ProteinParser—A community based tool for the generation of a detailed protein consensus and FASTA output

Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase

“…We located consensus mutations by counting amino acid frequencies at each position of a Clustal alignment of 100 plant peroxidase sequences [37] using our Protein Parser programme [23] (Approach 1). We validated this approach by two alternative methodologies, Approaches 2 and 3, described above in Methods.…”

“…Approach 1: The peroxidase consensus sequence was generated in silico by the 'Protein Parser' software [23]. One hundred fully confirmed peroxidase protein sequences were downloaded from the NCBI homepage [http://www.ncbi.nlm.nih.gov/], using the following search terms "((((((Peroxidase) AND (plant))) NOT (precursor)) NOT (putative)) NOT (segment)) NOT (catalase)".…”

“…The sequences were then aligned via the Clustal W alignment package [36], using the default parameters. The alignment was saved as a ".aln" file and subsequently processed by Protein Parser [23] with a tolerance level of "50% Consensus" (i.e. ≥ 50% frequency of occurrence of a particular amino acid) to generate the consensus sequence.…”

“…A consensus peroxidase protein sequence was developed "in silico" from aligned sequences of Class III secretory plant peroxidases downloaded from NCBI utilising custom-built bioinformatic software that scores the most frequent amino acid in a particular position [23]. Using this consensus sequence, five HRP residues were mutated to the corresponding consensus residue.…”