Mitochondrial targeting prediction of selected proteins in S. cerevisiae.

The whole amino acid sequence and the whole amino acid sequence with the 5′ upstream region of the ORF of each protein was analyzed up to the first in-frame stop codon with MitoProt II. In case of the Hfa1p, the identified upstream start codon with the addition of the methionine for the convenience of the calculation with MitoProt II was used. The whole amino acid sequence with the 5′ upstream region of the ORF of each protein was analyzed up to the first in-frame stop codon with Target P. In case of Acp1p, the whole amino acid sequence was used for the calculation with Target P. mTP, SP: Final NN scores on which the final prediction is based. Note that the scores are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class, see below) may be an indication of how certain the prediction is. Loc: S: Secretory pathway, i.e. the sequence contains SP, a signal peptide M: Mitochondrion, i.e. the sequence contains mTP, a mitochondrial targeting peptide; -: Any other location; RC: Reliability class, from 1 to 5, where 1 indicates the strongest prediction. RC is a measure of the size of the difference ('diff') between the highest (winning) and the second highest output scores. There are 5 reliability classes, defined as follows: 1: diff>0.800, 2: 0.800>diff>0.600, 3: 0.600> diff>0.400, 4: 0.400> diff>0.200, 5: 0.200> diff HFA1 and ACP1 are listed as controls for the prediction calculation of MitoProt II and target P.Mitochondrial targeting prediction of selected proteins in S. cerevisiae.