List of Regulated Genes

These genes are classified according to the functional classification of their gene products by SubtiList.

 1 Cell envelope and cellular processes
 1.1 Cell wall
 1.2 Transport/binding proteins and lipoproteins
 1.3 Sensors (signal transduction)
 1.4 Membrane bioenergetics (electron transport chain and ATP synthase)
 1.5 Mobility and chemotaxis
 1.6 Protein secretion
 1.7 Cell division
 1.8 Sporulation
 1.9 Germination
 1.10 Transformation/competence
 2 Intermediary metabolism
 2.1 Metabolism of carbohydrates and related molecules
 2.1.1 Specific pathways
 2.1.2 Main glycolytic pathways
 2.1.3 TCA cycle
 2.2 Metabolism of amino acids and related molecules
 2.3 Metabolism of nucleotides and nucleic acids
 2.4 Metabolism of lipids
 2.5 Metabolism of coenzymes and prosthetic groups
 2.6 Metabolism of phosphate
 2.7 Metabolism of sulfur
 3 Information pathways
 3.1 DNA replication
 3.2 DNA restriction/modification and repair
 3.3 DNA recombination
 3.4 DNA packaging and segregation
 3.5 RNA synthesis
 3.5.1 Initiation
 3.5.2 Regulation
 3.5.3 Elongation
 3.5.4 Termination
 3.6 RNA modification
 3.7 Protein synthesis
 3.7.1 Ribosomal proteins
 3.7.2 Aminoacyl-tRNA synthetases
 3.7.3 Initiation
 3.7.4 Elongation
 3.7.5 Termination
 3.8 Protein modification
 3.9 Protein folding
 4 Other functions
 4.1 Adaptation to atypical conditions
 4.2 Detoxification
 4.3 Antibiotic production
 4.4 Phage-related functions
 4.5 Transposon and IS
 4.6 Miscellaneous
 5 Similar to unknown proteins
 5.1 From B. subtilis
 5.2 From other organisms
 6 No similarity
  Category not assigned


1 Cell envelope and cellular processes

1.1 Cell wall
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
murAA murA murAA UDP-N-acetylglucosamine 1-carboxyvinyltransferase
0
0
dltD ipa-2r dltABCDE
3
3
yrvJ yrvJ
0
0
mbl usd-spoIIID-mbl-flhOP MreB-like protein
1
1
gcaD tms, tms26 gcaD-prs-ctc UDP-N-acetylglucosamine pyrophosphorylase
2
2
dacB dacB-spmAB D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*)
1
1
dacC pbp yoxA-dacC penicillin-binding protein (D-alanyl-D-alanine carboxypeptidase)
2
2
dacF dacF-spoIIAAB-sigF penicilin binding protein (putative D-alanyl-D-alanine carboxypeptidase)
5
7
tuaF yvhF tuaABCDEFGH
2
2
tuaG yvhG tuaABCDEFGH
2
2
tuaD yvhD tuaABCDEFGH UDP-glucose 6-dehydrogenase
2
2
tuaE yvhE tuaABCDEFGH
2
2
mreB divIVB mreBCD-minCD cell-shape determining protein
1
1
cwlD ybaK-cwlD N-acetylmuramoyl-L-alanine amidase
3
3
cwlC cwlC N-acetylmuramoyl-L-alanine amidase
1
1
cwlJ ycbQ cwlJ
1
1
cwlH yqeE cwlH N-acetylmuramoyl-L-alanine amidase
2
2
ywhE pbpG ywhE
2
2
gtaB gtaB UTP-glucose-1-phosphate uridylyltransferase
2
2
dltA ipa-5r, dae dltABCDE D-alanyl-D-alanine carrier protein ligase (Dcl)
3
3
dltB ipa-4r dltABCDE
3
3
dltC ipa-3r dltABCDE D-alanyl carrier protein (Dcp)
3
3
dltE ipa-1r dltABCDE
3
3
ywtD ywtD
0
0
spoVD spoVD penicillin-binding protein
2
3
lytE papQ, cwlF lytE cell wall hydrolase; phosphatase-associated protein (major autolysin) (CWBP33)
2
2
lytD cwlG lytD N-acetylglucosaminidase (major autolysin) (CWBP90)
1
1
lytF cwlE, yhdD lytF gamma-D-glutamate-meso-diaminopimelate muropeptidase (major autolysin) (CWBP49')
1
1
lytC cwlB lytABC N-acetylmuramoyl-L-alanine amidase (major autolysin) (CWBP49)
4
2
lytB cwbA lytABC modifier protein of major autolysin LytC (CWBP76)
4
2
ymaG ymaG
1
0
yqfY yqfZY
2
1
yabE yabE
0
0
tagD tagDEF glycerol-3-phosphate cytidylyltransferase
3
5
tagE rodD, gtaA, gtaD tagDEF UDP-glucose:polyglycerol phosphate glucosyltransferase
3
5
tagF rodC tagDEF CDP-glycerol:polyglycerol phosphate glycero-phosphotransferase
3
5
tagA tagAB
2
4
tagB tagAB
2
4
tagC dinC tagC
1
2
tuaH yvhH tuaABCDEFGH
2
2
tuaB yvhB tuaABCDEFGH
2
2
tuaC yvhC tuaABCDEFGH
2
2
tuaA yvhA tuaABCDEFGH
2
2
yfnG yfnHGFED
2
3
ponA recU-ponA penicillin-binding proteins 1A and 1B
0
0
ytcC ytcC
1
0
ggaA ggaAB membrane-bound protein
1
1
ggaB ggaAB membrane-bound protein
1
1
mreC mreBCD-minCD cell-shape determining protein
1
1
mreD rodB mreBCD-minCD cell-shape determining protein
1
1
wprA yisM wprA cell wall-associated protein precursor (CWBP23, CWBP52)
1
0
pbpF ponA pbpF penicillin-binding protein 2C
1
1
pbpD pbpD-yuxK penicillin-binding protein 4
1
1
pbpE pbpE-racX penicillin-binding protein 4*
2
3
pbpB yllB-ylxA-ftsL-pbpB penicillin-binding protein 2B
0
0
murE murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp UDP-N-acetylmuramoylalanyl-D-glutamate-2,6- diaminopimelate ligase
3
5
yocH yocH
3
2
pbpX pbpX penicillin-binding protein
2
2
wapA wapA-yxxG cell wall-associated protein precursor (CWBP200, 105, 62)
3
3
yrrR pbpI yrrRS
2
1
murB ylxC murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp UDP-N-acetylenolpyruvoylglucosamine reductase
3
5
murC ytxF murC UDP-N-acetyl muramate-alanine ligase
0
0
murD murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp UDP-N-acetylmuramoylalanyl-D-glutamate ligase
3
5
murG murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
3
5
mraY murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp phospho-N-acetylmuramoyl-pentapeptide transferase
3
5

