Table 5 Functional profiles of genes lost in different eukaryotic lineages
From: A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
Functional category | Lost genes (KOGs) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | Hs* | Dm* | Coelomates/ Ecdysozoa | Ce* | Animals | Sc | Sp | Yeasts | Ec | Fungi-Ec |
Total | 162/114 | 520/369 | 37/188 | 541/751 | 193 | 299 | 202 | 55 | 1,969 | 802 |
RNA processing and modification | 2/3 | 9/8 | 1/2 | 10/11 | 4 | 15 | 7 | 1 | 88 | 32 |
Translation | 3/3 | 16/11 | 0/5 | 13/10 | 9 | 9 | 6 | 3 | 122 | 10 |
Transcription | 5/2 | 16/12 | 0/4 | 29/33 | 2 | 16 | 9 | 4 | 83 | 40 |
Replication and repair | 4/5 | 28/14 | 1/15 | 29/14 | 2 | 9 | 7 | 3 | 60 | 16 |
Chromatin structure and dynamics | 1/1 | 8/6 | 0/2 | 8/6 | 0 | 5 | 3 | 1 | 29 | 11 |
Energy production and conversion | 7/10 | 9/10 | 5/4 | 12/10 | 7 | 6 | 13 | 1 | 110 | 37 |
Cell cycle control and mitosis | 3/3 | 11/6 | 0/5 | 15/11 | 3 | 12 | 3 | 1 | 61 | 16 |
Amino acid metabolism and transport | 5/6 | 16/9 | 1/8 | 15/7 | 38 | 6 | 9 | 0 | 110 | 18 |
Nucleotide metabolism and transport | 3/3 | 6/3 | 0/3 | 8/5 | 5 | 0 | 3 | 1 | 38 | 9 |
Carbohydrate metabolism and transport | 3/3 | 13/10 | 1/4 | 18/14 | 8 | 10 | 16 | 3 | 70 | 41 |
Coenzyme metabolism | 0/2 | 5/5 | 2/2 | 14/12 | 11 | 1 | 1 | 0 | 51 | 12 |
Lipid metabolism | 1/5 | 27/19 | 4/12 | 18/6 | 4 | 9 | 19 | 2 | 74 | 33 |
Membrane and cell wall structure and biogenesis | 5/4 | 10/10 | 2/2 | 9/11 | 7 | 5 | 3 | 0 | 37 | 15 |
Post-translational modification, protein turnover, chaperone functions | 3/5 | 22/15 | 2/9 | 44/40 | 8 | 29 | 21 | 4 | 167 | 69 |
Inorganic ion transport and metabolism | 2/4 | 8/8 | 2/2 | 8/7 | 9 | 2 | 6 | 4 | 50 | 14 |
Secondary metabolites biosynthesis, transport and catabolism | 1/2 | 6/5 | 1/2 | 5/3 | 2 | 4 | 1 | 0 | 23 | 5 |
Signal transduction | 5/3 | 32/22 | 0/10 | 30/37 | 4 | 16 | 7 | 3 | 110 | 52 |
Intracellular trafficking and secretion | 4/3 | 10/8 | 0/2 | 14/14 | 3 | 5 | 11 | 0 | 116 | 22 |
Nuclear structure | 0/0 | 3/3 | 0/0 | 5/6 | 0 | 1 | 0 | 0 | 16 | 5 |
Cytoskeleton | 0/0 | 2/2 | 0/0 | 6/8 | 0 | 9 | 0 | 3 | 44 | 6 |
General functional prediction only (typically, prediction of biochemical activity) | 14/13 | 79/55 | 5/29 | 88/72 | 30 | 55 | 24 | 11 | 241 | 134 |
Function unknown | 91/34 | 184/128 | 10/66 | 143/414 | 37 | 75 | 33 | 10 | 269 | 205 |