Computational approach towards finding evolutionary distance and gene order using promoter sequences of central metabolic pathway.
The comparative analysis of motifs of promoter sequences of the genes encoding enzymes of metabolic pathways such as glycolysis and kreb cycle in different genomes can give insights into the understanding of evolutionary and organizational relationships among both the species as well as enzymes. The comparison of resulting analysis with those of the evolutionary distances drawn considering coding regions of the genes allows one to measure the evolution of complete processes. In the present study we have collected promoter sequences of the glycolysis and kreb cycle genes encoding the respective enzymes from the standard EMBL database and extracted ten Transcription factors (TFs) using the TFsearch tool. This information was put together to develop a database CMPP database both offline and online (http://cmpp.sbbiotech.com). The matrix was developed by calculating the distances based on the presence or absence of motifs (TFs). The phylogenetic tree was obtained by using the NJ method by calculating the distances both within and between the enzymes of glycolysis and kreb cycle individually. The present study could also be extended to pathways such as carbohydrate and lipid metabolic networks.
A
Meera
M
B.M.S College of Engineering, Bull temple road, Bangalore, 560 019, India.
Rangarajan
Lalitha
L
Bhat
Savithri
S
D000465:Algorithms; D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000378:metabolism; D001671:Biochemistry / Q000379:methods; D002241:Carbohydrates / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism; D006801:Humans; D008055:Lipids / Q000737:chemistry; D055432:Metabolomics / Q000379:methods; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D012440:Saccharomyces / Q000378:metabolism; D012984:Software
D002241:Carbohydrates; D008055:Lipids