1.2 Transport/binding proteins and lipoproteins
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ybcL ybcL
0
0
yttB yttB
0
0
yxeR yxeR-yxxB
0
0
braB braB branched-chain amino acid transporter
0
0
glnH glnQHMP glutamine ABC transporter (glutamine-binding protein)
1
1
glnM glnQHMP glutamine ABC transporter (integral membrane protein)
1
1
glnQ glnQHMP glutamine ABC transporter (ATP-binding protein)
1
1
glnP glnQHMP glutamine ABC transporter (integral membrane protein)
1
1
ptsG ptsX, crr ptsGHI phosphotransferase system (PTS) glucose-specific enzyme IICBA component
2
2
mscL ywpC mscL large conductance mechanosensitive channel protein
0
0
yvrP yvrPON
1
2
yyzE yyzE-bglA
0
0
ycdH ycdHI-yceA
2
2
rocE rocDEF amino acid permease
3
4
rocC ipa-78d rocABC amino acid permease
3
4
glcU ycxE glcU-gdh
2
1
yvrN yziB, yvrM yvrPON
1
2
ydbO ydbO
0
0
glcP yhjI ntdABC-glcP glucose/mannose:H+ symporter
2
1
rbsA rbsRKDACB ribose ABC transporter (ATP-binding protein)
3
4
kdgT kdgRKAT 2-keto-3-deoxygluconate permease
3
2
ytrF ytrABCDEF
2
1
pbuG yebB pbuG hypoxanthine/guanine permease
1
1
pbuX ypaQ xpt-pbuX xanthine permease
2
2
yfnI yetP yfnI
0
0
mntH ydaR mntH manganese transporter
1
1
mntA ytgA mntABCD manganese ABC transporter (membrane protein)
1
1
mntD ytgD mntABCD manganese ABC transporter
1
1
nrgA nrgAB ammonium transporter
2
2
rbsC rbsRKDACB ribose ABC transporter (permease)
3
4
rbsB rbsRKDACB ribose ABC transporter (ribose-binding protein)
3
4
rbsD rbsRKDACB ribose ABC transporter (membrane protein)
3
4
oppA spo0KA oppABCDF oligopeptide ABC transporter (binding protein)
2
1
yfmI yfmIJ
0
0
yceA ycdHI-yceA
2
2
gntP gntRKPZ gluconate permease
4
5
yjmB uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA
4
4
gabP nrg-21 gabP gamma-aminobutyrate (GABA) permease
3
3
ptsI ptsGHI phosphotransferase system (PTS) enzyme I
2
2
dppB dciAB dppABCDE dipeptide ABC transporter (permease)
3
3
dppC dciAC dppABCDE dipeptide ABC transporter (permease)
3
3
dppD dciAD dppABCDE dipeptide ABC transporter (ATP-binding protein)
3
3
dppE dciAE dppABCDE dipeptide ABC transporter (dipeptide-binding protein)
3
3
fhuD fhuD ferrichrome ABC transporter (ferrichrome-binding protein)
1
1
pyrP pyrRPBCAAABKDFE uracil permease
3
5
feuA feuABC-ybbA iron-binding protein
2
2
feuB feuABC-ybbA integral membrane protein
2
2
feuC feuABC-ybbA integral membrane protein
2
2
glpT ybeE glpTQ glycerol-3-phosphate permease
3
4
glpF glpFK glycerol uptake facilitator
3
3
yciC yciABC
2
4
narK narK-fnr nitrite extrusion protein
4
4
yfhI yfhI
0
0
yybF yybF
0
0
sacP ipa-49d sacPA-ywdA phosphotransferase system (PTS) sucrose-specific enzyme IIBC component
3
3
yfiS yfiSR
0
0
arsB yqcL arsR-yqcK-arsBC membrane-associated protein
2
2
mrpA yufT, shaA, ntrA mrpABCDEFG Na+/H+ antiporter
0
0
bglP sytA bglPH-yxiE phosphotransferase system (PTS) beta-glucoside-specific enzyme IIBCA component
3
3
yabM yabMNOPQ-divIC-yabR
4
3
appC appDFABC oligopeptide ABC transporter (permease)
1
0
appB appDFABC oligopeptide ABC transporter (permease)
1
0
appA appDFABC oligopeptide ABC transporter (oligopeptide-binding protein)
1
0
nupC deoR-dra-nupC-pdp pyrimidine-nucleoside transport protein
3
3

