Table 2.
Functional categories of protein clusters inferred to have been gained and lost in the LD12 clade
| Information storage and processing | Gains | Losses | |
|---|---|---|---|
| A |
RNA processing and modification |
0 |
0 |
| J |
Translation, ribosomal structure and biogenesis |
1 |
2 |
| K |
Transcription |
5 |
0 |
| B |
Chromatin structure and dynamics |
0 |
1 |
| L |
Replication, recombination and repair |
7 |
2 |
| |
Total |
13 |
5 |
|
Metabolism |
|
|
|
| H |
Coenzyme transport and metabolism |
2 |
0 |
| F |
Nucleotide transport and metabolism |
0 |
2 |
| Q |
Secondary metabolites biosynthesis, transport and catabolism |
11 |
9 |
| C |
Energy production and conversion |
8 |
8 |
| P |
Inorganic ion transport and metabolism |
9 |
16 |
| I |
Lipid transport and metabolism |
4 |
5 |
| G |
Carbohydrate transport and metabolism |
12 |
12 |
| E |
Amino acid transport and metabolism |
23 |
22 |
| |
Total |
69 |
74 |
|
Cellular processes and signaling | |||
| O |
Posttranslational modification, protein turnover, chaperones |
5 |
7 |
| W |
Extracellular structures |
0 |
0 |
| T |
Signal transduction mechanisms |
5 |
4 |
| N |
Cell motility |
2 |
1 |
| Y |
Nuclear structure |
0 |
0 |
| V |
Defense mechanisms |
3 |
1 |
| Z |
Cytoskeleton |
0 |
0 |
| M |
Cell wall/membrane/envelope biogenesis |
22 |
6 |
| D |
Cell cycle control, cell division, chromosome partitioning |
0 |
0 |
| U |
Intracellular trafficking, secretion, and vesicular transport |
3 |
1 |
| |
Total |
40 |
20 |
|
Poorly characterized | |||
| S |
Function unknown |
15 |
14 |
| R |
General function prediction only |
26 |
31 |
| |
Total |
41 |
45 |
|
Unmapped to the COG database |
103 |
17 |
|
| Mapped to the COG database | 135 | 113 | |