BMC Genomics 2005, 6:103 http://www.biomedcentral.com/1471-2164/6/103 - - - - replication-associated protein replication-associated protein - CAAX N-terminal protease - transcriptional regulator TetR IS231 transposase bacitracin transport permease - sensor histidine kinase IS231 transposase DNA-damage repair protein Page 8 of 14 (page number not for citation purposes) LFiingeuarreal2ignment of pXO2, pAW63 and pBT9727 Linear alignment of pXO2, pAW63 and pBT9727. CDSs are represented by block arrows. Several CDS numbers (see Table 1) are indicated for reference on each plasmid, just above or below their representation. Predicted functions/homologies are indicated by the color key featured below. Well conserved segments of the plasmids are paired by shaded regions (>40% amino acid identity); percentages for specific CDS pairs can be found in Tables 1 and 2. The proposed PAI of pXO2 is raised above the rest of the sequence for clarity. Scale is indicated by the bar in the lower right-hand corner. Table 2: Comparison of pXO2 and pBT9727 CDSs with no homologs on pAW63 B.t. konkukian CDS Putative gene functions While the copy of the Tn916 CDS 14-like element present on pAW63 had been found to be encoded by two CDSs (CDSs 6 and 8) due to the insertion of the group II intron B.th.I1 (see above), the corresponding homologs of this element were uninterrupted on pBT9727 and pXO2. The sequence comparison of these 'native' versions of the gene with the one containing the intron allowed for the precise site of insertion to be determined. This region of the Tn916 CDS 14-like element was then aligned with its clos- est homologs as identified by BLAST search, revealing that the insertion had taken place in a relatively well-con- served domain of the gene. This is consistent with the B. anthracis CDS GBAA_pXO2_0011 GBAA_pXO2_0012 GBAA_pXO2_0028 GBAA_pXO2_0035 GBAA_pXO2_0040 GBAA_pXO2_0041 GBAA_pXO2_0052 GBAA_pXO2_0053 GBAA_pXO2_0054 GBAA_pXO2_0055 GBAA_pXO2_0056 GBAA_pXO2_0057 GBAA_pXO2_0061 GBAA_pXO2_0075 GBAA_pXO2_0086 GBAA_pXO2_0094 id % 65% 60% 67% 64% 91% 79% 89% 72% 92% 97% 96% 66% 39% 36% 81% 93% pBT9727_0011 pBT9727_0012 pBT9727_0024 pBT9727_0038 pBT9727_0047 pBT9727_0048 pBT9727_0039 pBT9727_0040 pBT9727_0041 pBT9727_0042 pBT9727_0043 genomic? genomic? genomic? pBT9727_0043 pBT9727_0061