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A BLAST search identified a predicted protein from O. granulosus (OgOGA) that not only shows improved sequence identity (37%) with the hOGA catalytic domain without any alignment gaps, but also, intriguingly, possesses a 200-residue C-terminal domain that shares approx. 20% identity with the hOGA middle domain.
In the absence of a hOGA structure to guide our substrate-specificity studies, we aimed to identify new bacterial OGAs with improved sequence identity and extending to beyond just the catalytic domain.
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Such alterations in amino-acid sequence frequently improve sequence identity to other homologous proteins, suggesting that RNA editing is a process to repair 'damaged' codons.
The process is required for gene expression in plant organelles, because this conversion alters the encoded amino acid residues and improves the sequence identity to homologous proteins.
MOSAIC achieves massive gains in the number of retrieved orthologs while slightly improving average levels of sequence identity.
As RNA editing improves the amino-acid sequence identity of the edited sequence for homologous sequences, if a well-conserved position in the amino-acid sequence from the chloroplast gene is not conserved and C-to-U conversion within the codon can amend this difference, then the nucleotide is a candidate for an RNA editing site.
We also compared the Infinium 450K data to reduced representation bisulfite sequencing data generated on the same samples and found a high level of concordance between the two independent methodologies, which can be further improved by filtering for probe sequence identity and mismatch location.
Our membrane-specific ESSTs consistently improve alignment quality, especially at low sequence identity.
We found that INTREPID is better able to exploit the diversity in such families and that accuracy improves when homologs with very low sequence identity are included in an alignment.
On average, in the 10 25% sequence identity range, alignments are improved by 28 correctly aligned residues compared with alignments made using FUGUE's default substitution tables.
In particular for the easier targets with many alternative templates with a high degree of sequence identity, quality is readily improved with a few percentages over the highest ranked model built on a single template.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com