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

Similar protocols

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 ( 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 ( 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 ( Multiple sequence alignments were carried out using the CLUSTALW algorithm of the NPSA server ( 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