In silico analysis of hydrolytic enzyme genes in rumen microbial genomes

Ruminants have been serving humans in almost every geography of the world with their various productivity characteristics for thousands of years. Rumen microorganisms, which are in a symbiotic relationship in the digestive system of ruminant animals, provide a great benefit in the digestion and utilization of roughage sources with high cellulose content by ruminant animals. For this reason, it is of great importance to investigate both rumen microorganisms and enzymes, vitamins, metabolites, and similar products produced by these organisms in order to benefit ruminant animals at a maximum level. In today's era of molecular genetics, studies on the identification of these microorganisms and the enzymes they produce at the molecular level have gained momentum. Analyzing the data obtained from these studies with bioinformatics tools and modelling the relationships between them in detail provides additional contributions to molecular genetic studies. In this thesis, in silico analyses of rumen microorganisms and hydrolytic enzymes such as cellulase and xylanase produced by these microorganisms were carried out. Nucleotide, NCBI-BLAST, CDD, COBALT, UniProt, AlphaFold, STRING, Expasy, ProtParam, and ProtScale databases were used for bioinformatic analyses of nucleotide and amino acid sequences. With BLAST, multiple sequence alignments and phylogenetic tree structures were generated and the existing main and outgroups were determined. BLASTn, BLASTp, and BLASTx analyses identified many identical microorganisms with different accession numbers and different bacterial names. It was observed that the microorganisms generally had very low estimated alignment errors and according to their physicochemical properties, most of them were stable and almost all of them had negative GRAVY values. High thermostability was observed for cellulase enzymes and low thermostability for xylanase enzymes. In addition, functional characterization of protein-protein interactions and prediction of protein structures were obtained.