Difference between revisions of "Part:BBa K808005"
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K808005 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K808005 SequenceAndFeatures</partinfo>
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*[1] Sasoh, M., E. Masai, et al. (2006). "Characterization of the terephthalate degradation genes of Comamonas sp. strain E6." Appl Environ Microbiol 72(3): 1825-1832.
 
  
 
PHYRE2 - http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index  
 
PHYRE2 - http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index  
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Protein structure prediction on the web: a case study using the    PhyreKelley LA and Sternberg MJE.Nature Protocols 4, 363 - 371 (2009 server
  
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'''Protein structure prediction on the web: a case study using the Phyre,''' Kelley LA and Sternberg MJE.Nature Protocols 4, 363 - 371 (2009 server
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I-TaSSER server - http://zhanglab.ccmb.med.umich.edu/I-TASSER/
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Yang Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, vol 9, 40 (2008).
 +
Ambrish Roy, Alper Kucukural, Yang Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, vol 5, 725-738 (2010).
 +
Ambrish Roy, Jianyi Yang, Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, doi:10.1093/nar/gks372 (2012)
  
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http://www.cbs.dtu.dk/services/TatP/ - Prediction of Twin-arginine signal peptides  
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*http://www.cbs.dtu.dk/services/TatP/ - Prediction of Twin-arginine signal peptides  
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'''Prediction of twin-arginine signal peptides.''' Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak. BMC bioinformatics 2005 6: 167.  
 
'''Prediction of twin-arginine signal peptides.''' Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak. BMC bioinformatics 2005 6: 167.  
  
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*http://www.cbs.dtu.dk/services/SignalP/  - Prediction of Signal peptide and cleavage sites in gram+,           gram- and eukaryotic amino acid sequences  
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http://www.cbs.dtu.dk/services/SignalP/  - Prediction of Signal peptide and cleavage sites in gram+,           gram- and eukaryotic amino acid sequences  
  
 
'''SignalP 4.0: discriminating signal peptides from transmembrane regions''' Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011
 
'''SignalP 4.0: discriminating signal peptides from transmembrane regions''' Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011
  
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*http://www.cbs.dtu.dk/services/TMHMM/  - Prediciton of transmembrane helices in proteins
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http://www.cbs.dtu.dk/services/TMHMM/  - Prediciton of transmembrane helices in proteins
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'''Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh''':A hidden Markov model for predicting      transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182,Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, CA: AAAI Press, 1998
+
  
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*http://www.sciencegateway.org/tools/proteinmw.htm - Protein Molecular Weight Caltulator
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'''Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh''':A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182,Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, CA: AAAI Press, 1998
  
 +
http://www.sciencegateway.org/tools/proteinmw.htm - Protein Molecular Weight Caltulator
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Revision as of 11:55, 24 September 2012

tctB_197: small subunit B2 of the tripartite tricarboxylate transporter family

The small subunit B1 of the tripartite tricarboxylate transporter family (tctB_197, 20,44 kDa) was isolated from Comamonas testosteroni KF-1. The tripartite tricarboxylate transporter system consists of three different proteins: a periplasmatic solute binding receptor, a membrane protein with 12 putative transmembrane alpha-helical spanners (in this case tctB_197), and a small poorly conserved membrane proteine with four putative transmembrane alpha-helical spanners.[1] The strain was purchased from Leibniz Institute DMSZ-German Collection of Microorganism and Cell Cultures (DMSZ no. 14576). To characterized the structure of the tctB_197 bioinformatic tools like Protein Homology/anologY Recognition Engine V 2.0 (PHYRE2), I-TASSER servers, and TMHMM was used. The TMHMM predicted a transmembrane protein with 4 alpha-helical spanners (Fig. 1). The NCBI Protein BLAST results shows that the tctB_197 subunit B2 belongs to the tctB superfamily. Phyre2 an I-Tasser server homology modelling did not give a significant result for the structure of the tctB_197 subunit B2.

Figure 1. TMHMM prediction of the tctB_197 subunit B1. It shows 4 alpha-helical spanners.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 18
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 522
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 345

PHYRE2 - http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index Protein structure prediction on the web: a case study using the PhyreKelley LA and Sternberg MJE.Nature Protocols 4, 363 - 371 (2009 server

I-TaSSER server - http://zhanglab.ccmb.med.umich.edu/I-TASSER/ Yang Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, vol 9, 40 (2008). 

Ambrish Roy, Alper Kucukural, Yang Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, vol 5, 725-738 (2010).

Ambrish Roy, Jianyi Yang, Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, doi:10.1093/nar/gks372 (2012)

http://www.cbs.dtu.dk/services/TatP/ - Prediction of Twin-arginine signal peptides

Prediction of twin-arginine signal peptides. Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak. BMC bioinformatics 2005 6: 167.

http://www.cbs.dtu.dk/services/SignalP/ - Prediction of Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences

SignalP 4.0: discriminating signal peptides from transmembrane regions Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011

http://www.cbs.dtu.dk/services/TMHMM/ - Prediciton of transmembrane helices in proteins

Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh:A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182,Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, CA: AAAI Press, 1998

http://www.sciencegateway.org/tools/proteinmw.htm - Protein Molecular Weight Caltulator