSTAL STRUCTURE OF THE SAM DEPENDENT METHYLTRANSFERASE FROM AGROBACTERIUM TUMEFACIENS
Solved by: X-RAY, Resolution: 1.89A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

185-363 2igtC 14%
[Model]
199-363 2igtB 15%
[Model]
200-363 2igtA 15%
[Model]

3tlj: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMADENOSYL-L-HOMOCYSTEINE
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-405 3tljB 13%
[Model]
1-405 3tljA 13%
[Model]

3tm5: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMSINEFUNGIN
Solved by: X-RAY, Resolution: 2.27A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-404 3tm5B 13%
[Model]
1-404 3tm5A 13%
[Model]

3tm4: CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMADENOSYLMETHIONINE
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-405 3tm4B 13%
[Model]
1-405 3tm4A 13%
[Model]

1vlm: CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE, POSSIBLE HISTAMINE N-METHYLTRANSFERASE (TM1293) FROM THERMOTOGA MARITIMA AT 2.20 A RESOLUTION
Solved by: X-RAY, Resolution: 2.20A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

204-366 1vlmA 13%
[Model]
205-367 1vlmB 13%
[Model]

3hm2: CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN-6Y C5,15- METHYLTRANSFERASE TARGETED DOMAIN FROM CORYNEBACTERIUM DIPHTHERIAE
Solved by: X-RAY, Resolution: 2.21A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

195-387 3hm2D 10%
[Model]
195-368 3hm2A 12%
[Model]
200-367 3hm2B 12%
[Model]
196-367 3hm2C 11%
[Model]
201-367 3hm2H 11%
[Model]
202-367 3hm2G 12%
[Model]
200-367 3hm2E 11%
[Model]
196-367 3hm2F 10%
[Model]

3e05: CRYSTAL STRUCTURE OF PRECORRIN-6Y C5,15-METHYLTRANSFERASE FROM GEOBACTER METALLIREDUCENS GS-15
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

194-380 3e05D 10%
[Model]
194-381 3e05G 10%
[Model]
194-381 3e05E 10%
[Model]
195-368 3e05A 10%
[Model]
185-367 3e05C 10%
[Model]
195-380 3e05H 10%
[Model]
187-381 3e05B 10%
[Model]
195-368 3e05F 10%
[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.




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