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

From: Analysis of Aspergillus nidulans metabolism at the genome-scale

Functional annotation (A)
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