1.3 Sensors (signal transduction)
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
cheA cheN fla-che two-component sensor histidine kinase
2
3
ydfH ydfHI
0
0
dctS ydbF dctSRP two-component sensor histidine kinase
3
2
luxS ytjB luxS autoinducer-2 production protein
0
0
yxdK yxdJK
0
0
yhjL ntdA ntdABC-glcP
2
1
yycG yycFGHIJ-yyxA
0
0
citS yflR citST-yflP two-component sensor histidine kinase
0
0
degS sacU degSU two-component sensor histidine kinase
1
1
ycbM ycbLM
0
0
comP comP two-component sensor histidine kinase
0
0
resE ypxE resABCDE two-component sensor histidine kinase
3
4
yccG yccG
0
0
ytrP ytrP
0
0
ybdK ybdK
1
2
kinE ykrQ kinE-ogt two-component sensor histidine kinase
1
1
kinB kinB-kapB two-component sensor histidine kinase
2
2
kinC ssb kinC two-component sensor histidine kinase
2
2
kinA spoIIF, spoIIJ, gsiC, scoB, scoD kinA two-component sensor histidine kinase
2
2
yocF desK yocFG
0
0
phoR phoPR two-component sensor histidine kinase
6
11
yfiJ yfiJK
0
0
cssS yvqB cssRS two-component sensor histidine kinase
2
3

1.4 Membrane bioenergetics (electron transport chain and ATP synthase)
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ctaD ctaBCDEFG cytochrome caa3 oxidase (subunit I)
1
1
ykuP ykuNOP
2
3
etfA lcfA-ysiAB-etfBA electron transfer flavoprotein (alpha subunit)
3
3
etfB lcfA-ysiAB-etfBA electron transfer flavoprotein (beta subunit)
3
3
cccB yvjA-cccB cytochrome c551
0
0
yhfW yhfW
1
1
ycnD ycnED
0
0
ccdA ccdA-yneIJ integral membrane protein
1
3
yneN yneN
0
0
yqjM yqjM
0
0
trxA trx trxA thioredoxin
3
2
ykuN ykuNOP
2
3
yqiG yqiG
0
0
ykvV spoIVH, stoA ykvUV
3
2
resB ypxB resABCDE
3
4
resC ypxC resABCDE
3
4
resA ypxA resABCDE essential protein similar to cytochrome c biogenesis protein
3
4
ywjF ywjF-acdA-rpoE
2
3
cydB yxkL cydABCD cytochrome bd ubiquinol oxidase (subunit II)
4
6
atpI atp ATP synthase (subunit i)
0
0
atpH atp ATP synthase (subunit delta)
0
0
atpC atp ATP synthase (subunit epsilon)
0
0
atpB atp ATP synthase (subunit a)
0
0
atpA atp ATP synthase (subunit alpha)
0
0
atpG atp ATP synthase (subunit gamma)
0
0
atpF atp ATP synthase (subunit b)
0
0
atpE atp ATP synthase (subunit c)
0
0
atpD atp ATP synthase (subunit beta)
0
0
yvaB acpD yvaB
1
1
yfmJ yfmIJ
0
0
ctaF ctaBCDEFG cytochrome caa3 oxidase (subunit IV)
1
1
ctaE ctaBCDEFG cytochrome caa3 oxidase (subunit III)
1
1
ctaC ctaBCDEFG cytochrome caa3 oxidase (subunit II)
1
1
ldh lctE ldh-lctP L-lactate dehydrogenase
5
3
ycgT ycgT
1
1
yfkO yfkO
0
0
cydA yxkK cydABCD cytochrome bd ubiquinol oxidase (subunit I)
4
6
nfrA ywcG, ipa-43d nfrA-ywcH FMN-containing NADPH-linked nitro/flavin reductase
2
2
ctaB ctaBCDEFG cytochrome caa3 oxydase assembly factor
1
1
ctaA ctaA heme-containing membrane protein
3
4
ywrO ywrO
0
0
narI narGHJI nitrate reductase (gamma subunit)
2
2
narH narGHJI nitrate reductase (beta subunit)
2
2
narJ narGHJI nitrate reductase (protein J)
2
2
narG narGHJI nitrate reductase (alpha subunit)
2
2
hmp ykiA hmp flavohemoglobin
4
2
qoxD ipa-40d qoxD cytochrome aa3 quinol oxidase (subunit IV)
0
0
ydbP ydbP
1
1
qcrB bfcB, petB qcrABC menaquinol:cytochrome c oxidoreductase (cytochrome b subunit)
2
1
qcrC bfcC, petD qcrABC menaquinol:cytochrome c oxidoreductase (cytochrome b/c subunit)
2
1
qcrA bfcA, petC qcrABC menaquinol:cytochrome c oxidoreductase (iron-sulfur subunit)
2
1

