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Fig. 9 | BMC Microbiology

Fig. 9

From: Carbohydrate metabolic systems present on genomic islands are lost and gained in Vibrio parahaemolyticus

Fig. 9

Analysis of the 26-kb l-rhamnose utilization island. a. Gene cluster of the l-rhamnose utilization in V. parahaemolyticus AQ3810. b. Genomic locus of the 26-kb l-rhamnose region in AQ3810. c. A Tn7-like transposon and a mini CRISPR-Cas system associated with T3SS-2α and a transposon like region associated with the 26-kb L-rhamnose region. d. Schematic of the L- rhamnose genomic loci in AQ4037, S03-S05, S08-S13 VPA1309 in chromosome 2 that is also the location of T3SS-2α in RIMD2210633. Location of the 26-kb l-rhamnose island in FORC_023 and the empty site at VPA1309. Parenthesis indicates homologous ORFs. e. Phylogenetic analysis of RhaA protein from FORC_022 and AQ3810 among members of the family Vibrionaceae. The evolutionary history was inferred by using the Maximum Likelihood method and Le_Gascuel_2008 model [40]. The tree with the highest log likelihood (− 6340.56) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.4168)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 29 amino acid sequences. All positions with less than 95% site coverage were eliminated, i.e., fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position (partial deletion option). There were a total of 418 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [29]

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