Chlamydia pneumoniae-specific genes
Using tblastx and tblastn, we searched other genomes for orthologs of the genes identified from individual gene-by-gene comparisons of the five C. pneumoniae genomes. The comparative approach identified 140 genes that were specific to C. pneumoniae and for which no significant similarity was detected in any other organism (Additional file 2). Many of these species-specific genes are short open reading frames (ORFs) that have been annotated as genes. The large number of short hypothetical ORFs makes it difficult to determine whether these genes are 'real' or artefacts of the genome annotation or sequencing process. Until these proteins are systematically studied in the future, it cannot be determined whether these proteins are valid or too short to be protein-coding genes. Genes with suggested or predicted functions include putative lipoproteins and chlamydial inclusion membrane proteins (IncA). Several hypothetical proteins are clustered together (including CPK_ORF00340-343, 389-401, 496-498, 567-569, 658-661, 969-980: LPCoLN locus designation, CPK), suggesting that they may exist in an operon and might be functionally related.