Table 2.
Summary of the genomic and functional features of the core-genome of the 56 PHBifs.
| Feature | Feature Count * | Sub-Feature | Sub Feature Count # |
|---|---|---|---|
| Protein Encoding Genes (PEGs) | 613 (100%) | ||
| PEGs predicted with the COGs functions | 442 (72.1%) | Cellular Processes and Signaling | 57 (9.3%) |
| Information Storage and Processing | 135 (22.02%) | ||
| Metabolism | 179 (29.2%) | ||
| Multiple Classes | 31 (5.06%) | ||
| Poorly Characterized | 40 (6.53%) | ||
| PEGs mapped to the KEGG functions | 488 (79.61%) | ||
| PEGs assigned to the Transporter Proteins | 60 (9.79%) | ||
| PEGs assigned to the Virulence Factors | 118 (19.25%) | ||
| Subcellular Localization of PEGs | 613 (100%) | Cell Wall | 1 (0.16%) |
| Cytoplasmic | 497 (81.08%) | ||
| Extracellular | 29 (4.73%) | ||
| Membrane | 86 (14.03%) | ||
| PEGs predicted with the Transmembrane Helices | 78 (12.72%) | ||
| PEGs predicted with the Signal Peptide Cleavage Sites | 9 (1.47%) | ||
| PEGs predicted with the Lipoprotein Signal Peptides | 613 (100%) | Cytoplasmic Proteins | 561 (91.52%) |
| SPaseI-cleaved Proteins | 12 (1.96%) | ||
| Lipoproteins (SPaseII-cleaved Proteins) | 1 (0.16%) | ||
| Transmembrane Proteins | 39 (6.36%) | ||
| PEGs predicted with the Non-Classical (Not Signal Peptide Triggered) Secretion | 94 (15.33%) | ||
| PEGs assigned to the Effector Proteins | 69 (11.26%) | Endoplasmic Reticulum as an Effector Target | 34 (5.55%) |
| Mitochondrion as an Effector Target | 7 (1.14%) | ||
| Endoplasmic Reticulum as a Possible Effector Target | 9 (1.47%) | ||
| Mitochondrion as a Possible Effector Target | 19 (3.1%) | ||
| PEGs assigned to the Essential Genes | 496 (80.91%) | ||
| PEGs assigned to the Types of Other DNA-binding Proteins | 1 (0.16%) | ||
| PEGs assigned to the Types of Transcription Factors | 19 (3.1%) | ||
| PEGs assigned to the Types of Two-Component Systems | 7 (1.14%) | ||
| PEGs assigned to the Carbohydrate Active Enzymes | 11 (1.8%) | Carbohydrate-Binding Modules | 2 (0.32%) |
| Glycoside Hydrolases | 6 (0.97%) | ||
| Glycosyl Transferases | 3 (0.48%) |
*, # are calculated out of 613 PEGs. KEGG: Kyoto Encyclopedia of Genes and Genomes.