Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 4.0 --

Collection of regulogs in Lactobacillaceae taxonomic group

General statistics
Genomes 15
TF regulogs 82
TF regulons 485
TF binding sites 1848
RNA regulogs 39
RNA regulons 409
RNA sites 581

This collection involves all regulons that were tentatively predicted by applying integrative comparative genomic approach to a single taxonomic group of closely-related genomes. To infer the regulons operated by transcription factors (TFs), we combined the identification of TF binding sites and cross-genome comparison of regulons with the analysis of the genomic and functional context of candidate target genes. To infer the regulons operated by regulatory RNAs such as riboswitches, we identified candidate RNA regulatory elements using HMM profiles and further analyzed their genomic and functional context.

Studied genomes and reconstructed regulon statistics
TF RNA Total
Genomes Regulons Sites Regulons Sites Regulons Sites
Lactobacillus acidophilus NCFM 26 116 26 41 52 157
Lactobacillus brevis ATCC 367 40 159 30 46 70 205
Lactobacillus casei ATCC 334 41 149 28 36 69 185
Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 18 53 26 33 44 86
Lactobacillus fermentum IFO 3956 30 116 25 41 55 157
Lactobacillus helveticus DPC 4571 20 70 25 36 45 106
Lactobacillus johnsonii NCC 533 26 116 27 38 53 154
Lactobacillus plantarum WCFS1 47 210 31 50 78 260
Lactobacillus reuteri JCM 1112 32 118 28 43 60 161
Lactobacillus rhamnosus GG 42 132 29 37 71 169
Lactobacillus sakei subsp. sakei 23K 37 126 29 36 66 162
Lactobacillus salivarius subsp. salivarius UCC118 31 119 27 33 58 152
Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 32 117 29 49 61 166
Oenococcus oeni PSU-1 25 92 19 23 44 115
Pediococcus pentosaceus ATCC 25745 38 155 30 39 68 194
Genomic distribution of regulons
Family Type Regulator Function
ArgR TF ArgR
1 ArgR

Lactobacillus brevis ATCC 367
2 ArgR

Lactobacillus casei ATCC 334
4 ArgR

Lactobacillus fermentum IFO 3956
4 ArgR

Lactobacillus plantarum WCFS1
3 ArgR

Lactobacillus reuteri JCM 1112
2 ArgR

Lactobacillus rhamnosus GG
1 ArgR

Lactobacillus sakei subsp. sakei 23K
2 ArgR

Lactobacillus salivarius subsp. salivarius UCC118
4 ArgR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 ArgR

Pediococcus pentosaceus ATCC 25745
Arginine degradation; Arginine biosynthesis
ArsR TF CzcR1
2 CzcR1

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 CzcR1

Lactobacillus johnsonii NCC 533
1 CzcR1

Lactobacillus reuteri JCM 1112
Zinc resistance; Cobalt resistance; Cadmium resistance
TF CzcR2
2 CzcR2

Lactobacillus brevis ATCC 367
1 CzcR2

Lactobacillus rhamnosus GG
2 CzcR2

Pediococcus pentosaceus ATCC 25745
Zinc resistance; Cobalt resistance; Cadmium resistance
BglG TF CelR
1 CelR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Cellobiose utilization
TF GutR
1 GutR

Lactobacillus casei ATCC 334
2 GutR

Lactobacillus plantarum WCFS1
1 GutR

Lactobacillus rhamnosus GG
1 GutR

Lactobacillus salivarius subsp. salivarius UCC118
Sorbitol utilization
TF MtlR
1 MtlR

Lactobacillus casei ATCC 334
1 MtlR

Lactobacillus plantarum WCFS1
1 MtlR

Lactobacillus rhamnosus GG
1 MtlR

Lactobacillus salivarius subsp. salivarius UCC118
Mannitol utilization
BirA TF BirA
1 BirA

Lactobacillus fermentum IFO 3956
2 BirA

Lactobacillus plantarum WCFS1
1 BirA

Lactobacillus reuteri JCM 1112
1 BirA

Lactobacillus salivarius subsp. salivarius UCC118
2 BirA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 BirA

Oenococcus oeni PSU-1
1 BirA

Pediococcus pentosaceus ATCC 25745
Biotin biosynthesis
CRP TF FlpA
2 FlpA

Lactobacillus acidophilus NCFM
2 FlpA

Lactobacillus casei ATCC 334
1 FlpA

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
4 FlpA

Lactobacillus fermentum IFO 3956
2 FlpA

Lactobacillus johnsonii NCC 533
4 FlpA

Lactobacillus plantarum WCFS1
2 FlpA

Lactobacillus reuteri JCM 1112
2 FlpA

Lactobacillus rhamnosus GG
2 FlpA

Lactobacillus sakei subsp. sakei 23K
4 FlpA

Lactobacillus salivarius subsp. salivarius UCC118
2 FlpA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 FlpA

Oenococcus oeni PSU-1
2 FlpA

Pediococcus pentosaceus ATCC 25745
Heavy metal resistance
TF NihR
2 NihR

Lactobacillus brevis ATCC 367
2 NihR

Lactobacillus fermentum IFO 3956
2 NihR

Lactobacillus plantarum WCFS1
2 NihR

Lactobacillus sakei subsp. sakei 23K
2 NihR

Pediococcus pentosaceus ATCC 25745
Nickel homeostasis
CcpN TF CcpN
1 CcpN

Lactobacillus casei ATCC 334
1 CcpN

Lactobacillus rhamnosus GG
2 CcpN

Lactobacillus sakei subsp. sakei 23K
1 CcpN

Oenococcus oeni PSU-1
Gluconeogenesis
CopY TF CopR
1 CopR

Lactobacillus acidophilus NCFM
2 CopR

Lactobacillus brevis ATCC 367
2 CopR

Lactobacillus casei ATCC 334
1 CopR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 CopR

Lactobacillus fermentum IFO 3956
2 CopR

Lactobacillus helveticus DPC 4571
1 CopR

Lactobacillus johnsonii NCC 533
2 CopR

Lactobacillus plantarum WCFS1
2 CopR

Lactobacillus reuteri JCM 1112
1 CopR

Lactobacillus rhamnosus GG
1 CopR

Lactobacillus sakei subsp. sakei 23K
1 CopR

Lactobacillus salivarius subsp. salivarius UCC118
1 CopR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 CopR

Oenococcus oeni PSU-1
1 CopR

Pediococcus pentosaceus ATCC 25745
Copper homeostasis
CtsR TF CtsR
4 CtsR

Lactobacillus brevis ATCC 367
3 CtsR

Lactobacillus casei ATCC 334
4 CtsR

Lactobacillus fermentum IFO 3956
5 CtsR

Lactobacillus plantarum WCFS1
4 CtsR

Lactobacillus reuteri JCM 1112
4 CtsR

Lactobacillus rhamnosus GG
5 CtsR

Lactobacillus sakei subsp. sakei 23K
4 CtsR

Lactobacillus salivarius subsp. salivarius UCC118
6 CtsR

Oenococcus oeni PSU-1
5 CtsR

Pediococcus pentosaceus ATCC 25745
Heat shock response
DeoR TF FruR
1 FruR

Lactobacillus acidophilus NCFM
1 FruR

Lactobacillus casei ATCC 334
1 FruR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 FruR

