Similarity searches using BLASTX revealed that eleven of the 16 regions contained sequences associated with phage proteins found in H. influenzae and related species. The remaining five regions encoded a putative tRNA-dihydrouridine synthase C, a predicted transcriptional regulator (NikR), a transport protein, and Hia and Hap proteins. Table 2 Regions in the H. influenzae strain RM7060 genome not found in strain 10810 Accession number Highest match by BLASTX analysis Species ZP_01791522 NikR predicted transcriptional regulator H. influenzae PittAA AAL79955 Hia/YadA-like similar to neisserial GNA992 H. influenzae nontypeable strain

1860A AAM74927 Hap peptidase S6 H. influenzae HK274 ZP_05977792 putative carboxylate/amino acid/amine transporter Neisseria mucosa P46495 Putative

buy VE-822 integrase/recombinase HI_1572 H. influenzae ZP_00134779 Phage-related PARP inhibitor protein, tail component Actinobacillus pleuropneumoniae YP_001968298 Phage-related protein, tail component Actinobacillus pleuropneumoniae ZP_01791539 Mu-like prophage protein H. influenzae PittAA YP_003007008 Phage-related minor tail protein SN-38 research buy Aggregatibacter aphrophilus NJ8700 ZP_01791533 putative phage tail component H. influenzae PittAA YP_001290203.1 tRNA-dihydrouridine synthase C H. influenzae PittEE YP_001053216.1 predicted bacteriophage tail assembly protein Actinobacillus pleuropneumoniae L20 ZP_05990265 hypothetical protein COK_2151 Mannheimia haemolytica ZP_04753126 possible prophage antirepressor Actinobacillus minor NM305 ZP_04464399 Phage Mu protein F like protein H. influenzae 6P18H1 YP_003007004 phage protein Aggregatibacter

aphrophilus Experimental assessment of H. influenzae transformation High throughput sequencing provides a useful experimental tool to examine in detail the recombination events associated with the transfer and exchange of DNA between H. influenzae strains through transformation. To this end, we investigated the transformation of DNA from a Hib strain donor into a high efficiency recipient GPX6 strain. To ensure that each transformant was the result of a recombination event we used a spontaneous, high level streptomycin resistant (strR) derivative of strain Eagan (EaganstrR), possessing a point mutation in rpoB. Spontaneous strR mutants were infrequent (<10-10 in control transformations of Rd using streptomycin-sensitive Eagan DNA). Compared to strain Rd, the donor strain Eagan genome sequence had 18,789 SNPs relatively uniformly distributed throughout the genome (an average density of 10.3 SNPs per kbp) including the region around rpoB, the location of the strR mutation. Following transformation and selection on streptomycin, 200 independent Rd+EaganstrR colonies were pooled, the genomic DNA sequenced and mapped to the Rd reference genome sequence using the MAQ programme to identify SNPs.