Table 2.
SMR subclass member diversity within putative metabolite operons and their association to common metabolite ORF based on genomic loci surveys of sequenced Archaeal and Bacterial chromosomes.
| SMR association to the following operons | |||||||||||
| Amino Acid Transport/Metabolism | Multidrug Resistance | Lipid Mtabolism | |||||||||
| SMR Subclass | Subclass Member | Total number of Loci | Lys/Arg | Trp/Tyr/Phe | Other Amino Acids | Polyamine (spe/cad/put) & Betaine | Glyco-peptide & Poly-ketide | β-lactam metabolism | Sn-G3P | Fatty Acid synthesis | |
| SUG | sugE | ||||||||||
| Putative operons | 118 | lys | trp/aro | liv/ilv/pro | put/spe/bet | MFS/ABC/ecn/bleo | tetR/pbp | ugp/pls | fab/acc | ||
| Frequency in operon/total surveyed loci | 0.8% | 4.2% | 1.7%/0.8%/0.8% | 0.8%/1.7%/0.8% | 3.4%/2.5%/3.4%/0.8% | 5.1%/0.8% | 0.8%/2.5% | 1.7%/0.8% | |||
| Frequency of occurrence in each locus (10 gene radius) | 29.7% | 20.3% | 2.0% | 5.1% | 22.9% | 23.7% | 7.6% | 17.8% | |||
| SMP | emrE/smr | ||||||||||
| Putative operons | 92 | lys | tyr | pro/his/met/cys | put/bet/dpp | ABC/bleo/hlx | tetR/pbp | glp | fab/ech | ||
| Frequency in operon/total surveyed loci | 1.1% | 1.1% | 1.1%/1.1%/1.1%/2.2% | 1.1%/3.3%/1.1% | 1.1%/1.1%/2.2% | 8.7%/1.1% | 3.3% | 1.1%/2.2% | |||
| Frequency of occurrence in each locus (10 gene radius) | 22.8% | 14.1% | 12.0% | 14.1% | 28.3% | 10.9% | 9.8% | 22.8% | |||
| PSMR | yvaE** | ||||||||||
| Putative operons | 16 | --- | --- | pro | --- | MFS/ABC | tetR | --- | acp/fab | ||
| Frequency in operon/total surveyed loci | --- | --- | 12.5% | --- | 6.3%/18.8% | 1.1% | --- | 12.5%/6.3% | |||
| Frequency of occurrence in each locus (10 gene radius) | 25.0% | 18.8% | --- | 43.8% | 12.5% | 6.3% | 18.8% | ||||
| PSMR | yvaD** | ||||||||||
| Putative operons | 7 | arg | --- | --- | --- | --- | tetR | --- | acp/fab | ||
| Frequency in operon/total surveyed loci | 14.3% | --- | --- | --- | --- | 14.3% | --- | 28.6% | |||
| Frequency of occurrence in each locus (10 gene radius) | 14.3% | --- | --- | --- | --- | 28.6% | --- | 42.9% | |||
| PSMR | ydgE/ydgF | ||||||||||
| Putative operons | 22 | lysR | --- | --- | spe* | --- | --- | --- | --- | ||
| Frequency in operon/total surveyed loci | 4.5% | --- | --- | --- | --- | --- | --- | --- | |||
| Frequency of occurrence in each locus (10 gene radius) | 54.5% | --- | --- | 31.8% | 22.7% | --- | --- | 22.7% | |||
| PSMR | ebrA/ebrB | ||||||||||
| Putative operons | 16 | --- | --- | --- | --- | --- | --- | --- | --- | ||
| Frequency in operon/total surveyed loci | --- | --- | --- | --- | --- | --- | --- | --- | |||
| Frequency of occurrence in each locus (10 gene radius) | 12.5% | 6.3% | --- | 6.3% | 31.3% | 43.8% | --- | 50.0% | |||
| PSMR | ykkC/ykkD | ||||||||||
| Putative operons | 9 | --- | aro | liv | spe | MFS | --- | --- | --- | ||
| Frequency in operon/total surveyed loci | --- | 11.1% | 11.1% | 11.1% | 11.1% | --- | --- | --- | |||
| Frequency of occurrence in each locus (10 gene radius) | 22.2% | 55.6% | 11.1% | 11.1% | 33.3% | 33.3% | 11.1% | 44.4% | |||
| PSMR | yvdR/yvdS | 3 | NA | NA | NA | NA | NA | NA | NA | NA | |
| Total loci | 283 | ||||||||||
| SMR association to the following operons | |||||||||||
| Vitamin Metabolism | Nucleotide Metabolism | Horizontal Gene Transfer System | |||||||||
| SMR Subclass | Subclass Member | Total number of Loci | Vitamin (Vit.) B1, B2, & BB3 (thi, rib, nia) | Vit. B7 & BB9 (bio/fol) | Vit. B6 & BB12 (Pyd & Cob) | Coenz. Q10 (Ubi) & F420 | Pur | Pyr | Int/Tn/Mat | Plasmid | Phage genes |
| SUG | sugE | ||||||||||
| Putative operons | 118 | thi/nad | fol | --- | ubi | pur | ctp | tn/rve | vap/kill | --- | |
| Frequency in operon/total surveyed loci | 0.8/2.5% | 0.8% | --- | 1.7% | 4.2% | 0.8% | 2.5% | 2.5% | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | 7.6% | 1.7% | 2.5% | 11.9% | 22.0% | 3.4% | 21.2% | 9.3% | 5.9% | ||
| SMP | emrE/smr | ||||||||||
| Putative operons | 92 | thi/nad | bio/fol | cob | --- | pur | --- | tn/rve | --- | Pro-phage DLP12 | |
