Annotation of Five Genes in DNA Mismatch Repair Pathway of Kytococcus Sedentarius
Joseph M. Gawron, Rama Dey-Rao, Ph.D., Stephen T. Koury, Ph.D.
Department of Biotechnical and Clinical Laboratory Sciences, School of Medicine and Biomedical Sciences, State University of New York University at Buffalo, 26 Cary Hall, 3435 Main Street, Buffalo, NY 14214
Background information: Kytococcus sedentarius is an opportunistic pathogen that can survive on and inside humans. Understanding the genetics of this organism and its biologic pathways can lead to better treatments in addition to possible uses of the gene protein products it produces.
Purpose: The purpose of this study was to use in silico gene annotation to characterize five genes in the DNA mismatch repair pathway of K. sedentarius.
Methods: This study used the IMG-ACT website to record data in a digital notebook. The gene details page was accessed for basic information on each gene. Databases such as BLAST, CDD, TIGRFAM, PDB, PSORT-B, MetaCyc, and Prosite were used to collect qualitative and quantitative data for the five genes, including similar genes in other organisms, functional families, crystal structures, localization, and the presence of necessary functional residues. Websites like Phylogeny.fr, Pfam, KEGG, TMHMM, SignalP, Web Logo, and Phobius were used to generate diagrams that used in the analysis.
Conclusions: The proposed annotations for all five genes were confirmed. The genes were found to be phylogenetically conserved between K. sedentarius and multiple orthologs.
Keywords: Gene annotation, Kytococcus sedentarius, DNA mismatch repair, BLAST, orthologs, horizontal gene transfer, DNA sequence conservation