SWISS-MODEL Repository - Model Details

Model Overview
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1
152

Sequence
UniProt P0AAS3
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P0AAS3: 511145.b0488

Domain
Link to: [ InterPro ]
NfeD

Model 3D Structure
Model information:
Modelled residue range: 92 to 151
Based on template: [ 2k5h ]  
Sequence Identity [%]: 27%
Model date: 2012-10-28
Revision date: 2012-10-15

Quaternary structure information: [details]
Template (2k5h): MONOMER
Model: MONOMER

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 ]

This model has not been updated since 2012-10-15. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1                                             RGQ QLIGRRFVLE
2k5h_1#8  1     mgsshhhhhh ssgrenlyfq ghmaaritge pskka--vsd rligrkgvvm
                                                                      
TARGET                                                          ssssss
2k5h_1#8                                                        ssssss


TARGET    14    SPLV-NGRGH MRVGDSSWPV SASEDLGAGT HVEVIAIEGI TLHIRAVS -
2k5h_1#8  49    eaispqnsgl vkvdgetwra tsgtvldvge evsvkaiegv klvvekleeq
                                                                      
TARGET                  ss sss  sssss s        s ssssssss   sssssss   
2k5h_1#8                ss sss  sssss s        s ssssssss   sssssss   


TARGET          ---                                                   
2k5h_1#8  99    kgs                                                   
                                                                      
TARGET                                                                
2k5h_1#8

Quality 


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

 
Quaternary Structure Annotation of the Template 
 2k5h is annotated as MONOMER 
 The template structure (2k5h) was solved by NMR and does not contain any quaternary structure annotation 
 The template is annotated by the number of chains found in the PDB file 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.684 (>0.5 indicates similarity) 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:22cceb8ea8572d920b6ea0113afe5ddb on BC2-cluster at Sun Oct 28 00:32:04
2012 


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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - Proof template(s) selection compared to previous Repository update
 - Selected template(s): no changes compared to previous version of the Repository:
 -  Template: 2k5hA (92-151) Sequence Identity: 27.869
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                 ********************************
 - building model based on 2k5hA (92-151) 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:22cceb8ea8572d920b6ea0113afe5ddb on BC2-cluster at Sun Oct 28 00:37:59
2012


Template Description
Match Chain SeqId

2k5h: SOLUTION NMR STRUCTURE OF PROTEIN ENCODED BY MTH693 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM: NORTHEAST STRUCTURAGENOMICS CONSORTIUM TARGET TT824A
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

92-151 2k5hA 28%
[Model]

3cp0: CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF MEMBRANE PROTEIIMPLICATED IN REGULATION OF MEMBRANE PROTEASE ACTIVITY FROM CORYNEBACTERIUM GLUTAMICUM
Solved by: X-RAY, Resolution: 1.65A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

93-151 3cp0A 23%
[Model]

2k14: SOLUTION STRUCTURE OF THE SOLUBLE DOMAIN OF THE NFED PROTEIN YUAF FROM BACILLUS SUBTILIS
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

84-151 2k14A 19%
[Model]

2exd: THE SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF A NFED HOMOLOG FROM PYROCOCCUS HORIKOSHII
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

93-151 2exdA 19%
[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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