1.5 Mobility and chemotaxis
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
flhP yvyB usd-spoIIID-mbl-flhOP flagellar hook-basal body protein
1
1
yvyF yviB comFABC-yvyF-flgM-yvyG-flgKL
3
4
yvyC yviH yvyC-fliDST
1
1
cheV cheV
1
1
cheW fla-che
2
3
cheD ylxK fla-che
2
3
yvyG yviC comFABC-yvyF-flgM-yvyG-flgKL
3
4
flgK comFABC-yvyF-flgM-yvyG-flgKL flagellar hook-associated protein 1 (HAP1)
3
4
cheC ylxJ fla-che
2
3
hag hag flagellin protein
2
2
mcpA tlpA-mcpA methyl-accepting chemotaxis protein
1
2
hemAT yhfV hemAT haem-based aerotactic transducer
1
1
tlpA tlpA-mcpA methyl-accepting chemotaxis protein
1
2
fliL fla-che flagellar protein
2
3
tlpB tlpB methyl-accepting chemotaxis protein
1
1
tlpC tlpC methyl-accepting chemotaxis protein
1
1
fliK fla-che
2
3
fliJ cheF fla-che flagellar protein
2
3
yfmS yfmTS
1
1
yoaH yoaH
1
1
motA mot motAB motility protein A
1
1
motB mot motAB motility protein B
1
1
flgC fla-che flagellar basal-body rod protein
2
3
flgB fla-che flagellar basal-body rod protein
2
3
flgE flgG fla-che flagellar hook protein
2
3
flgM comFABC-yvyF-flgM-yvyG-flgKL anti-sigma factor repressor of sigma-D-dependent transcription
3
4
flgL yviD comFABC-yvyF-flgM-yvyG-flgKL flagellar hook-associated protein 3 (HAP3)
3
4
ytxE motS ccpA-motPS
0
0
ytxD motP ccpA-motPS
0
0
ylxG fla-che
2
3
ylxH fla-che
2
3
fliT yvyC-fliDST flagellar protein
1
1
flhB fla-che flagella-associated protein
2
3
flhA fla-che flagella-associated protein
2
3
flhF fla-che flagella-associated protein
2
3
flhO flgG, yvyA usd-spoIIID-mbl-flhOP flagellar basal-body rod protein
1
1
yvzB yvzB
0
0
fliY cheD fla-che flagellar motor switch protein
2
3
fliZ fla-che flagellar protein
2
3
fliQ fla-che flagellar protein
2
3
fliP fla-che flagellar protein
2
3
fliS yvyC-fliDST flagellar protein
1
1
fliR fla-che flagellar protein
2
3
fliM fla-che flagellar motor switch protein
2
3
mcpB mcpB methyl-accepting chemotaxis protein
1
1
mcpC prg71 mcpC methyl-accepting chemotaxis protein
1
1
fliI fla-che flagellar-specific ATP synthase
2
3
fliH fla-che flagellar assembly protein
2
3
fliE fla-che flagellar hook-basal body protein
2
3
fliD yvyC-fliDST flagellar hook-associated protein 2 (HAP2)
1
1
fliG flaA15 fla-che flagellar motor switch protein
2
3
fliF fla-che flagellar basal-body M-ring protein
2
3

1.6 Protein secretion
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ftsY srb rnc-smc-ftsY signal recognition particle (docking protein)
3
3
secA div, div-341, ts-341 secA-prfB translocase binding subunit (ATPase)
1
1
lytA lppX lytABC membrane bound lipoprotein
4
2
ffh ylxM-ffh signal recognition particle-like (SRP) component
1
1
sipT sipT type I signal peptidase
1
1
sipU ycsB sipU type I signal peptidase
0
0
sipV yhjF yhjE-sipV type I signal peptidase
1
1
sipW yqhE yqxM-sipW-tasA type I signal peptidase
3
3
sipS sipS type I signal peptidase
2
4

1.7 Cell division
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
gidA thdF-gidAB-yyaA glucose-inhibited division protein
1
2
gidB thdF-gidAB-yyaA glucose-inhibited division protein
1
2
ftsA spoIIN ftsAZ cell-division protein
4
6
ftsL ylxB, yllD yllB-ylxA-ftsL-pbpB cell-division protein
0
0
ftsH ftsH cell-division protein and general stress protein (class III heat-shock)
1
1
ftsW ylaO, ylaO ftsW-pycA cell-division protein
1
0
minC mreBCD-minCD
1
1
minD divIVB1 mreBCD-minCD ATPase activator of MinC
1
1
ezrA ytwP ezrA
1
2
ftsZ ts-1 ftsAZ cell-division initiation protein
4
6
yjoB yjoB
1
1
rodA ywcF, ipa-42d rodA
0
0
divIC yabMNOPQ-divIC-yabR cell-division initiation protein
4
3
divIB dds, tms-12 murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp cell-division initiation protein
3
5
yfhK yfhKLM
2
2
yfhF yfhFED
1
0

