TABLE 4.
PseudoCAP function classification of deleted genes identified in isolates collected from three patients (A, D, F).
| PseudoCAP manually assigned functions | A-isolates | D-isolates | F-isolates | A- and F- isolates |
| Adaptation, Protection | 1% | 0% | 1% | 0% |
| Amino acid biosynthesis and metabolism | 2% | 0% | 3% | 4% |
| Antibiotic resistance and susceptibility | 1% | 0% | 3% | 2% |
| Biosynthesis of cofactors, prosthetic groups and carriers | 2% | 0% | 6% | 8% |
| Carbon compound catabolism | 5% | 0% | 13% | 16% |
| Cell wall/LPS/Capsule | 0% | 0% | 1% | 0% |
| Central intermediary metabolism | 2% | 0% | 2% | 2% |
| Chaperones and heat shock proteins | 1% | 0% | 1% | 1% |
| DNA replication, recombination, modification and repair | 1% | 0% | 0% | 0% |
| Energy metabolism | 1% | 0% | 1% | 1% |
| Fatty acid and phospholipid metabolism | 1% | 0% | 1% | 1% |
| Membrane protein | 7% | 0% | 9% | 10% |
| Motility and Attachment | 1% | 0% | 5% | 0% |
| Nucleotide biosynthesis and metabolism | 0% | 0% | 0% | 0% |
| Putative enzymes | 7% | 0% | 7% | 8% |
| Secreted Factors (toxins, enzymes, alginate) | 0% | 0% | 0% | 0% |
| Transcriptional regulators | 7% | 0% | 11% | 11% |
| Translation, post-translational modification, degradation | 0% | 0% | 1% | 1% |
| Transport of small molecules | 7% | 0% | 9% | 6% |
| Two-component regulatory systems | 1% | 0% | 4% | 5% |
| Hypothetical, unclassified, unknown | 52% | 100% | 24% | 23% |
Percent of deleted genes per gene function are presented here. PseudoCAP functions are available on the Pseudomonas Genome Database (https://www.pseudomonas.com/). A convergent evolution by deletion was identified in a common region between A- and F- isolates. Percent of deleted genes per gene function are indicated by “A- and F- isolates.” When over than 5% of genes for a given PseudoCAP function were affected (except for “Hypothetical, unclassified, unknown” function), values were indicated in bold.