TABLE 3.
Functional classification of ORFs in the M. caseolyticus JCSC5402 chromosome and taxonomic distribution of BLAST best-hit entries to the ORFs
| Class | Functional classification | No. of most similar genes in a taxonomic family to each M. caseolyticus ORF
|
|||
|---|---|---|---|---|---|
| Total | Family Bacillaceae | Family Staphylococceae | Others | ||
| I-1 | Cell wall | 58 | 4 | 49 | 5 |
| I-2 | Transport/binding proteins | 196 | 44 | 129 | 23 |
| I-3 | Sensors | 16 | 1 | 13 | 2 |
| I-4 | Membrane bioenergetics | 63 | 28 | 30 | 5 |
| I-5 | Protein secretion | 8 | 1 | 7 | 0 |
| I-6 | Cell division | 15 | 0 | 15 | 0 |
| I-7 | Transformation/competence | 10 | 1 | 8 | 1 |
| II-1-1 | Specific pathways | 92 | 28 | 55 | 9 |
| II-1-2 | Main glycolytic pathways | 18 | 3 | 15 | 0 |
| II-1-3 | Tricarboxylic acid cycle | 11 | 3 | 8 | 0 |
| II-2 | Metabolism of amino acids | 81 | 10 | 63 | 8 |
| II-3 | Metabolism of nucleotides and nucleic acids | 63 | 7 | 54 | 2 |
| II-4 | Metabolism of lipids | 35 | 6 | 19 | 10 |
| II-5 | Metabolism of coenzymes and prosthetic groups | 80 | 8 | 64 | 8 |
| II-6 | Metabolism of phosphate | 8 | 2 | 6 | 0 |
| II-7 | Metabolism of sulfur | 2 | 1 | 1 | 0 |
| III-1 | DNA replication | 24 | 1 | 22 | 1 |
| III-2 | DNA restriction/modification and repair | 47 | 6 | 31 | 10 |
| III-3 | DNA recombination | 15 | 2 | 12 | 1 |
| III-4 | DNA packaging and segregation | 7 | 2 | 5 | 0 |
| III-5-1 | RNA synthesis initiation | 7 | 1 | 6 | 0 |
| III-5-2 | RNA synthesis regulation | 97 | 22 | 66 | 9 |
| III-5-3 | RNA synthesis elongation | 2 | 0 | 2 | 0 |
| III-5-4 | RNA synthesis termination | 5 | 0 | 5 | 0 |
| III-6 | RNA modification | 41 | 4 | 34 | 3 |
| III-7-1 | Ribosomal proteins | 48 | 5 | 43 | 0 |
| III-7-2 | Aminoacyl-tRNA synthetases | 25 | 1 | 24 | 0 |
| III-7-3 | Protein synthesis initiation | 4 | 0 | 4 | 0 |
| III-7-4 | Protein synthesis elongation | 5 | 0 | 5 | 0 |
| III-7-5 | Protein synthesis termination | 3 | 1 | 2 | 0 |
| III-8 | Protein modification | 71 | 12 | 48 | 11 |
| III-9 | Protein folding | 11 | 2 | 9 | 0 |
| IV-1 | Adaptation to atypical conditions | 29 | 2 | 25 | 2 |
| IV-2 | Detoxification | 58 | 14 | 39 | 5 |
| IV-3 | Antibiotic production | 1 | 1 | 0 | 0 |
| IV-4 | Phage-related functions | 69 | 16 | 9 | 44 |
| IV-5 | Transposon and IS | 6 | 0 | 0 | 6 |
| IV-6 | Miscellaneous | 89 | 20 | 55 | 14 |
| V | Similar to unknown proteins | 408 | 74 | 288 | 48 |
| VI | No similarity | 129 | |||
| Total | 1,957 | 333 | 1,270 | 227 | |