In silico analysis of a Rhizobium sp. RC1 putative haloalkanoic permease sequence motif and classification

ABSTRACT

Aims@#The transport of haloalkanoic acids (haloacids) is important in the metabolism of haloacid pollutants by bacteria. In this study, a computational analysis of Rhizobium sp. RC1 haloacid permease (DehrP) amino acid sequence was conducted to identify its subfamily, sequence motifs and evolutionary position among closely related transporters. @*Conclusion, significance and impact of study@#Blast search in the Pfam and Transmembrane Classification Databases was used to establish the classification and the subfamily of DehrP. Clustal omega sequence alignment approach and MEME Suite motif-based analysis tools were used to locate the transporter motifs of DehrP. Dotplots of DehrP sequence was computed using the EMBOSS Dotmatcher. MEGA7 software was used to analyze the phylogenetic position of DehrP among closely related symporters in the Transmembrane Classification Database. Comparative analysis by Pfam shows that DehrP is a member of the Major Facilitator Superfamily (#2.A.1). PSI-Blast against the Transmembrane Classification Database shows that DehrP is significantly aligned with a subfamily of transporters called the Metabolite H+ Symporters (#2.A.1.6). DehrP has six similar sequence motifs with the Metabolite H+ Symporter proteins including the functional motif of GXXXDRXGRR. DehrP is evolutionarily related to Burkholderia caribensis MBA4 Haloacid H+ Symporters (Dehp2 and Deh4p). @*Methodology and results@#Based on sequence similarity, DehrP is a Major Facilitator Superfamily protein that belongs to the Metabolite H+ Symporter protein subfamily which might coordinate the transport of a haloacid coupled with a proton (H+). Mutagenesis of DehrP sequence motifs might be useful in the engineering of Rhizobium sp. RC1 for efficient uptake and degradation of haloacids.