02369nas a2200265   4500000000100000008004100001260001300042653001500055653003800070653003800108653001900146653002200165653001800187653001100205653002700216653002400243100001000267700002100277700002300298245008500321300001200406490000800418520166300426022001402089       2010                            d  c2010 Aug10aAlgorithms10aBacterial Outer Membrane Proteins10aComparative Genomic Hybridization10aDNA, Bacterial10aGenome, Bacterial10aMycobacterium10aPorins10aSequence Analysis, DNA10aSpecies Specificity1 aMah N1 aPerez-Iratxeta C1 aAndrade-Navarro MA00aOuter membrane pore protein prediction in mycobacteria using genomic comparison.  a2506-150 v1563 a<p>Proteins responsible for outer membrane transport across the unique membrane structure of Mycobacterium spp. are attractive drug targets in the treatment of human diseases caused by the mycobacterial pathogens, Mycobacterium tuberculosis, M. bovis, M. leprae and M. ulcerans. In contrast with Escherichia coli, relatively few outer-membrane proteins (OMPs) have been identified in Mycobacterium spp., largely due to the difficulties in isolating mycobacterial membrane proteins and our incomplete understanding of secretion mechanisms and cell wall structure in these organisms. To further expand our knowledge of these elusive proteins in mycobacteria, we have improved upon our previous method of OMP prediction in mycobacteria by taking advantage of genomic data from seven mycobacteria species. Our improved algorithm suggests 4333 sequences as putative OMPs in seven species with varying degrees of confidence. The most virulent pathogenic mycobacterial species are slightly enriched in these selected sequences. We present examples of predicted OMPs involved in horizontal transfer and paralogy expansion. Analysis of local secondary structure content allowed identification of small domains predicted to perform as OMPs; some examples show their involvement in events of tandem duplication and domain rearrangements. We discuss the taxonomic distribution of these discovered families and architectures, often specific to mycobacteria or the wider taxonomic class of Actinobacteria. Our results suggest that OMP functionality in mycobacteria is richer than expected and provide a resource to guide future research of these understudied proteins.</p>  a1465-2080