Lactobacillus helveticus DPC 4571
1 FruR

Lactobacillus johnsonii NCC 533
1 FruR

Lactobacillus plantarum WCFS1
1 FruR

Lactobacillus rhamnosus GG
1 FruR

Lactobacillus sakei subsp. sakei 23K
1 FruR

Lactobacillus salivarius subsp. salivarius UCC118
1 FruR

Pediococcus pentosaceus ATCC 25745
Fructose utilization
TF FucR
1 FucR

Lactobacillus rhamnosus GG
Fucose utilization
TF IolR
2 IolR

Lactobacillus rhamnosus GG
Inositol utilization
TF LacR
1 LacR

Lactobacillus casei ATCC 334
1 LacR

Lactobacillus rhamnosus GG
Lactose utilization
TF PflR
3 PflR

Lactobacillus plantarum WCFS1
Formate metabolism
DtxR TF MntR
2 MntR

Lactobacillus brevis ATCC 367
2 MntR

Lactobacillus casei ATCC 334
1 MntR

Lactobacillus fermentum IFO 3956
2 MntR

Lactobacillus plantarum WCFS1
1 MntR

Lactobacillus reuteri JCM 1112
2 MntR

Lactobacillus rhamnosus GG
3 MntR

Lactobacillus sakei subsp. sakei 23K
1 MntR

Lactobacillus salivarius subsp. salivarius UCC118
Manganese homeostasis
FUR TF PerR
6 PerR

Lactobacillus brevis ATCC 367
5 PerR

Lactobacillus casei ATCC 334
4 PerR

Lactobacillus fermentum IFO 3956
6 PerR

Lactobacillus plantarum WCFS1
4 PerR

Lactobacillus reuteri JCM 1112
4 PerR

Lactobacillus rhamnosus GG
4 PerR

Lactobacillus sakei subsp. sakei 23K
5 PerR

Lactobacillus salivarius subsp. salivarius UCC118
2 PerR

Pediococcus pentosaceus ATCC 25745
Manganese homeostasis; Oxidative stress response; Iron homeostasis
TF Zur
3 Zur

Lactobacillus brevis ATCC 367
5 Zur

Lactobacillus casei ATCC 334
3 Zur

Lactobacillus fermentum IFO 3956
6 Zur

Lactobacillus plantarum WCFS1
2 Zur

Lactobacillus reuteri JCM 1112
4 Zur

Lactobacillus rhamnosus GG
1 Zur

Lactobacillus sakei subsp. sakei 23K
3 Zur

Lactobacillus salivarius subsp. salivarius UCC118
2 Zur

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
3 Zur

Oenococcus oeni PSU-1
2 Zur

Pediococcus pentosaceus ATCC 25745
Zinc homeostasis
GntR/MocR TF LAR_1807
2 LAR_1807

Lactobacillus reuteri JCM 1112
2 LAR_1807

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
TF PdxR
2 PdxR

Lactobacillus brevis ATCC 367
2 PdxR

Lactobacillus sakei subsp. sakei 23K
Pyridoxine biosynthesis
TF YdfD/YisV
1 YdfD/YisV

Lactobacillus plantarum WCFS1
Metabolite transport
GntR/Others TF AgaR2
1 AgaR2

Lactobacillus helveticus DPC 4571
2 AgaR2

Lactobacillus johnsonii NCC 533
1 AgaR2

Lactobacillus rhamnosus GG
1 AgaR2

Pediococcus pentosaceus ATCC 25745
N-acetylgalactosamine utilization
TF AraR
1 AraR

Lactobacillus brevis ATCC 367
3 AraR

Lactobacillus fermentum IFO 3956
2 AraR

Lactobacillus plantarum WCFS1
1 AraR

Lactobacillus reuteri JCM 1112
1 AraR

Lactobacillus sakei subsp. sakei 23K
1 AraR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 AraR

Oenococcus oeni PSU-1
1 AraR

Pediococcus pentosaceus ATCC 25745
Arabinose utilization
TF BusR
2 BusR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Betaine utilization
TF Lp_2742
1 Lp_2742

Lactobacillus brevis ATCC 367
1 Lp_2742

Lactobacillus fermentum IFO 3956
1 Lp_2742

Lactobacillus plantarum WCFS1
1 Lp_2742

Lactobacillus reuteri JCM 1112
1 Lp_2742

Lactobacillus sakei subsp. sakei 23K
1 Lp_2742

Lactobacillus salivarius subsp. salivarius UCC118
2 Lp_2742

Pediococcus pentosaceus ATCC 25745
Multidrug efflux; Multidrug resistance
TF NagR
7 NagR

Lactobacillus acidophilus NCFM
4 NagR

Lactobacillus brevis ATCC 367
3 NagR

Lactobacillus casei ATCC 334
4 NagR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 NagR

Lactobacillus fermentum IFO 3956
4 NagR

Lactobacillus helveticus DPC 4571
4 NagR

Lactobacillus johnsonii NCC 533
5 NagR

Lactobacillus plantarum WCFS1
2 NagR

Lactobacillus reuteri JCM 1112
3 NagR

Lactobacillus rhamnosus GG
4 NagR

Lactobacillus sakei subsp. sakei 23K
3 NagR

Lactobacillus salivarius subsp. salivarius UCC118
2 NagR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
3 NagR

Oenococcus oeni PSU-1
5 NagR

Pediococcus pentosaceus ATCC 25745
N-acetylglucosamine utilization
TF TreR
2 TreR

Lactobacillus acidophilus NCFM
1 TreR

Lactobacillus casei ATCC 334
2 TreR

Lactobacillus johnsonii NCC 533
1 TreR

Lactobacillus plantarum WCFS1
1 TreR

Lactobacillus rhamnosus GG
2 TreR

Lactobacillus sakei subsp. sakei 23K
2 TreR

Lactobacillus salivarius subsp. salivarius UCC118
1 TreR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 TreR

Oenococcus oeni PSU-1
2 TreR

Pediococcus pentosaceus ATCC 25745
Trehalose utilization
TF UxuR
3 UxuR

Lactobacillus brevis ATCC 367
Glucuronate utilization; Galacturonate utilization
TF YhcF
2 YhcF

Lactobacillus acidophilus NCFM
1 YhcF

Lactobacillus brevis ATCC 367
1 YhcF

Lactobacillus casei ATCC 334
3 YhcF

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 YhcF

Lactobacillus helveticus DPC 4571
2 YhcF

Lactobacillus johnsonii NCC 533
1 YhcF

Lactobacillus plantarum WCFS1
1 YhcF

Lactobacillus rhamnosus GG
1 YhcF

Pediococcus pentosaceus ATCC 25745
Multidrug resistance; Multidrug efflux
TF YtrA
1 YtrA

Lactobacillus brevis ATCC 367
1 YtrA

Lactobacillus casei ATCC 334
1 YtrA

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 YtrA

Lactobacillus plantarum WCFS1
1 YtrA

Lactobacillus rhamnosus GG
1 YtrA

Lactobacillus sakei subsp. sakei 23K
1 YtrA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 YtrA