1.8 Sporulation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ypeB joeB, yzuA sleB-ypeB
1
1
yyaA thdF-gidAB-yyaA
1
2
cotJA cotJABC-yesJK
2
2
cotJB cotJABC-yesJK
2
2
spoIVCA cisA spoIVCA site-specific DNA recombinase
2
3
spoVAC spoVAABCDEF-lysA
2
1
spoVAB spoVAABCDEF-lysA
2
1
spoVAA spoVAABCDEF-lysA
2
1
spoVAF spoVAABCDEF-lysA
2
1
spoVAE spoVAABCDEF-lysA
2
1
spoVAD spoVAABCDEF-lysA
2
1
phrK rapK-phrK regulator of the activity of phosphatase RapK
1
1
phrI rapI-phrI regulator of the activity of phosphatase RapI
2
2
phrC rapC-phrC regulator of the activity of phosphatase RapC and competence and sporulation stimulating factor (CSF)
4
3
phrA gsiAB rapA-phrA inhibitor of the activity of phosphatase RapA
2
2
phrF ywhI rapF-phrF regulator of the activity of phosphatase RapF
2
1
phrG yycL rapG-phrG regulator of the activity of phosphatase RapG
3
3
phrE rapE-phrE regulator of the activity of phosphatase RapE
3
3
yaaH yaaH
1
1
cgeC cgeBA cgeCDE
2
2
cgeB cgeAB cgeAB
3
6
cgeD cgeBB cgeCDE
2
2
obg spo0B-obg GTPase activity
1
1
yqjG yqjG
0
0
soj spo0JA soj-spo0J chromosome partitioning protein; transcriptional regulator
0
0
spoIIAA dacF-spoIIAAB-sigF anti-anti-sigma factor (antagonist of SpoIIAB)
5
7
spoVFA dpaA spoVFAB-asd-dapG-dapA dipicolinate synthase subunit A
2
3
spoVS spoVS
1
1
cotJC cotJABC-yesJK
2
2
ykuD ykuD
1
1
spoIIAB dacF-spoIIAAB-sigF anti-sigma factor (antagonist of sigma-F) and serine kinase
5
7
spoVR spoVR
1
1
spoVK spoVJ spoVK
3
2
spoVM spoVM
2
1
spoVB spoIIIF spoVB
2
1
spoVG 0.4 kb gene spoVG
2
2
spoVE murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp
3
5
seaA yphB yphA-seaA
1
0
ytaA cotI ytaA
1
0
ykvU ykvUV
3
2
spmB ypuK dacB-spmAB spore maturation protein
1
1
spmA ypuJ dacB-spmAB spore maturation protein
1
1
spoIVFA bofB, spoVL spoIVFAB
2
1
spoIVFB spoIVFAB membrane metalloprotease
2
1
safA yrbA safA-coxA morphogenetic protein associated with SpoVID
1
1
spsL ipa-73d sps
1
1
spsI ipa-71d sps
1
1
spsJ ipa-72d sps
1
1
spsD ipa-66d sps
1
1
spsE ipa-67d sps
1
1
spsF ipa-68d sps
1
1
spsG ipa-69d, spsH sps
1
1
spsA ipa-63d sps
1
1
spsB ipa-64d sps
1
1
spsC ipa-65d sps
1
1
kapB kinB-kapB kinase-associated protein B
2
2
spo0E spo0E negative sporulation regulatory phosphatase
2
2
yqfD yqfCD
2
1
splB spl splAB spore photoproduct (thymine dimer) lyase
2
2
spoIIGA spoIIGA-sigE-sigG protease
6
7
spoVID spoVID-ysxE
1
1
csgA csgA-ybxH sporulation-specific SASP protein
2
1
spoIID spoIIC spoIID
2
2
spoIIE spoIIH, spoIIK spoIIE serine phosphatase
2
5
spoIIM spoIIM
2
1
spoIIP spoIIP-yqxA
2
1
spoIIQ ywnI spoIIQ
1
1
spoIIR ipc-27d, csfX spoIIR
2
1
cgeE cgeBC cgeCDE
2
2
kipA ycsFGI-kipIAR-ycsK
3
0
kipI ycsJ ycsFGI-kipIAR-ycsK
3
0
spoVFB dpaB spoVFAB-asd-dapG-dapA dipicolinate synthase subunit B
2
3
spoIIIAH yqhV-spoIIIAABCDEFGH
3
3
sspN sspN-tlp small acid-soluble spore protein
2
2
spoIIIAA yqhV-spoIIIAABCDEFGH
3
3
spoIIIAB yqhV-spoIIIAABCDEFGH
3
3
spoIIIAC yqhV-spoIIIAABCDEFGH
3
3
spoIIIAD yqhV-spoIIIAABCDEFGH
3
3
spoIIIAE yqhV-spoIIIAABCDEFGH
3
3
spoIIIAF yqhV-spoIIIAABCDEFGH
3
3
spoIIIAG yqhV-spoIIIAABCDEFGH
3
3
sspO cotK sspOP small acid-soluble spore protein
1
1
rapA gsiAA, spo0L rapA-phrA response regulator aspartate phosphatase
2
2
sspL sspL small acid-soluble spore protein
1
1
sspJ sspJ small acid-soluble spore protein
1
1
sspH yfjU acoR-sspH small acid-soluble spore protein
2
2
sspI ysfA sspI small acid-soluble spore protein
1
2
sspF 0.3 kb gene sspF small acid-soluble spore protein (alpha/beta-type SASP)
1
1
sspD sspD small acid-soluble spore protein (alpha/beta-type SASP)
2
1
sspE yfhQ-fabL-sspE small acid-soluble spore protein (gamma-type SASP)
5
5
sspB sspB small acid-soluble spore protein (beta-type SASP)
2
1
sspC sspC small acid-soluble spore protein (alpha/beta-type SASP)
1
1
sspA sspA small acid-soluble spore protein (alpha-type SASP)
2
1
sspP cotL sspOP small acid-soluble spore protein
1
1
spoIVA spoVP spoIVA
2
2
spoIVB spoIVB serine peptidase of the SA clan
3
2
cotV cotVWX spore coat protein (insoluble fraction)
3
6
cotW cotVWX spore coat protein (insoluble fraction)
3
6
cotT cotT spore coat protein (inner)
2
1
cotZ cotYZ spore coat protein (insoluble fraction)
3
3
cotX cotVWX spore coat protein (insoluble fraction)
3
6
cotY cotYZ spore coat protein (insoluble fraction)
3
3
cotF cotF spore coat protein
2
1
cotG cotG morphogenetic protein
3
2
bofA bofA
2
3
cotE cotE morphogenic protein
2
2
cotC cotC spore coat protein (outer)
3
4
cotA pig cotA spore coat protein (outer)
3
1
cotM yneL cotM spore coat protein (outer)
2
3
cotH ywrH cotH spore coat protein (inner)
2
2
tgl yuxF, yugV tgl transglutaminase
1
1
tasA cotN, yqhF yqxM-sipW-tasA translocation-dependent antimicrobial spore component
3
3
sinI sinIR antagonist of SinR
4
7
ydhD ydhD
1
0
spoIIIE spoIIIE DNA translocase
1
1
rsfA ywfN, ipa-92r rsfA probable transcriptional regulatory protein
3
0
cgeA cgeAA cgeAB
3
6
yobW csk22 yobW
1
1
cotSA ytxN, ytbA cotSA-cotS-ytxO spore coat protein
1
1
sda sda
3
3
spo0B spo0D spo0B-obg sporulation initiation phosphotransferase
1
1
spo0J spo0JB soj-spo0J site-specific DNA-binding protein
0
0
spo0M ygaI spo0M
1
1
sspM sspM small acid-soluble spore protein
1
1
sspK sspK small acid-soluble spore protein
1
1
sspG sspG-yurS small acid-soluble spore protein
2
3
spsK ipa-73d sps
1
1
usd usd-spoIIID-mbl-flhOP
1
1
cotB cotB spore coat protein (outer)
2
3
rapK yobG rapK-phrK response regulator aspartate phosphatase
1
1
rapJ ycdE rapJ response regulator aspartate phosphatase
0
0
rapI yddL rapI-phrI response regulator aspartate phosphatase
2
2
rapH yeeH, yzqA rapH-phrH response regulator aspartate phosphatase
3
4
rapC yclL rapC-phrC response regulator aspartate phosphatase
4
3
rapB spo0P, ywmE rapB response regulator aspartate phosphatase
1
1
rapG yycM rapG-phrG response regulator aspartate phosphatase
3
3
rapF ywhJ rapF-phrF response regulator aspartate phosphatase
2
1
rapE yqcH rapE-phrE response regulator aspartate phosphatase
3
3
rapD ywpA rapD response regulator aspartate phosphatase
3
2
cotS cotSA-cotS-ytxO spore coat protein
1
1
cotP ydfT ydgBA-cotP spore coat protein
2
2
cotD cotD spore coat protein (inner)
3
6
yraF yraGF-adhB-yraED
1
1
yraG yraGF-adhB-yraED
1
1
yraD yraGF-adhB-yraED
1
1
yraE yraGF-adhB-yraED
1
1
yknT cse15 yknT
1
1
jag spoIIIJ-jag SpoIIIJ-associated protein
1
1
tlp sspN-tlp small acid-soluble spore protein (thioredoxin-like protein)
2
2
coxA yrbB safA-coxA spore cortex protein
1
1
spoIIIJ spo0J87 spoIIIJ-jag
1
1
yabG yabG
1
1
bofC csbX-bofC
4
3

