Table 4

Estimating transcriptome completeness by comparison toNematostellaa
Pathway Number of predicted proteins assigned to this pathway inNematostella Number of orthologs inAiptasiatranscriptome Average% ofNematostellacoding sequence covered by best alignment Average predicted amino acid similarity (%)b
Glycolysis and gluconeogenesis 30 25 89 87
Amino-sugar and nucleotide-sugar metabolism 28 25 68 85
Regulation of autophagy 13 10 63 85
Pentose-phosphate pathway 18 14 81 89
Citrate cycle 28 24 90 89
Valine, leucine, and isoleucine degradation 37 34 80 88
Purine metabolism 92 78 62 86
Fatty acid biosynthesis 5 3 62 79

aAiptasia orthologs to Nematostella proteins in each pathway (as identified in KEGG) were predicted by best-reciprocal-BLAST analysis (see text).

b Using BLOSUM62 similarity matrix [41].

Lehnert et al.

Lehnert et al. BMC Genomics 2012 13:271   doi:10.1186/1471-2164-13-271

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