Table 4.
Functional categories of genome-unique Pfam domain annotations for genomes of six Rhodopseudomonas palustris strains.*
| Functional category | BisA53 | BisB18 | BisB5 | CGA009 | HaA2 | TIE-1 |
|---|---|---|---|---|---|---|
| Information processing and storage | ||||||
| Translation, ribosomal structure and biogenesis [J] | 0 | 0 | 0 | 0 | 0 | 1 |
| RNA processing and modification [A] | 0 | 0 | 0 | 0 | 0 | 0 |
| Transcription [K] | 1 | 0 | 0 | 2 | 2 | 1 |
| Replication, recombination and repair [L] | 1 | 1 | 1 | 0 | 0 | 2 |
| Chromatin structure and dynamics [B] | 0 | 0 | 0 | 0 | 0 | 0 |
| Cellular processes and signaling | ||||||
| Cell cycle control, cell division, chromosome partitioning [D] | 2 | 1 | 0 | 0 | 0 | 0 |
| Nuclear structure [Y] | 0 | 0 | 0 | 0 | 0 | 0 |
| Defense mechanisms [V] | 0 | 1 | 1 | 0 | 0 | 0 |
| Signal transduction mechanisms [T] | 2 | 2 | 1 | 0 | 0 | 1 |
| Cell wall/membrane/envelope biogenesis [M] | 0 | 2 | 0 | 0 | 0 | 0 |
| Cell motility [N] | 1 | 0 | 0 | 0 | 0 | 0 |
| Cytoskeleton [Z] | 0 | 0 | 0 | 0 | 0 | 0 |
| Extracellular structures [W] | 0 | 0 | 0 | 0 | 1 | 0 |
| Intracellular trafficking, secretion, and vesicular transport [U] | 0 | 0 | 0 | 0 | 1 | 0 |
| Posttranslational modification, protein turnover, chaperones [O] | 0 | 0 | 2 | 0 | 0 | 0 |
| Metabolism | ||||||
| Energy production and conversion [C] | 3 | 6 | 0 | 0 | 0 | 0 |
| Carbohydrate transport and metabolism [G] | 5 | 3 | 0 | 0 | 1 | 0 |
| Amino acid transport and metabolism [E] | 0 | 3 | 0 | 0 | 4 | 0 |
| Nucleotide transport and metabolism [F] | 1 | 1 | 0 | 0 | 0 | 0 |
| Coenzyme transport and metabolism [H] | 2 | 1 | 0 | 0 | 1 | 0 |
| Lipid transport and metabolism [I] | 2 | 1 | 0 | 0 | 0 | 0 |
| Inorganic ion transport and metabolism [P] | 2 | 1 | 0 | 0 | 1 | 0 |
| Secondary metabolites biosynthesis, transport and catabolism [Q] | 0 | 4 | 0 | 1 | 4 | 0 |
| Poorly characterized | ||||||
| General function prediction only [R] | 2 | 3 | 2 | 0 | 4 | 12 |
| Function unknown [S] | 6 | 4 | 1 | 1 | 8 | 6 |
| Unmapped | 29 | 33 | 11 | 5 | 25 | 26 |
| Total Genome-Unique Pfam Domain Annotations | 59 | 67 | 19 | 9 | 52 | 49 |
Notes:
*
Pfam domains are genome-unique based on comparison of the six R. palustris genomes. Inclusion of additional genomes may change the count of genome-unique Pfam domains. To facilitate comparison of unique annotations for biological insights, a visual representation of the data in Table 3 is presented in Figure 4.