1.9 Germination
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
gerPC yisF gerPABCDEF spore germination protein
2
1
sleB ypeA sleB-ypeB spore cortex-lytic enzyme
1
1
gerKA gerKACB
2
1
yndE yndDEF
1
1
yndD yndDEF
1
1
yndF yndDEF
1
1
gerPD yisE gerPABCDEF spore germination protein
2
1
ykvT ykvT
1
1
gerKB gerKACB
2
1
gerKC gerKACB
2
1
gpr gpr spore protease
4
2
gerBA gerBABC probable component of a germinant receptor
2
1
gerBC gerBABC
2
1
gerBB gerBABC probable component of a germinant receptor
2
1
gerM gerM
2
1
gerD gerD
2
1
gerAA gerAABC
3
2
gerAB gerAABC
3
2
gerAC gerAABC
3
2
gerPF yisC gerPABCDEF spore germination protein
2
1
gerPB yisG gerPABCDEF spore germination protein
2
1
gerPA yisH gerPABCDEF spore germination protein
2
1
gerPE yisD gerPABCDEF spore germination protein
2
1

1.10 Transformation/competence
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
med yjaW med-comZ
1
2
smf smf DNA processing Smf protein homolog
1
2
rok ykuW rok
4
2
comX comQX competence pheromone precursor (pheromone peptide aa 46->55, modified)
1
1
comZ yjzA med-comZ
1
2
comS srfAA-srfAB-comS-srfAC-srfAD
4
5
comC comC DNA-binding protein
2
3
mecA mecA
1
1
comEA comD comEABC unspecific high-affinity DNA-binding protein
2
3
comEC comD comEABC putative integral membrane protein
2
3
comEB comD comEABC
2
3
comER comD, comED comER
0
0
comGC comGABCDEFG-yqzE
3
3
comGB comGABCDEFG-yqzE probably part of the DNA transport machinery
3
3
comGA comGABCDEFG-yqzE
3
3
comGG comGABCDEFG-yqzE probably part of the DNA transport machinery
3
3
comGF comGABCDEFG-yqzE probably part of the DNA transport machinery
3
3
comGE comGABCDEFG-yqzE probably part of the DNA transport machinery
3
3
comGD comGABCDEFG-yqzE probably part of the DNA transport machinery
3
3
comFA comFABC-yvyF-flgM-yvyG-flgKL late competence protein
3
4
comFB comFABC-yvyF-flgM-yvyG-flgKL
3
4
comFC comFABC-yvyF-flgM-yvyG-flgKL
3
4