Oenococcus oeni PSU-1
Hypothetical ABC transporter
HrcA TF HrcA
6 HrcA

Lactobacillus acidophilus NCFM
3 HrcA

Lactobacillus brevis ATCC 367
5 HrcA

Lactobacillus casei ATCC 334
5 HrcA

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
4 HrcA

Lactobacillus fermentum IFO 3956
5 HrcA

Lactobacillus helveticus DPC 4571
6 HrcA

Lactobacillus johnsonii NCC 533
3 HrcA

Lactobacillus plantarum WCFS1
4 HrcA

Lactobacillus reuteri JCM 1112
5 HrcA

Lactobacillus rhamnosus GG
4 HrcA

Lactobacillus sakei subsp. sakei 23K
2 HrcA

Lactobacillus salivarius subsp. salivarius UCC118
4 HrcA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
3 HrcA

Pediococcus pentosaceus ATCC 25745
Heat shock response
LacI TF BfrR
1 BfrR

Lactobacillus acidophilus NCFM
Fructooligosaccharides utilization
TF CcpA
37 CcpA

Lactobacillus acidophilus NCFM
32 CcpA

Lactobacillus brevis ATCC 367
31 CcpA

Lactobacillus casei ATCC 334
5 CcpA

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
30 CcpA

Lactobacillus fermentum IFO 3956
17 CcpA

Lactobacillus helveticus DPC 4571
35 CcpA

Lactobacillus johnsonii NCC 533
56 CcpA

Lactobacillus plantarum WCFS1
29 CcpA

Lactobacillus reuteri JCM 1112
29 CcpA

Lactobacillus rhamnosus GG
29 CcpA

Lactobacillus sakei subsp. sakei 23K
33 CcpA

Lactobacillus salivarius subsp. salivarius UCC118
32 CcpA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
22 CcpA

Oenococcus oeni PSU-1
42 CcpA

Pediococcus pentosaceus ATCC 25745
Carbon catabolism
TF CcpB
1 CcpB

Lactobacillus casei ATCC 334
1 CcpB

Lactobacillus plantarum WCFS1
1 CcpB

Lactobacillus rhamnosus GG
1 CcpB

Lactobacillus sakei subsp. sakei 23K
unknown
TF ExuR
1 ExuR

Lactobacillus brevis ATCC 367
1 ExuR

Lactobacillus sakei subsp. sakei 23K
Glucuronate utilization; Galacturonate utilization
TF GalR
3 GalR

Lactobacillus brevis ATCC 367
1 GalR

Lactobacillus casei ATCC 334
1 GalR

Lactobacillus fermentum IFO 3956
3 GalR

Lactobacillus plantarum WCFS1
4 GalR

Lactobacillus reuteri JCM 1112
1 GalR

Lactobacillus rhamnosus GG
3 GalR

Lactobacillus sakei subsp. sakei 23K
3 GalR

Lactobacillus salivarius subsp. salivarius UCC118
1 GalR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 GalR

Oenococcus oeni PSU-1
5 GalR

Pediococcus pentosaceus ATCC 25745
Galactosides utilization; Galactose utilization
TF GntR2
1 GntR2

Lactobacillus fermentum IFO 3956
1 GntR2

Lactobacillus reuteri JCM 1112
Gluconate utilization
TF HxlR
1 HxlR

Lactobacillus brevis ATCC 367
1 HxlR

Oenococcus oeni PSU-1
Hexulose metabolism
TF LBA1472
2 LBA1472

Lactobacillus acidophilus NCFM
2 LBA1472

Lactobacillus johnsonii NCC 533
Sugar utilization
TF LJ1265
2 LJ1265

Lactobacillus acidophilus NCFM
2 LJ1265

Lactobacillus johnsonii NCC 533
Pentose utilization
TF LSEI_0368
2 LSEI_0368

Lactobacillus casei ATCC 334
2 LSEI_0368

Lactobacillus rhamnosus GG
Sugar utilization
TF LacR
1 LacR

Lactobacillus acidophilus NCFM
2 LacR

Lactobacillus fermentum IFO 3956
1 LacR

Lactobacillus helveticus DPC 4571
2 LacR

Lactobacillus johnsonii NCC 533
2 LacR

Lactobacillus plantarum WCFS1
1 LacR

Lactobacillus reuteri JCM 1112
2 LacR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Lactose utilization
TF Lp_3221
2 Lp_3221

Lactobacillus casei ATCC 334
2 Lp_3221

Lactobacillus plantarum WCFS1
2 Lp_3221

Lactobacillus rhamnosus GG
Sugar utilization
TF MalR
1 MalR

Lactobacillus brevis ATCC 367
1 MalR

Lactobacillus fermentum IFO 3956
3 MalR

Lactobacillus plantarum WCFS1
1 MalR

Lactobacillus reuteri JCM 1112
1 MalR

Lactobacillus salivarius subsp. salivarius UCC118
2 MalR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 MalR

Pediococcus pentosaceus ATCC 25745
Maltose utilization; Maltodextrin utilization
TF MalR3
2 MalR3

Lactobacillus brevis ATCC 367
2 MalR3

Lactobacillus fermentum IFO 3956
4 MalR3

Lactobacillus plantarum WCFS1
2 MalR3

Lactobacillus reuteri JCM 1112
3 MalR3

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 MalR3

Oenococcus oeni PSU-1
Maltose utilization; Maltodextrin utilization
TF MdxR
2 MdxR

Lactobacillus acidophilus NCFM
2 MdxR

Lactobacillus casei ATCC 334
1 MdxR

Lactobacillus helveticus DPC 4571
2 MdxR

Lactobacillus johnsonii NCC 533
2 MdxR

Lactobacillus plantarum WCFS1
2 MdxR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Maltose utilization; Maltodextrin utilization
TF NigR
2 NigR

Lactobacillus johnsonii NCC 533
2 NigR

Lactobacillus salivarius subsp. salivarius UCC118
Nigerose utilization
TF OglR2
1 OglR2

Lactobacillus casei ATCC 334
Oligoglucoside utilization
TF RbsR
3 RbsR

Lactobacillus brevis ATCC 367
1 RbsR

Lactobacillus casei ATCC 334
3 RbsR

Lactobacillus fermentum IFO 3956
1 RbsR

Lactobacillus plantarum WCFS1
1 RbsR

Lactobacillus reuteri JCM 1112
1 RbsR

Lactobacillus rhamnosus GG
1 RbsR

Lactobacillus sakei subsp. sakei 23K
2 RbsR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 RbsR

Oenococcus oeni PSU-1
1 RbsR

Pediococcus pentosaceus ATCC 25745
Ribose utilization
TF ScrR
2 ScrR

Lactobacillus acidophilus NCFM
2 ScrR

Lactobacillus fermentum IFO 3956
2 ScrR

Lactobacillus johnsonii NCC 533
2 ScrR

Lactobacillus plantarum WCFS1
2 ScrR

Lactobacillus sakei subsp. sakei 23K
2 ScrR

Lactobacillus salivarius subsp. salivarius UCC118
2 ScrR

Pediococcus pentosaceus ATCC 25745
Sucrose utilization
TF ScrR2
2 ScrR2

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Sucrose utilization
LexA TF LexA
4 LexA

