Table 2.
Pathema curation assertions
| Pathema clade | Total organisms | Predicted genes | Evidence types supporting manual curation |
Curated specialty genes |
Annotation data types |
Curation assertions |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sequence similarity | Mutant phenotype | Expression pattern | Direct assay | Genome context | Epitopes | Virulence factors | Multidrug exporters | Protein interactions | Experimentally verified | Protein name (%) | Gene symbol (%) | EC number (%) | Molecular function (%) | Biological process (%) | Cellular component (%) | |||
| Bacillus | 40 | 217 352 | 10 645 | 61 | 0 | 57 | 12 | 758 | 74 | 6473 | 163 | 343 | 69 | 20 | 14 | 91 | 94 | 36 |
| Burkholderia | 41 | 245 739 | 48 142 | 104 | 11 | 72 | 110 | 418 | 122 | 5448 | 52 | 714 | 70 | 19 | 15 | 82 | 80 | 40 |
| Clostridium | 36 | 131 359 | 28 803 | 3 | 1 | 32 | 55 | 345 | 17 | 2897 | 1 | 227 | 73 | 22 | 16 | 74 | 73 | 34 |
| Entamoeba | 3 | 28 560 | 2537 | 1 | 0 | 14 | 0 | 0 | 176 | 141 | 0 | 31 | 12 | 1 | 14 | 16 | 10 | 5 |
| Total | 120 | 623 010 | 90 127 | 169 | 12 | 175 | 177 | 1521 | 389 | 14 959 | 216 | 1315 | 68 | 19 | 15 | 80 | 80 | 36 |
Only a subset of annotation data types and curation assertions used by Pathema to describe predicted genes based on supporting evidence are included.