Table 6 Classification of candidate ORFs into categories, according to several criteria.

Comparison of the previous functional annotations for the candidate ORFs [5] with the function of interest

   A

function assigned to the candidate ORF consistent with function of interest

   A*

function assigned to the candidate ORF not contradicting function of interest (e.g. aldose reductase versus xylose reductase; mitochondrial isocitrate dehydrogenase versus cytosolic isocitrate dehydrogenase)

   A-NA

no function assigned to the candidate ORF (e.g. hypothetical protein)

   A-X

function assigned to the candidate ORF not consistent with function of interest

Protein families (F)

Comparison of the protein domains originally predicted for the candidate ORF [5] with those of the enzymes catalysing the function of interest [6]

   F

protein family of candidate ORF consistent with protein family of function of interest

   F-NA

no protein family associated to the candidate ORF

   F-X

protein family of candidate ORF not consistent with protein family of function of interest

Comparative genomics with yeast (Y)

BLASTP searches of all proteins in S. cerevisiae [35] against all predicted proteins in A. nidulans [5]

   Y

function of the protein in yeast (that has a match with the candidate ORF) consistent with missing function

   Y*

function of the protein in yeast (that has a match with the candidate ORF) not contradicting missing function (e.g. aldose reductase versus xylose reductase; mitochondrial isocitrate dehydrogenase versus cytosolic isocitrate dehydrogenase)

   Y-NA

no match of protein in yeast with the candidate ORF

   Y-X

function of the protein in yeast (that has a match with the candidate ORF) not consistent with missing function

Comparative genomics with other organisms (O)

BLASTP searches of candidate ORF in A. nidulans against (non-redundant) protein database at NCBI [26]

   O

functions of proteins in other organisms (that have a match with the candidate ORF) consistent with missing function

   O*

functions of proteins in other organisms (that have a match with the candidate ORF) not contradicting missing function (e.g. aldose reductase versus xylose reductase; mitochondrial isocitrate dehydrogenase versus cytosolic isocitrate dehydrogenase)

   O-NA

no matches of candidate ORF with proteins in other organisms

   O-X

functions of proteins in other organisms (that have a match with the candidate ORF) not consistent with missing function