Lactobacillus acidophilus NCFM
8 LexA

Lactobacillus brevis ATCC 367
9 LexA

Lactobacillus casei ATCC 334
4 LexA

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
5 LexA

Lactobacillus fermentum IFO 3956
5 LexA

Lactobacillus helveticus DPC 4571
4 LexA

Lactobacillus johnsonii NCC 533
9 LexA

Lactobacillus plantarum WCFS1
6 LexA

Lactobacillus reuteri JCM 1112
9 LexA

Lactobacillus rhamnosus GG
6 LexA

Lactobacillus sakei subsp. sakei 23K
2 LexA

Lactobacillus salivarius subsp. salivarius UCC118
8 LexA

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
6 LexA

Oenococcus oeni PSU-1
6 LexA

Pediococcus pentosaceus ATCC 25745
SOS response
LysR TF MleR
1 MleR

Lactobacillus acidophilus NCFM
2 MleR

Lactobacillus brevis ATCC 367
2 MleR

Lactobacillus casei ATCC 334
2 MleR

Lactobacillus plantarum WCFS1
2 MleR

Lactobacillus reuteri JCM 1112
2 MleR

Lactobacillus rhamnosus GG
2 MleR

Lactobacillus sakei subsp. sakei 23K
2 MleR

Lactobacillus salivarius subsp. salivarius UCC118
2 MleR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 MleR

Oenococcus oeni PSU-1
2 MleR

Pediococcus pentosaceus ATCC 25745
Malate utilization
TF MtaR
2 MtaR

Lactobacillus plantarum WCFS1
Methionine biosynthesis
MarR TF AdcR
1 AdcR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Zinc homeostasis
TF FabT
1 FabT

Lactobacillus brevis ATCC 367
1 FabT

Lactobacillus casei ATCC 334
1 FabT

Lactobacillus fermentum IFO 3956
1 FabT

Lactobacillus helveticus DPC 4571
2 FabT

Lactobacillus reuteri JCM 1112
2 FabT

Lactobacillus rhamnosus GG
1 FabT

Lactobacillus salivarius subsp. salivarius UCC118
1 FabT

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 FabT

Oenococcus oeni PSU-1
Fatty acid biosynthesis
TF LBA0573
1 LBA0573

Lactobacillus acidophilus NCFM
1 LBA0573

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 LBA0573

Lactobacillus helveticus DPC 4571
1 LBA0573

Lactobacillus salivarius subsp. salivarius UCC118
Multidrug resistance
TF YybA
1 YybA

Lactobacillus acidophilus NCFM
1 YybA

Lactobacillus johnsonii NCC 533
unknown
MerR TF GlnR
3 GlnR

Lactobacillus brevis ATCC 367
4 GlnR

Lactobacillus casei ATCC 334
4 GlnR

Lactobacillus plantarum WCFS1
4 GlnR

Lactobacillus rhamnosus GG
1 GlnR

Lactobacillus sakei subsp. sakei 23K
5 GlnR

Lactobacillus salivarius subsp. salivarius UCC118
4 GlnR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 GlnR

Oenococcus oeni PSU-1
2 GlnR

Pediococcus pentosaceus ATCC 25745
Nitrogen assimilation
NiaR TF NiaR
1 NiaR

Lactobacillus casei ATCC 334
2 NiaR

Lactobacillus plantarum WCFS1
1 NiaR

Lactobacillus rhamnosus GG
1 NiaR

Lactobacillus sakei subsp. sakei 23K
2 NiaR

Pediococcus pentosaceus ATCC 25745
NAD biosynthesis
NrdR TF NrdR
4 NrdR

Lactobacillus acidophilus NCFM
5 NrdR

Lactobacillus brevis ATCC 367
5 NrdR

Lactobacillus casei ATCC 334
3 NrdR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
3 NrdR

Lactobacillus fermentum IFO 3956
4 NrdR

Lactobacillus helveticus DPC 4571
3 NrdR

Lactobacillus johnsonii NCC 533
5 NrdR

Lactobacillus plantarum WCFS1
4 NrdR

Lactobacillus reuteri JCM 1112
5 NrdR

Lactobacillus rhamnosus GG
3 NrdR

Lactobacillus sakei subsp. sakei 23K
2 NrdR

Lactobacillus salivarius subsp. salivarius UCC118
4 NrdR

Pediococcus pentosaceus ATCC 25745
Deoxyribonucleotide biosynthesis
NrtR TF NrtR
1 NrtR

Lactobacillus casei ATCC 334
1 NrtR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 NrtR

Lactobacillus fermentum IFO 3956
1 NrtR

Lactobacillus helveticus DPC 4571
1 NrtR

Lactobacillus plantarum WCFS1
1 NrtR

Lactobacillus reuteri JCM 1112
1 NrtR

Lactobacillus rhamnosus GG
1 NrtR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
NAD biosynthesis
PadR TF PadR
2 PadR

Lactobacillus brevis ATCC 367
2 PadR

Lactobacillus plantarum WCFS1
1 PadR

Lactobacillus sakei subsp. sakei 23K
1 PadR

Pediococcus pentosaceus ATCC 25745
Phenolic acid stress response
TF YwzG
1 YwzG

Lactobacillus brevis ATCC 367
1 YwzG

Lactobacillus plantarum WCFS1
1 YwzG

Lactobacillus reuteri JCM 1112
1 YwzG

Lactobacillus salivarius subsp. salivarius UCC118
1 YwzG

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 YwzG

Pediococcus pentosaceus ATCC 25745
Transport
PurR TF PurR
7 PurR

Lactobacillus acidophilus NCFM
4 PurR

Lactobacillus brevis ATCC 367
5 PurR

Lactobacillus casei ATCC 334
4 PurR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
5 PurR

Lactobacillus fermentum IFO 3956
5 PurR

Lactobacillus helveticus DPC 4571
5 PurR

Lactobacillus johnsonii NCC 533
5 PurR

Lactobacillus plantarum WCFS1
3 PurR

Lactobacillus reuteri JCM 1112
5 PurR

Lactobacillus rhamnosus GG
6 PurR

Lactobacillus sakei subsp. sakei 23K
4 PurR

Lactobacillus salivarius subsp. salivarius UCC118
3 PurR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 PurR

Oenococcus oeni PSU-1
6 PurR

Pediococcus pentosaceus ATCC 25745
Purine metabolism
ROK TF XylR
6 XylR

Lactobacillus brevis ATCC 367
3 XylR

Lactobacillus fermentum IFO 3956
2 XylR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 XylR

