S. gordonii genome regions. The S. gordonii genome region is shown for each of the 3 genes of interest identified in these studies, SGO_1242 (camG) (A), SGO_1089 (lspA) (B), and SGO_1852 (eep) (C). The top line in each panel indicates the nucleotide numbers in the genome sequence in GenBank (accession number CP000725); the arrows at the end of each line show the ascending direction of the nucleotide numbers, indicating the orientation of the genome region pictured with respect to the chromosomal origin of replication. Beneath the genome nucleotide number line, each gene locus is indicated by the SGO number, which appears within an open arrow indicating the 5-prime-to-3-prime direction. The putative functional descriptions are based on the NCBI genome annotation and include conserved hypothetical (CHP) and hypothetical (HP) proteins. Putative bacterial promoters (forward arrows) and Rho-independent bacterial terminators (stem-loops) were identified in silico with the Bprom and FindTerm online software programs. Beneath camG, lspA, and eep are expansions that show the relevant features of the deduced CamG, LspA, and Eep proteins from the amino terminus (designated 1) to the carboxyl terminus. The filled blocks represent regions of conserved amino acids that share sequence homology to predicted functional domains identified in Prosite (PS) or pFam (PF) () or to signal sequences predicted by Signal P (). The hatched bars represent the region of each encoded protein that was genetically manipulated in the construction of the isogenic mutant strains used in these studies (see Materials and Methods). (A) SGO_1242, which was designated camG, encodes a 116-amino-acid predicted lipoprotein with a processed signal sequence containing a peptide similar to cAM373. In silico analysis predicted that camG has its own promoter. Upstream of camG are two conserved hypothetical proteins, each with its own predicted promoter. Downstream of camG are two overlapping open reading frames with a single putative promoter; based upon sequence similarities, SGO_1241 encodes a 32.2-kDa protein similar to an aminoglycoside adenlytransferase (pFam04439) and SGO_1240 encodes a 27.2-kDa protein similar to CAAX amino-terminal proteases (pFam 02517) (). No rho-independent terminators were detected in silico within the SGO_1244-through-SGO_1240 gene cluster. (B) SGO_1089, designated lspA, encodes a signal II peptidase signature motif (PF01252 and PS0085), as well as a conserved multicopper oxidase signature (PS00079). The lspA gene is located between two overlapping open reading frames with a single upstream promoter identified by both MacVector and Softberry promoter prediction software. In silico analysis of this operon indicated that the upstream gene (SGO_1088) encodes a putative transcriptional regulator of the LysR family. The downstream gene, SGO_1090, with its putative ribosomal binding site and start codon located within the lspA ORF, encodes a putative pseudouridine synthase. (C) SGO_1852, designated eep, encodes a 417-amino-acid protein with sequence similarity to E. faecalis Eep. The S. gordonii Eep carries a conserved zinc metalloprotease M-50 superfamily domain thought to be associated with the ability of a protein to cleave the transmembrane domains of substrate proteins, thereby transferring information and signals across bacterial membranes ().