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Effect of expect-value cutoff is a function of gene conservation, conserved domain number and gene length.
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The extent of gene conservation is likely to reflect function.
Evolutionary persistence of a pathological peptide sequence may depend on the functions of the precursor gene, conservation or mutation of nucleotides or peptide domains within the precursor gene, or a species-specific physiological environment.
The ability to assess sequence conservation within and between species is informative regarding sequence evolution and is critical to understanding the function of gene products.
In cases of selection three major outcomes have been described: evolution of a new beneficial function in one duplicate (neofunctionalization), partitioning of ancestral functions between the duplicates (subfunctionalization), or conservation of ancestral function(s) in both duplicates (gene conservation) [ 2, 5– 7].
Different approaches have been used to analyse gene organization in bacterial genomes through the development of new algorithm or prediction programs, which are based on characteristics such as intergenic distance, closely related gene function, conservation of gene order in phylogenetically close genomes, or even the prediction of promoter region and transcriptional terminators.
The impacts of nsSNPs on gene functions were predicted based on gene conservation profiles as described by Paterson et al.[ 21].
Calculation of cross species gene conservation.
Despite gene conservation, the possibility of altered functions of homologous genes due to sequence divergence cannot be excluded.
To determine if there is a relationship between gene block conservation and the function of the gene blocks, we assigned each operon keywords based on its function.
The extremely high-level sequence conservation found for this gene in this study may reflect the necessity of sequence conservation in maintaining the function of this gene.
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