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Online Journal of Bioinformatics©
Volume 22 (2): 136-152, 2021.
Phylogenetic assignment of proteins in entomopathogenic bacteria (Photorhabdus luminescens subsp. laumondii TT01).
Razia M1, Karthik Raja R1, Padmanaban K1, Chellapandi P2 and Sivaramakrishnan S1
Razia M, Raja KR, Padmanaban K, Chellapandi P, Sivaramakrishnan S., Phylogenetic assignment of proteins in entomopathogenic bacteria (Photorhabdus luminescens subsp. laumondii TT01), Onl J Bioinform., 22 (2): 136-152, 2021. Polyketides (KA) are structurally diverse natural products with a broad range of biological activity. Polyketide synthase gene in bacteria synthetizes polyketides. We describe sequence and structural similarities of proteins of Photorhabdus luminescens subsp. laumondii TT01 with polyketide synthases (PKSs). PSI-BLAST revealed proteins homologous to PKS at 2247626-2249476 bp in chromosome 1 with similarity to ketoacyl synthase and acyl carrier protein. Ketosynthase-acyltransferase domain module 5 (2HG4) of Saccharopolyspora erythraea orthologs was used as template for 3D structure. ProFunc and Castp servers revealed structure-function similarity with KA synthase homologs. Phylogenetic analysis showed that β-KA synthase evolutionary relationship with soil and enteric bacteria with horizontal gene transfer to P. luminescence genome. We find that PKS gene in entomopathogenic bacteria may protect host nematodes.
Keywords entomopathogenic nematodes, Heterorhabdus, Photorhabdus, ketoacyl synthase, phylogenetics, polyketides, gene annotation, functional assignment.