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 ]

Model 3D Structure
Model information:
Modelled residue range: 204 to 366
Based on template: [ 1vlm ]  
Sequence Identity [%]: 12%
Model date: 2015-08-12
Revision date: 2015-07-24

Quaternary structure information: [details]
Template (1vlm): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: NA: 1.
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                                        IAQVKPGT IMYDPFAGTG
1vlmA     0     hxwhiferfv neyerwflvh rfaylselqa --vkcllpeg rgveigvgtg
                                                                      
TARGET                                                      ssssss    
1vlmA             hhhhh    hhhhhhhh    hhhhhhhhh   hhhh     ssssss    


TARGET    19    SFLVAGGHFG SLVIGSDIDG RMIRGKGAQV NISANFKKYG ESSQFLDVLT
1vlmA     48    rfavpl---- kikigvepse rxaeiark-- ----r----- ----gvfvlk
                                                                      
TARGET          hhhhh        sssss  h hhhhhh  ss sss   ssss ss    ssss
1vlmA           hhhhhh       sssss  h hhhhhhhh       h            ssss


TARGET    69    MDFTNNALRN NLVIDTILCD PPYGIRESIK VLGAKDPERF LGKEDMEIDG
1vlmA     79    gtaenlplk- desfdfalxv tti------- ---------- ----------
                                                                      
TARGET          s              ssssss s   sssss               hhh     
1vlmA           s              ssssss s                               


TARGET    119   EKAYLRRDYI PTKKPYALDS LLDDLLQYSS ERLPIGGRLA FWMPT ----
1vlmA     101   -------cfv d--------d -peralkeay rilkkggyli vgivdresfl
                                                                      
TARGET             sssss                hhhhhhhh hh     sss ss        
1vlmA                                  hhhhhhhhh h     ssss sssss   hh


TARGET          ---------- ---------- ---------- ---------- ----------
1vlmA     135   greyeknkek vfyknarffs teelxdlxrk agfeefkvvq tlfkhpsels
                                                                      
TARGET                                                                
1vlmA           hhhhhh                hhhhhhhhhh h     ssss ss        


TARGET          ---------- ---------- --                              
1vlmA     186   eiepvkegyg egafvvirgt kk                              
                                                                      
TARGET                                                                
1vlmA                sss     ssssssss s                               



Quality


Template's ligands section
Ligands in the template: NA: 1.
Ligands in the template that will be assessed: NA300.
Model's ligands section
NA300
Not all the residues interacting with the ligand are completely conserved between model and template.
No RMSD calculation will be performed.
Given the properties calculated previously, the ligand A.NA300 will not be included in the final model.
NA300: conservation:False, RMSD:False, included: False

No ligands were included in the model.


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

Quaternary Structure Modelling of the Target Protein
The target and template sequences are too diverse (seqid: 12.883) to infer a conservation of the oligomeric state
Please use the advancend features of the SwissModel Project Mode

The target structure was calculated as SINGLE CHAIN


Template Selection
 - Start SMR-Pipeline for:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Wed Aug 12 17:58:26
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 H found
 - No template with D found
 - No template with E found
 - No template with G found
 - No template with A found
 - No template with C found
 - No template with F 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 1vlmA (204-366) 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:5adc1525bec1bd32481fd3c31e7f43d0 on BC2-cluster at Wed Aug 12 17:59:27
2015 




Template Description
Match Chain SeqId

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 ]  

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

1nkv: X-RAY STRUCTURE OF YJHP FROM E.COLI NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER13
Solved by: X-RAY, Resolution: 2.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

191-373 1nkvC 13%
[Model]
192-372 1nkvA 13%
[Model]
185-372 1nkvB 11%
[Model]

5bxy: CRYSTAL STRUCTURE OF RNA METHYLTRANSFERASE FROM SALINIBACTCOMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
Solved by: X-RAY, Resolution: 1.75A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

194-363 5bxyB 11%
[Model]
194-362 5bxyA 11%
[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 ]  

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

5bp7: CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE FROM SULFURREDUCENS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

185-362 5bp7C 9%
[Model]
185-362 5bp7A 9%
[Model]
184-363 5bp7B 9%
[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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