2 Intermediary metabolism

2.1 Metabolism of carbohydrates and related molecules

2.1.1 Specific pathways
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yngE yngJIHGFE
1
1
yxbG yxaU yxbG
0
0
treA treC trePAR trehalose-6-phosphate hydrolase
3
4
adhB yraGF-adhB-yraED alcohol dehydrogenase
1
1
uxaA yjmJ uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA altronate hydrolase
4
4
uxaB yjmI uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA tagaturonate reductase (altronate oxidoreductase)
4
4
aldY yxkE aldY aldehyde dehydrogenase
1
1
aldX yxaS, yxbE aldX aldehyde dehydrogenase
0
0
ybaN ybxG ybaN
2
1
ydaD ydaDEFG
1
2
ydaF ydaDEFG
1
2
ydaP ydaP
1
1
abfA araABDLMNPQ-abfA alpha-L-arabinofuranosidase
3
5
amyX amyX pullulanase
0
0
araB araABDLMNPQ-abfA L-ribulokinase
3
5
araA araABDLMNPQ-abfA L-arabinose isomerase
3
5
araD araABDLMNPQ-abfA L-ribulose-5-phosphate 4-epimerase
3
5
araM yseB araABDLMNPQ-abfA
3
5
fruK fruB fruRKA fructose-1-phosphate kinase
1
0
yvfC epsL eps
2
3
yvfO yvfKLM-lacA-yvfO
1
0
acoL yfjH acoABCL acetoin dehydrogenase E3 component (dihydrolipoamide dehydrogenase)
3
3
acoA yfjK acoABCL acetoin dehydrogenase E1 component (TPP-dependent alpha subunit)
3
3
acoC yfjI acoABCL acetoin dehydrogenase E2 component (dihydrolipoamide acetyltransferase)
3
3
araL yseA araABDLMNPQ-abfA
3
5
yhxD yhxD
0
0
yhxC yhxC
1
0
uxaC yjmA uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA glucuronate isomerase
4
4
melA melA alpha-D-galactoside galactohydrolase
0
0
pmi yvyI pmi mannose-6-phosphate isomerase
1
1
yqkF yqkF
0
0
acoB yfjJ acoABCL acetoin dehydrogenase E1 component (TPP-dependent beta subunit)
3
3
xynB ynaK xynPB xylan beta-1,4-xylosidase
3
3
yxiM yxiM-deaD
0
0
yveP epsF eps
2
3
yveT epsJ eps
2
3
yveB sacB-yveBA
6
4
yveO epsE eps
2
3
ykuF ykuFG
2
2
licH celD, celF licBCAH 6-phospho-beta-glucosidase
3
2
hxlA yckG hxlAB 3-hexulose-6-phosphate synthase (HPS)
1
1
hxlB yckF hxlAB 6-phospho-3-hexuloisomerase (PHI)
1
1
yrhH yrhH
2
2
ycbF ycbCDEFGHJ
0
0
ycbD ycbCDEFGHJ
0
0
yqiQ mmgABCDE-yqiQ
2
2
iolS yxbF iolRS
2
3
iolD yxdD mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
iolE yxdE mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
iolC yxdC mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
iolH yxdG mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
iolI yxdH mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
ycbC ycbCDEFGHJ
0
0
kdgK kdgRKAT 2-keto-3-deoxygluconate kinase
3
2
kdgA kdgRKAT 2-keto-3-deoxygluconate-6-phosphate aldolase
3
2
ykvQ ykvPQ
1
0
gdh glcU-gdh glucose 1-dehydrogenase
2
1
ywjI ywjI
0
0
ywdH ipa-58r ywdH
0
0
iolB yxdB mmsA-iolBCDEF-idh-iolHI-fbaB
3
5
ytrC ytrABCDEF
2
1
ytrD ytrABCDEF
2
1
acsA acsA acetyl-CoA synthetase
3
2
pta ipa-88d, ywfJ pta phosphotransacetylase
2
3
lacA yvfN yvfKLM-lacA-yvfO beta-galactosidase
1
0
ylbB ylbBC
1
1
yfnH yfnHGFED
2
3
malA glvG, glvA malA-yfiA-malP 6-phospho-alpha-glucosidase
3
2
yhdN yhdNO
2
2
rbsK rbsRKDACB ribokinase
3
4
yitF yitGF
1
1
yvaM yvaM
1
0
gntK gntRKPZ gluconate kinase
4
5
gntZ gntRKPZ 6-phosphogluconate dehydrogenase
4
5
yjmF uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA
4
4
alsS alsSD alpha-acetolactate synthase (pH6)
5
2
alsD alsSD alpha-acetolactate decarboxylase
5
2
galT ipa-36d galKT galactose-1-phosphate uridyltransferase
1
1
galE galE UDP-glucose 4-epimerase
1
1
galK ipa-35d galKT galactokinase
1
1
yoaJ yoaJ
1
1
acuC acuABC acetoin dehydrogenase
2
2
acuB acuABC acetoin dehydrogenase
2
2
acuA acuABC acetoin dehydrogenase
2
2
uxuA yjmE uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA D-mannonate hydrolase
4
4
yjmD uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA
4
4
yfmT yfmTS
1
1
glgA glgBCDAP starch (bacterial glycogen) synthase
1
1
glgB glgBCDAP 1,4-alpha-glucan branching enzyme
1
1
glgC glgBCDAP glucose-1-phosphate adenylyltransferase
1
1
glgD glgBCDAP ADP-glucose pyrophosphorylase
1
1
glgP glgBCDAP glycogen phosphorylase
1
1
ywqF ywqF
0
0
ptsH ptsGHI histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein)
2
2
yolJ sunT-bdbA-yolJ-bdbB
2
0
pel pel pectate lyase
2
2
xynA xynA endo-1,4-beta-xylanase
1
1
idh iolG, iol mmsA-iolBCDEF-idh-iolHI-fbaB myo-inositol 2-dehydrogenase
3
5
abnA abnA arabinan-endo 1,5-alpha-L-arabinase
2
2
yxiA yxiA
0
0
amyE amyA amyE alpha-amylase
3
2
glpD glpD glycerol-3-phosphate dehydrogenase
2
2
glpK glpFK glycerol kinase
3
3
yhcV yhcV
1
1
yxnA yxnA
0
0
ydjL ydjL
0
0
yugT yugT
0
0
yfjS pdaA yfjS
1
0
yugF yugF
0
0
yugK yugK
0
0
yugJ yugJ
0
0
yxjF yxjC-scoAB-yxjF
2
2
sacA ipa-50d sacPA-ywdA sucrase-6-phosphate hydrolase
3
3
sacC sacL levDEFG-sacC levanase
3
4
sacB sacB-yveBA levansucrase
6
4
sacX ipa-14r, sacS sacXY negative regulatory protein of SacY
4
4
xylA xylAB xylose isomerase
4
3
xylB yncA xylAB xylulose kinase
4
3
yycR yycR
0
0
csrA yviG csrA carbon storage regulator
0
0
yckE yckE
0
0
ykrW mtnW mtnWXBD
1
2
ysfD ysfD
0
0
ackA ackA acetate kinase
2
3
phy yodV, yzxA phy phytase
0
0
mtlD mtlB mtlAD mannitol-1-phosphate dehydrogenase
0
0
gutB gutBP sorbitol dehydrogenase
2
2
xsa xsa alpha-L-arabinosidase
2
3
bglH bglPH-yxiE beta-glucosidase
3
3
bglA yyzE-bglA 6-phospho-beta-glucosidase
0
0
bglC eglS, gluB bglC endo-1,4-beta-glucanase
1
1
bglS bgl, licS licT-bglS endo-beta-1,3-1,4 glucanase
4
3
yfhM yfhKLM
2
2
yhdF yhdF
1
1

