TABLE 3.
Numbers of rpoC-, uvrB-, and recA-derived tags and the phylogenetic level at which they are able to discriminate the 168 sequenced microbial genomes
| Gene and tag sequence location | Enzyme | Recognition sequence | No. of tags at the level ofa:
|
No. of nonidentified organisms | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Domain | Phylum | Class | Order | Family | Genus | Species | ||||
| rpoC, upstream | HpyCH4IV | ACGT | 0 | 1 (4) | 0 | 1 (2) | 1 (3) | 7 (16) | 119 (119) | 2 |
| Sau3AI | GATC | 2 (8) | 4 (16) | 1 (2) | 1 (3) | 0 | 8 (18) | 99 (99) | 0 | |
| BamHI | GGATCC | 0 | 0 | 0 | 0 | 0 | 0 | 21 (21) | 125 | |
| Csp6I | GTAC | 4 (15) | 0 | 2 (5) | 1 (3) | 1 (4) | 6 (13) | 105 (105) | 1 | |
| rpoC, downstream | HpyCH4IV | ACGT | 8 (36) | 1 (4) | 3 (6) | 0 | 0 | 5 (11) | 86 (86) | 1 |
| Sau3AI | GATC | 0 | 3 (7) | 0 | 0 | 0 | 10 (24) | 115 (115) | 0 | |
| BamHI | GGATCC | 0 | 0 | 0 | 0 | 1 (3) | 7 (15) | 61 (61) | 67 | |
| Csp6I | GTAC | 6 (18) | 0 | 1 (3) | 1 (2) | 0 | 7 (17) | 104 (104) | 2 | |
| uvrB, upstream | HpyCH4IV | ACGT | 0 | 0 | 0 | 0 | 0 | 8 (17) | 113 (111) | 8 |
| Sau3AI | GATC | 0 | 1 (2) | 0 | 0 | 0 | 9 (20) | 114 (112) | 0 | |
| BamHI | GGATCC | 0 | 0 | 0 | 0 | 0 | 2 (4) | 31 (31) | 101 | |
| Csp6Ib | GTAC | 1 (9) | 1 (2) | 1 (4) | 0 | 0 | 4 (8) | 109 (107) | 4 | |
| uvrB, downstream | HpyCH4IVb | ACGT | 0 | 2 (7) | 1 (4) | 1 (2) | 0 | 5 (10) | 109 (107) | 3 |
| Sau3AI | GATC | 2 (7) | 1 (4) | 1 (2) | 1 (2) | 0 | 9 (19) | 104 (102) | 0 | |
| BamHI | GGATCC | 0 | 0 | 1 (2) | 0 | 0 | 2 (4) | 36 (36) | 94 | |
| Csp6I | GTAC | 0 | 1 (4) | 0 | 1 (3) | 0 | 5 (10) | 115 (113) | 6 | |
| recA, upstream | HpyCH4IV | ACGT | 1 (NE)c | 0 | 1 (2) | 0 | 0 | 10 (16) | 122 (93) | 2 |
| Sau3AI | GATC | 3 (7) | 0 | 0 | 2 (5) | 0 | 7 (11) | 117 (89) | 1 | |
| BamHI | GGATCC | 0 | 0 | 0 | 0 | 0 | 5 (10) | 59 (51) | 52 | |
| Csp6I | GTAC | 0 | 0 | 0 | 0 | 0 | 10 (17) | 122 (91) | 5 | |
| recA, downstream | HpyCH4IV | ACGT | 2 (4) | 0 | 0 | 0 | 0 | 7 (12) | 123 (94) | 3 |
| Sau3AI | GATC | 1 (4) | 0 | 1 (NE) | 1 (NE) | 0 | 9 (13) | 123 (96) | 0 | |
| BamHI | GGATCC | 0 | 0 | 0 | 0 | 0 | 1 (2) | 45 (36) | 75 | |
| Csp6I | GTAC | 0 | 0 | 0 | 0 | 1 (2) | 10 (17) | 123 (92) | 2 | |
Tags were generated in silico with an MmeI-containing linker cassette from the first position of the anchoring enzyme located upstream or downstream of the gene-specific primer annealing site. Data are presented for HpyCH4IV, Sau3AI, BamHI, and Csp6I as anchoring enzymes. Numbers in parentheses indicate the number of species that can be identified by SP-GSTs at a given phylogenetic level. In the case of multiple gene copies per species, as is the case for uvrB and recA with 138 and 151 occurrences in 136 and 113 strains, respectively, tag numbers at a phylogenetic level can be higher than the number of species distinguished at that level. Tags located at more than 3,000 nucleotides from the primer annealing sites were discarded, as a result of which some organisms were not identified.
For this specific restriction enzyme, tags were generated that did not distinguish between two or more organisms at the domain level (between Archaea and Bacteria).
NE, no effect. At this level the tag had no effect on the final identification of the species, as additional tags were generated from the same species that allowed for identification at a lower phylogenetic level.