Computational protocol: Genes Encoding Cher-TPR Fusion Proteins Are Predominantly Found in Gene Clusters Encoding Chemosensory Pathways with Alternative Cellular Functions

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Protocol publication

[…] Initially the CheR-TPR containing genomes were analyzed for sequences that match InterPro signatures IPR011990 (TPR-like helical) and IPR004089 (methylaccepting chemotaxis protein [MCP] signaling domain). Subsequently, all currently available chemoreceptor sequences were retrieved by a search for hits in all currently available genome sequences using IPR004089. This search resulted in the detection of 29 425 sequences. To verify whether these sequences contain a TPR domain, a series of batch searches were conducted using the “batch search” tool (http://pfam.sanger.ac.uk/search#tabview=tab1) of Pfam. The criterion for this search was the presence of members of the TPR clan (CL0020) and the E-value threshold for this search was set at 1.0 e−4. The transmembrane regions of chemoreceptor-TPR fusion proteins were determined using the TMHMM Server v. 2.0 (http://www.cbs.dtu.dk/services/TMHMM-2.0/). The sequence fragments of chemoreceptor predicted to form a TPR domain, flanked by 5 amino acids at each side, were submitted to the three-dimensional homology modeling server CPHmodels 3.2 (http://www.cbs.dtu.dk/services/CPHmodels/). Multiple sequence alignments were carried out using the CLUSTALW algorithm of the NPSA server (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_clustalw.html). The GONNET matrix was used and the gap opening and gap extension penalties were set at 10 and 0.1, respectively. […]

Pipeline specifications

Software tools TMHMM, CPHmodels, Clustal W
Applications Protein structure analysis, Membrane protein analysis
Organisms Pseudomonas putida, Escherichia coli
Diseases Hyperparathyroidism, Renal Insufficiency
Chemicals S-Adenosylhomocysteine, S-Adenosylmethionine