Pediococcus pentosaceus ATCC 25745
Xylose utilization
Rex TF Rex
3 Rex

Lactobacillus acidophilus NCFM
6 Rex

Lactobacillus brevis ATCC 367
3 Rex

Lactobacillus casei ATCC 334
2 Rex

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
4 Rex

Lactobacillus fermentum IFO 3956
2 Rex

Lactobacillus helveticus DPC 4571
2 Rex

Lactobacillus johnsonii NCC 533
3 Rex

Lactobacillus plantarum WCFS1
5 Rex

Lactobacillus reuteri JCM 1112
3 Rex

Lactobacillus rhamnosus GG
6 Rex

Lactobacillus sakei subsp. sakei 23K
3 Rex

Lactobacillus salivarius subsp. salivarius UCC118
5 Rex

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
3 Rex

Oenococcus oeni PSU-1
3 Rex

Pediococcus pentosaceus ATCC 25745
Energy metabolism
RpiR TF AguR
1 AguR

Lactobacillus brevis ATCC 367
1 AguR

Lactobacillus sakei subsp. sakei 23K
1 AguR

Pediococcus pentosaceus ATCC 25745
Agmatine utilization
TF GntR1
4 GntR1

Lactobacillus brevis ATCC 367
2 GntR1

Lactobacillus casei ATCC 334
1 GntR1

Lactobacillus plantarum WCFS1
2 GntR1

Lactobacillus rhamnosus GG
2 GntR1

Lactobacillus sakei subsp. sakei 23K
2 GntR1

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 GntR1

Oenococcus oeni PSU-1
2 GntR1

Pediococcus pentosaceus ATCC 25745
Gluconate utilization
TF MurR
1 MurR

Lactobacillus acidophilus NCFM
1 MurR

Lactobacillus johnsonii NCC 533
1 MurR

Lactobacillus plantarum WCFS1
1 MurR

Pediococcus pentosaceus ATCC 25745
N-acetylmuramate utilization
TF RpiR
2 RpiR

Lactobacillus acidophilus NCFM
2 RpiR

Lactobacillus casei ATCC 334
1 RpiR

Lactobacillus helveticus DPC 4571
2 RpiR

Lactobacillus salivarius subsp. salivarius UCC118
Sugar utilization
TF TagR
2 TagR

Lactobacillus casei ATCC 334
2 TagR

Lactobacillus johnsonii NCC 533
2 TagR

Lactobacillus rhamnosus GG
2 TagR

Pediococcus pentosaceus ATCC 25745
Tagatose utilization
SdaR TF SdaR
2 SdaR

Lactobacillus brevis ATCC 367
2 SdaR

Lactobacillus reuteri JCM 1112
1 SdaR

Lactobacillus sakei subsp. sakei 23K
Glycerate utilization
SorC TF CggR
1 CggR

Lactobacillus acidophilus NCFM
1 CggR

Lactobacillus brevis ATCC 367
1 CggR

Lactobacillus casei ATCC 334
1 CggR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 CggR

Lactobacillus helveticus DPC 4571
1 CggR

Lactobacillus johnsonii NCC 533
1 CggR

Lactobacillus plantarum WCFS1
1 CggR

Lactobacillus rhamnosus GG
1 CggR

Lactobacillus sakei subsp. sakei 23K
1 CggR

Lactobacillus salivarius subsp. salivarius UCC118
1 CggR

Pediococcus pentosaceus ATCC 25745
Glycolysis
TF DeoR
1 DeoR

Lactobacillus brevis ATCC 367
2 DeoR

Lactobacillus fermentum IFO 3956
1 DeoR

Lactobacillus plantarum WCFS1
2 DeoR

Lactobacillus reuteri JCM 1112
1 DeoR

Lactobacillus sakei subsp. sakei 23K
Deoxynucleoside utilization
TetR TF FatR
1 FatR

Lactobacillus casei ATCC 334
1 FatR

Lactobacillus rhamnosus GG
3 FatR

Oenococcus oeni PSU-1
Toxic fatty acid stress response
TF FlrR
2 FlrR

Lactobacillus brevis ATCC 367
2 FlrR

Lactobacillus plantarum WCFS1
2 FlrR

Lactobacillus sakei subsp. sakei 23K
Drug resistance
TF LBA1638
1 LBA1638

Lactobacillus acidophilus NCFM
1 LBA1638

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 LBA1638

Lactobacillus helveticus DPC 4571
1 LBA1638

Lactobacillus johnsonii NCC 533
Transport
TF LSEI_0081
2 LSEI_0081

Lactobacillus casei ATCC 334
2 LSEI_0081

Lactobacillus rhamnosus GG
2 LSEI_0081

Oenococcus oeni PSU-1
Transport
TF YxeR
1 YxeR

Lactobacillus acidophilus NCFM
1 YxeR

Lactobacillus brevis ATCC 367
1 YxeR

Lactobacillus casei ATCC 334
1 YxeR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 YxeR

Lactobacillus fermentum IFO 3956
1 YxeR

Lactobacillus helveticus DPC 4571
1 YxeR

Lactobacillus johnsonii NCC 533
1 YxeR

Lactobacillus reuteri JCM 1112
1 YxeR

Lactobacillus rhamnosus GG
1 YxeR

Oenococcus oeni PSU-1
1 YxeR

Pediococcus pentosaceus ATCC 25745
Antibiotic resistance
RF00050 RNA FMN
1 FMN

Lactobacillus acidophilus NCFM
2 FMN

Lactobacillus brevis ATCC 367
1 FMN

Lactobacillus casei ATCC 334
1 FMN

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 FMN

Lactobacillus fermentum IFO 3956
1 FMN

Lactobacillus helveticus DPC 4571
1 FMN

Lactobacillus johnsonii NCC 533
1 FMN

Lactobacillus plantarum WCFS1
1 FMN

Lactobacillus reuteri JCM 1112
1 FMN

Lactobacillus rhamnosus GG
1 FMN

Lactobacillus sakei subsp. sakei 23K
1 FMN

Lactobacillus salivarius subsp. salivarius UCC118
2 FMN

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 FMN

Oenococcus oeni PSU-1
2 FMN

Pediococcus pentosaceus ATCC 25745
Riboflavin biosynthesis
RF00059 RNA TPP
1 TPP

Lactobacillus acidophilus NCFM
2 TPP

Lactobacillus brevis ATCC 367
2 TPP

Lactobacillus casei ATCC 334
2 TPP

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
3 TPP

Lactobacillus fermentum IFO 3956
1 TPP

Lactobacillus johnsonii NCC 533
2 TPP

Lactobacillus plantarum WCFS1
3 TPP

Lactobacillus reuteri JCM 1112
2 TPP

Lactobacillus rhamnosus GG
3 TPP

Lactobacillus sakei subsp. sakei 23K
1 TPP

Lactobacillus salivarius subsp. salivarius UCC118
8 TPP

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 TPP

Oenococcus oeni PSU-1
3 TPP

Pediococcus pentosaceus ATCC 25745
Thiamine biosynthesis
RF00080 RNA yybP-ykoY
2 yybP-ykoY

