Because the maximum size of the loop region of known Inc pro teins is 22 amino acids, we set a threshold of 30 residues between the two transmembrane segments. Chlamydiae membrane proteins www.selleckchem.com/products/Bortezomib.html were collected from all 7 chlamydial proteomes using the Polyphobius predictor algorithm. Out of the 2904 sequences obtained, we eliminated the sequences that only contained one hydro phobic N terminus fragment identified as a signal pep tide or that contained a single transmembrane domain. The remaining polytopic Inhibitors,Modulators,Libraries membrane proteins were submitted to the domain recognition program rpsblast associated with the NCBI CDD data base. Proteins generating multi domain family hits, highly indicative of a conserved pro karyotic function, were removed. In addition, sequences containing a single domain covering the whole length of the protein were analyzed with Blast.
Among those, we retained as candidates only the proteins specific to the chlamydial genus. Finally at this stage, only sequences containing at least one set of transmembrane domains separated by a loop of less than 30 amino acids were retained. Altogether, the seven chlamydial proteomes generated 537 sequences that fulfilled these criteria. The number of putative Inc Inhibitors,Modulators,Libraries proteins per chlamydial species ranges from 76 out of 2031 proteins in P. amoebo phila to 107 out of 1052 proteins in C. pneumo niae. The list of putative C. trachomatis and C. pneumoniae Inc proteins are shown in Table 2 and 3, respectively, while putative Inc proteins from other gen omes are found in Additional files 1, 2, 3, 4 and 5.
We next studied the evolutionary relationship Inhibitors,Modulators,Libraries of the putative Inc proteins using InParanoid Multiparanoid programs, which can automatically find orthology rela tionships between proteins in multiple proteomes. From the 537 Inc candidates sequences, 126 are orphan sequences, showing no orthology relationship with other putative Inc. Most of these orphan putative Inc proteins are from P. amoebophila and from C. pneumoniae. The remaining 411 putative Inc proteins come into 109 groups of orthologs. Interestingly, 50 and 21 of the ortholog groups were specific of the Chlamydophila and of the Chlamydia Inhibitors,Modulators,Libraries families, respectively. This sug gests that many Inc proteins might fulfill species specific or family specific functions. Alternatively, and not exclu sively, Inc proteins that are involved in similar functions in distinct species might not be recognizable at the pri mary sequence level.
Genes coding for Inc proteins are scattered in the genomes with a few hot spots that cluster several con secutive inc genes. Transcription of the genes in operons has been demonstrated in a few cases. Finally, Inhibitors,Modulators,Libraries Inc proteins have an average length of 279 residues. Most members of Fluoro-Sorafenib the family have only two transmembrane segments.