| Frequency in operon/total surveyed loci | 1.1%/1.1% | 1.1%/1.1% | 2.2% | --- | 1.1% | --- | 3.3% | --- | 1.1% | ||
| Frequency of occurrence in each locus (10 gene radius) | 17.4% | 12.0% | 3.3% | 9.8% | 8.7% | 3.3% | 14.1% | 2.2% | 4.3% | ||
| PSMR | yvaE** | ||||||||||
| Putative operons | 16 | --- | --- | --- | --- | --- | --- | --- | --- | --- | |
| Frequency in operon/total surveyed loci | --- | --- | --- | --- | --- | --- | --- | --- | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | --- | 6.3% | --- | 25.0% | --- | --- | 12.5% | --- | --- | ||
| PSMR | yvaD** | ||||||||||
| Putative operons | 7 | --- | --- | --- | ubi | pur | --- | --- | --- | --- | |
| Frequency in operon/total surveyed loci | --- | --- | --- | 28.6% | 14.3% | --- | --- | --- | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | --- | 14.3% | --- | 42.9% | 42.9% | 28.6% | 14.3% | --- | --- | ||
| PSMR | ydgE/ydgF | ||||||||||
| Putative operons | 22 | --- | --- | --- | --- | --- | --- | tn/rve | tra/cop | --- | |
| Frequency in operon/total surveyed loci | --- | --- | --- | --- | --- | --- | 4.5% | 9.1% | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | 13.6% | 18.2% | --- | --- | 18.2% | 4.5% | 9.1% | 9.1% | 13.6% | ||
| PSMR | ebrA/ebrB | ||||||||||
| Putative operons | 16 | nad* | fol | --- | --- | pur | --- | --- | --- | --- | |
| Frequency in operon/total surveyed loci | 12.5% | 6.3% | --- | --- | 6.3% | --- | --- | --- | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | 18.8% | 25.0% | 12.5% | 6.3% | 25.0% | --- | 25.0% | --- | 6.3% | ||
| PSMR | ykkC/ykkD | ||||||||||
| Putative operons | 9 | rib | bio | --- | --- | pur | pyr | --- | cdt | --- | |
| Frequency in operon/total surveyed loci | 11.1% | 11.1% | --- | --- | 22.2% | 11.1% | --- | 11.1% | --- | ||
| Frequency of occurrence in each locus (10 gene radius) | 22.2% | 11.1% | 11.1% | --- | 33.3% | 11.1% | 11.1% | 11.1% | --- | ||
| PSMR | yvdR/yvdS | 3 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| Total loci | 283 | ||||||||||
* Indicates these SMR members have experimentally demonstrated transport involvement in the metabolite transport.
** Calculated value listed in table includes both isogenic gene occurances and gene pairs.
Abreviations of genes listed in table: ABC ABC-type antimicrobial peptide transport system; aro aromatic amino acid biosynthesis; bet transport and biosynthesis/degradation of glycine betaines; bleo bleomycin resistance genes; bio involved in biotin (vitamin B7) metabolism; cdt plasmid encoded cytotoxin genes; cob involved in cobalamin vitamin B6 metabolism; dpp ABC-type dipeptide/oligopeptide/nickel transport system; fol involved in folate metabolism; glp utilization of glycerol and sn-glycerol 3-phosphate (sn-G3P); hlx hemolysin genes involved in host virulence; lysR lysine transcriptional regulator; liv/ile branched amino acid biosynthesis (val, ile, leu); met/pro/his/cys amino acid biosynthetic genes; MFS multidrug efflux major facillitator superfamily genes; nad involved in nicotine and nicotinamide metabolism; nag GlcNAc uptake and metabolism; nai (niacin) vitamin B3 metabolism; pbp penicillin binding proteins/cell wall biosynthesis proteins; pls involved in sn-glycerol-3-phosphate phsopholipid biosynthesis; put transport and biosynthesis/degradation of putrescine; pts phosphoenolpyruvate-dependent phosphotransferase system; pur involved in purine nucleotide biosynthesis; pyd (pyridoxine) vitamin B12 metabolism pyr involved in pyrimidine nucleotide biosynthesis; rib involved in riboflavin metabolism; spe transport and biosynthesis/degradation of spermidine; tetR tetracyclin resistance transcriptional regulator; thi (thiamin) vitamin B1 metabolism; tn/rve transposons and integron maturases; trp/tyr biosynthesis of tryptophan/tyrosine; ubi involved in ubiquinone (coenzyme Q10) biosynthesis; ugp uptake of sn-glycerol-3-phosphate and glycerophosphoryl diesters; vap/kill host plasmid virulence and toxin genes.