Lactobacillus acidophilus NCFM
1 yybP-ykoY

Lactobacillus brevis ATCC 367
1 yybP-ykoY

Lactobacillus casei ATCC 334
1 yybP-ykoY

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 yybP-ykoY

Lactobacillus johnsonii NCC 533
1 yybP-ykoY

Lactobacillus plantarum WCFS1
1 yybP-ykoY

Lactobacillus rhamnosus GG
1 yybP-ykoY

Lactobacillus sakei subsp. sakei 23K
1 yybP-ykoY

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 yybP-ykoY

Oenococcus oeni PSU-1
1 yybP-ykoY

Pediococcus pentosaceus ATCC 25745
RF00114 RNA S15
1 S15

Lactobacillus brevis ATCC 367
1 S15

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 S15

Lactobacillus johnsonii NCC 533
1 S15

Lactobacillus reuteri JCM 1112
1 S15

Lactobacillus sakei subsp. sakei 23K
1 S15

Lactobacillus salivarius subsp. salivarius UCC118
1 S15

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 S15

Oenococcus oeni PSU-1
1 S15

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF00162 RNA SAM
1 SAM

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 SAM

Oenococcus oeni PSU-1
Methionine biosynthesis
RF00167 RNA Purine
2 Purine

Lactobacillus acidophilus NCFM
1 Purine

Lactobacillus brevis ATCC 367
1 Purine

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 Purine

Lactobacillus fermentum IFO 3956
2 Purine

Lactobacillus helveticus DPC 4571
2 Purine

Lactobacillus johnsonii NCC 533
2 Purine

Lactobacillus plantarum WCFS1
1 Purine

Lactobacillus reuteri JCM 1112
1 Purine

Lactobacillus salivarius subsp. salivarius UCC118
2 Purine

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 Purine

Oenococcus oeni PSU-1
1 Purine

Pediococcus pentosaceus ATCC 25745
Purine metabolism
RF00168 RNA Lysine
2 Lysine

Lactobacillus acidophilus NCFM
1 Lysine

Lactobacillus brevis ATCC 367
2 Lysine

Lactobacillus casei ATCC 334
1 Lysine

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 Lysine

Lactobacillus fermentum IFO 3956
2 Lysine

Lactobacillus helveticus DPC 4571
1 Lysine

Lactobacillus johnsonii NCC 533
1 Lysine

Lactobacillus plantarum WCFS1
2 Lysine

Lactobacillus reuteri JCM 1112
2 Lysine

Lactobacillus rhamnosus GG
1 Lysine

Lactobacillus sakei subsp. sakei 23K
1 Lysine

Lactobacillus salivarius subsp. salivarius UCC118
3 Lysine

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 Lysine

Oenococcus oeni PSU-1
2 Lysine

Pediococcus pentosaceus ATCC 25745
Lysine biosynthesis
RF00174 RNA Cobalamin
1 Cobalamin

Lactobacillus helveticus DPC 4571
Cobalamin biosynthesis
RF00230 RNA T-box(Ala)
1 T-box(Ala)

Lactobacillus acidophilus NCFM
1 T-box(Ala)

Lactobacillus brevis ATCC 367
1 T-box(Ala)

Lactobacillus casei ATCC 334
1 T-box(Ala)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Ala)

Lactobacillus fermentum IFO 3956
1 T-box(Ala)

Lactobacillus helveticus DPC 4571
1 T-box(Ala)

Lactobacillus johnsonii NCC 533
1 T-box(Ala)

Lactobacillus plantarum WCFS1
1 T-box(Ala)

Lactobacillus reuteri JCM 1112
1 T-box(Ala)

Lactobacillus rhamnosus GG
1 T-box(Ala)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Ala)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Ala)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Ala)

Oenococcus oeni PSU-1
1 T-box(Ala)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Arg)
1 T-box(Arg)

Lactobacillus acidophilus NCFM
2 T-box(Arg)

Lactobacillus brevis ATCC 367
1 T-box(Arg)

Lactobacillus casei ATCC 334
1 T-box(Arg)

Lactobacillus fermentum IFO 3956
1 T-box(Arg)

Lactobacillus helveticus DPC 4571
1 T-box(Arg)

Lactobacillus johnsonii NCC 533
1 T-box(Arg)

Lactobacillus plantarum WCFS1
1 T-box(Arg)

Lactobacillus reuteri JCM 1112
1 T-box(Arg)

Lactobacillus rhamnosus GG
1 T-box(Arg)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Arg)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Arg)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Arg)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Asn)
2 T-box(Asn)

Lactobacillus acidophilus NCFM
2 T-box(Asn)

Lactobacillus brevis ATCC 367
1 T-box(Asn)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Asn)

Lactobacillus fermentum IFO 3956
2 T-box(Asn)

Lactobacillus helveticus DPC 4571
1 T-box(Asn)

Lactobacillus johnsonii NCC 533
1 T-box(Asn)

Lactobacillus plantarum WCFS1
1 T-box(Asn)

Lactobacillus reuteri JCM 1112
2 T-box(Asn)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Asp)
1 T-box(Asp)

Lactobacillus acidophilus NCFM
1 T-box(Asp)

Lactobacillus brevis ATCC 367
1 T-box(Asp)

Lactobacillus casei ATCC 334
1 T-box(Asp)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Asp)

Lactobacillus fermentum IFO 3956
1 T-box(Asp)

Lactobacillus helveticus DPC 4571
2 T-box(Asp)

Lactobacillus johnsonii NCC 533
1 T-box(Asp)

Lactobacillus plantarum WCFS1
2 T-box(Asp)

Lactobacillus reuteri JCM 1112
1 T-box(Asp)

Lactobacillus rhamnosus GG
1 T-box(Asp)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Asp)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Asp)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Asp)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Cys)
1 T-box(Cys)

Lactobacillus sakei subsp. sakei 23K
Amino acid metabolism
RNA T-box(Gly)
1 T-box(Gly)

Lactobacillus acidophilus NCFM
1 T-box(Gly)

Lactobacillus brevis ATCC 367
1 T-box(Gly)

Lactobacillus casei ATCC 334
1 T-box(Gly)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Gly)

Lactobacillus fermentum IFO 3956
1 T-box(Gly)

Lactobacillus helveticus DPC 4571
1 T-box(Gly)

Lactobacillus johnsonii NCC 533
1 T-box(Gly)

Lactobacillus plantarum WCFS1
1 T-box(Gly)

Lactobacillus reuteri JCM 1112
1 T-box(Gly)

Lactobacillus rhamnosus GG
1 T-box(Gly)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Gly)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Gly)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Gly)

Oenococcus oeni PSU-1
1 T-box(Gly)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(His)
1 T-box(His)

Lactobacillus casei ATCC 334
1 T-box(His)

Lactobacillus fermentum IFO 3956
1 T-box(His)

Lactobacillus plantarum WCFS1
1 T-box(His)

Lactobacillus rhamnosus GG
Amino acid metabolism
RNA T-box(Ile)
4 T-box(Ile)

Lactobacillus acidophilus NCFM
3 T-box(Ile)

Lactobacillus brevis ATCC 367
1 T-box(Ile)

Lactobacillus casei ATCC 334
1 T-box(Ile)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 T-box(Ile)

Lactobacillus fermentum IFO 3956
2 T-box(Ile)

Lactobacillus helveticus DPC 4571
3 T-box(Ile)

Lactobacillus johnsonii NCC 533
2 T-box(Ile)

Lactobacillus plantarum WCFS1
2 T-box(Ile)

Lactobacillus reuteri JCM 1112
2 T-box(Ile)

Lactobacillus rhamnosus GG
1 T-box(Ile)

Lactobacillus sakei subsp. sakei 23K
2 T-box(Ile)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Ile)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Ile)

Oenococcus oeni PSU-1
1 T-box(Ile)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Leu)
1 T-box(Leu)

Lactobacillus acidophilus NCFM
2 T-box(Leu)

Lactobacillus brevis ATCC 367
1 T-box(Leu)

Lactobacillus casei ATCC 334
1 T-box(Leu)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Leu)

Lactobacillus fermentum IFO 3956
1 T-box(Leu)

Lactobacillus helveticus DPC 4571
1 T-box(Leu)

Lactobacillus johnsonii NCC 533
1 T-box(Leu)

