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Publication for TATFIND
Signal peptides for recombinant protein secretion in bacterial expression systems
[…] eby sequences possessing a D-score above 0.7 having a high probability that they in fact really do so .For the identification of Tat signal peptides, TatP (http://www.cbs.dtu.dk/services/TatP/ ), TatFind (http://signalfind.org/tatfind.html ), and PRED-Tat (http://www.compgen.org/tools/PRED-TAT/ ) are commonly used prediction programs. However, since twin-arginine residues can also occur in […]
Tracking Proteins Secreted by Bacteria: What's in the Toolbox?
[…] ://www.cbs.dtu.dk/services/SignalP) (Petersen et al., ), PSort (http://www.psort.org), which conveniently also provides a list of links toward other subcellular prediction programs, Pred-Tat, TatP or TatFind (see Berks, , for comparison). Lipoprotein signal peptides are a distinct class of Sec dependent signal peptides characterized by a C-terminal consensus sequence, the lipobox, which ends with […]
The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection
[…] Sequences were analyzed for transmembrane domains and signal peptides using TMHMM () and Signal P (). Previous analyses of the M. tuberculosis genome performed with LipoP, TatP, TATFIND, and TigrFAM were used to identify proteins with lipoprotein or Tat signal peptides (, ). PE/PPE proteins were analyzed for YxxxD/E motifs (). […]
Secretome Prediction of Two M. tuberculosis Clinical Isolates Reveals Their High Antigenic Density and Potential Drug Targets
[…] s that we used; however, they do not eliminate the transmembrane proteins in their secretome. While the secretome reported by Roy et al. (), only utilized the secreted proteins by SignalP followed by TATFIND1.4, PRED-LIPO, and the application of TMHMM analysis but only in a selected subgroup of proteins. Our bioinformatics pipeline could be useful to predict secretomes in other pathogen bacteria g […]
A unifying mechanism for the biogenesis of membrane proteins co operatively integrated by the Sec and Tat pathways
[…] A Perl script was used to run all proteins from all completed prokaryotic genomes available in Genbank at the time of analysis through the TATFind program (version 1.4; ) and the TMHMM program (version 2.0c; ). Conditions were included in the script to state that there should be an even number of TMD before the twin arginines, the nu […]
Physical, Chemical and Proteomic Evidence of Potato Suberin Degradation by the Plant Pathogenic Bacterium Streptomyces scabiei
[…] The extracellular localization of the protein was assessed using SignalP (), Phobius (), SecrotomeP (), TatP (), and Tatfind () programs, while NCBI, Uniprot, KEGG, and COG resources were used to predict protein function.The normalized spectral count (NSpC) was defined as the spectral count of a protein divided by i […]
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