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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.

From: Diversity and evolution of the small multidrug resistance protein family

   

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

         
  1. * Indicates these SMR members have experimentally demonstrated transport involvement in the metabolite transport.
  2. ** Calculated value listed in table includes both isogenic gene occurances and gene pairs.
  3. 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.