Lactobacillus plantarum WCFS1
1 T-box(Leu)

Lactobacillus reuteri JCM 1112
1 T-box(Leu)

Lactobacillus rhamnosus GG
1 T-box(Leu)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Leu)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Leu)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Leu)

Oenococcus oeni PSU-1
1 T-box(Leu)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Lys)
1 T-box(Lys)

Lactobacillus plantarum WCFS1
Amino acid metabolism
RNA T-box(Met)
4 T-box(Met)

Lactobacillus acidophilus NCFM
3 T-box(Met)

Lactobacillus brevis ATCC 367
4 T-box(Met)

Lactobacillus casei ATCC 334
3 T-box(Met)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
6 T-box(Met)

Lactobacillus fermentum IFO 3956
3 T-box(Met)

Lactobacillus helveticus DPC 4571
2 T-box(Met)

Lactobacillus johnsonii NCC 533
7 T-box(Met)

Lactobacillus plantarum WCFS1
6 T-box(Met)

Lactobacillus reuteri JCM 1112
4 T-box(Met)

Lactobacillus rhamnosus GG
1 T-box(Met)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Met)

Lactobacillus salivarius subsp. salivarius UCC118
6 T-box(Met)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
2 T-box(Met)

Oenococcus oeni PSU-1
2 T-box(Met)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Phe)
1 T-box(Phe)

Lactobacillus acidophilus NCFM
1 T-box(Phe)

Lactobacillus brevis ATCC 367
1 T-box(Phe)

Lactobacillus casei ATCC 334
1 T-box(Phe)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Phe)

Lactobacillus fermentum IFO 3956
1 T-box(Phe)

Lactobacillus helveticus DPC 4571
1 T-box(Phe)

Lactobacillus johnsonii NCC 533
1 T-box(Phe)

Lactobacillus plantarum WCFS1
1 T-box(Phe)

Lactobacillus reuteri JCM 1112
1 T-box(Phe)

Lactobacillus rhamnosus GG
1 T-box(Phe)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Phe)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Phe)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Phe)

Oenococcus oeni PSU-1
1 T-box(Phe)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Pro)
1 T-box(Pro)

Lactobacillus casei ATCC 334
1 T-box(Pro)

Lactobacillus reuteri JCM 1112
1 T-box(Pro)

Lactobacillus rhamnosus GG
Amino acid metabolism
RNA T-box(Ser)
1 T-box(Ser)

Lactobacillus acidophilus NCFM
1 T-box(Ser)

Lactobacillus brevis ATCC 367
1 T-box(Ser)

Lactobacillus casei ATCC 334
1 T-box(Ser)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Ser)

Lactobacillus fermentum IFO 3956
1 T-box(Ser)

Lactobacillus helveticus DPC 4571
1 T-box(Ser)

Lactobacillus johnsonii NCC 533
2 T-box(Ser)

Lactobacillus plantarum WCFS1
1 T-box(Ser)

Lactobacillus reuteri JCM 1112
1 T-box(Ser)

Lactobacillus rhamnosus GG
1 T-box(Ser)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Ser)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Ser)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Ser)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Thr)
1 T-box(Thr)

Lactobacillus acidophilus NCFM
1 T-box(Thr)

Lactobacillus brevis ATCC 367
1 T-box(Thr)

Lactobacillus casei ATCC 334
1 T-box(Thr)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Thr)

Lactobacillus fermentum IFO 3956
1 T-box(Thr)

Lactobacillus helveticus DPC 4571
1 T-box(Thr)

Lactobacillus johnsonii NCC 533
1 T-box(Thr)

Lactobacillus plantarum WCFS1
1 T-box(Thr)

Lactobacillus reuteri JCM 1112
1 T-box(Thr)

Lactobacillus rhamnosus GG
1 T-box(Thr)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Thr)

Lactobacillus salivarius subsp. salivarius UCC118
2 T-box(Thr)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Thr)

Oenococcus oeni PSU-1
1 T-box(Thr)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Trp)
2 T-box(Trp)

Lactobacillus brevis ATCC 367
3 T-box(Trp)

Lactobacillus casei ATCC 334
1 T-box(Trp)

Lactobacillus fermentum IFO 3956
3 T-box(Trp)

Lactobacillus plantarum WCFS1
1 T-box(Trp)

Lactobacillus reuteri JCM 1112
1 T-box(Trp)

Lactobacillus rhamnosus GG
1 T-box(Trp)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Trp)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Trp)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Trp)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Tyr)
2 T-box(Tyr)

Lactobacillus acidophilus NCFM
3 T-box(Tyr)

Lactobacillus brevis ATCC 367
1 T-box(Tyr)

Lactobacillus casei ATCC 334
2 T-box(Tyr)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 T-box(Tyr)

Lactobacillus fermentum IFO 3956
2 T-box(Tyr)

Lactobacillus helveticus DPC 4571
2 T-box(Tyr)

Lactobacillus johnsonii NCC 533
3 T-box(Tyr)

Lactobacillus plantarum WCFS1
2 T-box(Tyr)

Lactobacillus reuteri JCM 1112
1 T-box(Tyr)

Lactobacillus rhamnosus GG
2 T-box(Tyr)

Lactobacillus sakei subsp. sakei 23K
3 T-box(Tyr)

Lactobacillus salivarius subsp. salivarius UCC118
2 T-box(Tyr)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Tyr)

Oenococcus oeni PSU-1
2 T-box(Tyr)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RNA T-box(Val)
2 T-box(Val)

Lactobacillus acidophilus NCFM
2 T-box(Val)

Lactobacillus brevis ATCC 367
2 T-box(Val)

Lactobacillus casei ATCC 334
1 T-box(Val)

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 T-box(Val)

Lactobacillus fermentum IFO 3956
1 T-box(Val)

Lactobacillus helveticus DPC 4571
1 T-box(Val)

Lactobacillus johnsonii NCC 533
2 T-box(Val)

Lactobacillus plantarum WCFS1
1 T-box(Val)

Lactobacillus reuteri JCM 1112
2 T-box(Val)

Lactobacillus rhamnosus GG
1 T-box(Val)

Lactobacillus sakei subsp. sakei 23K
1 T-box(Val)

Lactobacillus salivarius subsp. salivarius UCC118
1 T-box(Val)

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 T-box(Val)

Oenococcus oeni PSU-1
1 T-box(Val)

Pediococcus pentosaceus ATCC 25745
Amino acid metabolism
RF00234 RNA glmS
1 glmS

Lactobacillus plantarum WCFS1
Amino sugar metabolism
RF00380 RNA ykoK
1 ykoK

Lactobacillus acidophilus NCFM
1 ykoK

Lactobacillus brevis ATCC 367
1 ykoK

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
2 ykoK

Lactobacillus helveticus DPC 4571
2 ykoK

Lactobacillus johnsonii NCC 533
1 ykoK

Lactobacillus plantarum WCFS1
1 ykoK

Lactobacillus rhamnosus GG
1 ykoK

Lactobacillus sakei subsp. sakei 23K
Magnesium homeostasis
RF00442 RNA ykkC-yxkD
1 ykkC-yxkD

Lactobacillus brevis ATCC 367
1 ykkC-yxkD

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
Multidrug resistance
RF00515 RNA PyrR
4 PyrR

Lactobacillus acidophilus NCFM
4 PyrR

Lactobacillus brevis ATCC 367
1 PyrR

Lactobacillus casei ATCC 334
4 PyrR

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
5 PyrR

Lactobacillus fermentum IFO 3956
4 PyrR

Lactobacillus helveticus DPC 4571
4 PyrR

Lactobacillus johnsonii NCC 533
4 PyrR

Lactobacillus plantarum WCFS1
4 PyrR

Lactobacillus reuteri JCM 1112
2 PyrR

Lactobacillus rhamnosus GG
4 PyrR

Lactobacillus sakei subsp. sakei 23K
2 PyrR

Lactobacillus salivarius subsp. salivarius UCC118
1 PyrR

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
3 PyrR

Pediococcus pentosaceus ATCC 25745
Pyrimidine metabolism
RF00522 RNA PreQ1
2 PreQ1

Lactobacillus plantarum WCFS1
2 PreQ1

Lactobacillus sakei subsp. sakei 23K
2 PreQ1

Lactobacillus salivarius subsp. salivarius UCC118
2 PreQ1

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 PreQ1

Pediococcus pentosaceus ATCC 25745
Queuosine biosynthesis
RF00555 RNA L13_leader
1 L13_leader

Lactobacillus acidophilus NCFM
1 L13_leader

Lactobacillus brevis ATCC 367
1 L13_leader

Lactobacillus casei ATCC 334
1 L13_leader

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 L13_leader

Lactobacillus helveticus DPC 4571
1 L13_leader

Lactobacillus johnsonii NCC 533
1 L13_leader

Lactobacillus plantarum WCFS1
1 L13_leader

Lactobacillus reuteri JCM 1112
1 L13_leader

Lactobacillus rhamnosus GG
1 L13_leader

Lactobacillus sakei subsp. sakei 23K
1 L13_leader

Lactobacillus salivarius subsp. salivarius UCC118
1 L13_leader

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 L13_leader

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF00556 RNA L19_leader
1 L19_leader

Lactobacillus acidophilus NCFM
1 L19_leader

Lactobacillus brevis ATCC 367
1 L19_leader

Lactobacillus casei ATCC 334
1 L19_leader

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 L19_leader

Lactobacillus fermentum IFO 3956
1 L19_leader

Lactobacillus helveticus DPC 4571
1 L19_leader

Lactobacillus johnsonii NCC 533
1 L19_leader

Lactobacillus plantarum WCFS1
1 L19_leader

Lactobacillus reuteri JCM 1112
1 L19_leader

Lactobacillus rhamnosus GG
1 L19_leader

Lactobacillus sakei subsp. sakei 23K
1 L19_leader

Lactobacillus salivarius subsp. salivarius UCC118
1 L19_leader

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 L19_leader

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF00557 RNA L10_leader
1 L10_leader

Lactobacillus acidophilus NCFM
1 L10_leader

Lactobacillus brevis ATCC 367
1 L10_leader

Lactobacillus casei ATCC 334
1 L10_leader

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 L10_leader

Lactobacillus fermentum IFO 3956
1 L10_leader

Lactobacillus helveticus DPC 4571
1 L10_leader

Lactobacillus johnsonii NCC 533
1 L10_leader

Lactobacillus plantarum WCFS1
1 L10_leader

Lactobacillus reuteri JCM 1112
1 L10_leader

Lactobacillus rhamnosus GG
1 L10_leader

Lactobacillus sakei subsp. sakei 23K
1 L10_leader

Lactobacillus salivarius subsp. salivarius UCC118
1 L10_leader

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 L10_leader

Oenococcus oeni PSU-1
1 L10_leader

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF00558 RNA L20_leader
1 L20_leader

Lactobacillus acidophilus NCFM
1 L20_leader

Lactobacillus brevis ATCC 367
1 L20_leader

Lactobacillus casei ATCC 334
1 L20_leader

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 L20_leader

Lactobacillus fermentum IFO 3956
1 L20_leader

Lactobacillus helveticus DPC 4571
1 L20_leader

Lactobacillus johnsonii NCC 533
1 L20_leader

Lactobacillus plantarum WCFS1
1 L20_leader

Lactobacillus reuteri JCM 1112
1 L20_leader

Lactobacillus rhamnosus GG
1 L20_leader

Lactobacillus sakei subsp. sakei 23K
1 L20_leader

Lactobacillus salivarius subsp. salivarius UCC118
1 L20_leader

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 L20_leader

Oenococcus oeni PSU-1
1 L20_leader

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF00559 RNA L21_leader
1 L21_leader

Lactobacillus acidophilus NCFM
1 L21_leader

Lactobacillus brevis ATCC 367
1 L21_leader

Lactobacillus casei ATCC 334
1 L21_leader

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 L21_leader

Lactobacillus fermentum IFO 3956
1 L21_leader

Lactobacillus helveticus DPC 4571
1 L21_leader

Lactobacillus johnsonii NCC 533
1 L21_leader

Lactobacillus plantarum WCFS1
1 L21_leader

Lactobacillus reuteri JCM 1112
1 L21_leader

Lactobacillus rhamnosus GG
1 L21_leader

Lactobacillus sakei subsp. sakei 23K
1 L21_leader

Lactobacillus salivarius subsp. salivarius UCC118
1 L21_leader

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 L21_leader

Oenococcus oeni PSU-1
1 L21_leader

Pediococcus pentosaceus ATCC 25745
Ribosome biogenesis
RF01054 RNA preQ1-II
1 preQ1-II

Lactobacillus casei ATCC 334
1 preQ1-II

Lactobacillus rhamnosus GG
1 preQ1-II

Pediococcus pentosaceus ATCC 25745
Queuosine biosynthesis
RF01767 RNA SMK_box_riboswitch
1 SMK_box_riboswitch

Lactobacillus acidophilus NCFM
1 SMK_box_riboswitch

Lactobacillus brevis ATCC 367
1 SMK_box_riboswitch

Lactobacillus casei ATCC 334
1 SMK_box_riboswitch

Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
1 SMK_box_riboswitch

Lactobacillus fermentum IFO 3956
1 SMK_box_riboswitch

Lactobacillus helveticus DPC 4571
1 SMK_box_riboswitch

Lactobacillus johnsonii NCC 533
1 SMK_box_riboswitch

Lactobacillus plantarum WCFS1
1 SMK_box_riboswitch

Lactobacillus reuteri JCM 1112
1 SMK_box_riboswitch

Lactobacillus rhamnosus GG
1 SMK_box_riboswitch

Lactobacillus sakei subsp. sakei 23K
1 SMK_box_riboswitch

Lactobacillus salivarius subsp. salivarius UCC118
1 SMK_box_riboswitch

Pediococcus pentosaceus ATCC 25745
Methionine metabolism
RF01831 RNA THF
1 THF

Lactobacillus brevis ATCC 367
1 THF

Lactobacillus casei ATCC 334
1 THF

Lactobacillus reuteri JCM 1112
1 THF

Lactobacillus rhamnosus GG
1 THF

Lactobacillus sakei subsp. sakei 23K
1 THF

Lactobacillus salivarius subsp. salivarius UCC118
1 THF

Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293
1 THF

Pediococcus pentosaceus ATCC 25745
Folate metabolism