2.1.2 Main glycolytic pathways
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ywlF ipc-32d ywlFG
1
1
fbaB iolJ, yxdI mmsA-iolBCDEF-idh-iolHI-fbaB fructose-1,6-bisphosphate aldolase
3
5
fbaA tsr, fba fbaA-ywjH fructose-1,6-bisphosphate aldolase
0
0
eno cggR-gapA-pgk-tpiA-pgm-eno enolase
2
3
pfkA pfk pfkA-pyk-ytzA 6-phosphofructokinase
0
0
zwf yqjJ zwf glucose-6-phosphate 1-dehydrogenase
0
0
pdhA aceA pdhABCD pyruvate dehydrogenase (E1 alpha subunit)
1
2
pdhB pdhABCD pyruvate dehydrogenase (E1 beta subunit)
1
2
pdhC pdhABCD pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit)
1
2
pdhD citL pdhABCD dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes
1
2
yqjI yqjHI
0
0
pckA ppc pckA phosphoenolpyruvate carboxykinase
2
2
tpiA tpi, tim cggR-gapA-pgk-tpiA-pgm-eno triose phosphate isomerase
2
3
gapA gap cggR-gapA-pgk-tpiA-pgm-eno glyceraldehyde-3-phosphate dehydrogenase
2
3
gapB gapB-speD glyceraldehyde-3-phosphate dehydrogenase
2
3
tkt tktA tkt transketolase
0
0
ywjH fbaA-ywjH
0
0
fbp fdp, yydE fbp fructose-1,6-bisphosphatase
1
1
pycA ylaP ftsW-pycA pyruvate carboxylase
1
0
pgm cggR-gapA-pgk-tpiA-pgm-eno phosphoglycerate mutase
2
3
pgk gerG cggR-gapA-pgk-tpiA-pgm-eno phosphoglycerate kinase
2
3
pgi yugL pgi-yugMN glucose-6-phosphate isomerase
0
0
pyk pykA pfkA-pyk-ytzA pyruvate kinase
0
0

2.1.3 TCA cycle
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
mmgD yqiO mmgABCDE-yqiQ citrate synthase III
2
2
citZ citA2 citZ-icd-mdh citrate synthase II
3
5
mdh citH citZ-icd-mdh malate dehydrogenase
3
5
citG fumC citG fumarate hydratase
2
3
icd citC citZ-icd-mdh isocitrate dehydrogenase
3
5
sucC sucCD succinyl-CoA synthetase (beta subunit)
0
0
sucD sucCD succinyl-CoA synthetase (alpha subunit)
0
0
citA citA1 citA citrate synthase I
2
1
citB citB aconitate hydratase (aconitase)
5
4
ytsJ ytsJ
0
0
malS malS malate dehydrogenase (decarboxylating)
0
0
ywkA maeA ywkAB
2
2
odhB citM odhAB 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit)
1
1
yjmC uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA
4
4
odhA citK odhAB 2-oxoglutarate dehydrogenase (E1 subunit)
1
1
sdhA citF sdhCAB succinate dehydrogenase (flavoprotein subunit)
1
1
sdhC sdhCAB succinate dehydrogenase (cytochrome b558 subunit)
1
1
sdhB sdhCAB succinate dehydrogenase (iron-sulfur protein)
1
1

2.2 Metabolism of amino acids and related molecules
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
speD ytcF gapB-speD S-adenosylmethionine decarboxylase
2
3
speE ywhF speE-speB spermidine synthase
1
1
speB ywhG speE-speB agmatinase
1
1
ypwA ypwA
0
0
patB patB aminotransferase
0
0
gltB gltAB glutamate synthase (small subunit)
4
5
argJ argA, argE argCJBD-carAB-argF amino-acid acetyltransferase
3
4
argC argCJBD-carAB-argF N-acetylglutamate gamma-semialdehyde dehydrogenase
3
4
goxB yjbR tenAI-goxB-thiSGF-yjbV glycine oxidase
1
0
ureC ureABC urease (alpha subunit)
5
5
gcvT yqhI gcvT-gcvPA-gcvPB aminomethyltransferase (glycine cleavage system protein T)
0
0
glyA glyC, ipc-34d glyA serine hydroxymethyltransferase
4
2
aprE sprE aprE serine alkaline protease (subtilisin E)
6
8
aprX aprX alkaline serine protease
2
2
yxeP yxeKLMNOPQ
3
2
ykrV mtnV mtnV
1
1
yaaE yaaDE
0
0
glnA glnRA glutamine synthetase
3
5
gltA gltAB glutamate synthase (large subunit)
4
5
mmsA iolA, yxdA mmsA-iolBCDEF-idh-iolHI-fbaB methylmalonate-semialdehyde dehydrogenase
3
5
epr ipa-15r epr extracellular serine protease
3
3
trpC trpEDCFBA-hisC-tyrA-aroE indol-3-glycerol phosphate synthase
3
2
trpA trpEDCFBA-hisC-tyrA-aroE tryptophan synthase (alpha subunit)
3
2
trpF trpEDCFBA-hisC-tyrA-aroE phosphoribosyl anthranilate isomerase
3
2
trpD trpEDCFBA-hisC-tyrA-aroE anthranilate phosphoribosyltransferase
3
2
trpE trpEDCFBA-hisC-tyrA-aroE anthranilate synthase
3
2
yvfD epsM eps
2
3
pheA pheBA prephenate dehydratase
0
0
yqjN yqjN
0
0
vpr ipa-45r vpr extracellular serine protease
2
1
dsdA yqjR yqjPQ-dsdA-coaA-yqjT D-serine dehydratase
0
0
cysH cysHP-sat-cysC-ylnDEF phosphoadenosine phosphosulfate
1
1
cysK cysK cysteine synthetase A
2
2
cysE cysA gltX-cysES-yazC-yacOP serine acetyltransferase
2
2
cysC ylnC cysHP-sat-cysC-ylnDEF adenylylsulfate kinase
1
1
ipi ipi intracellular proteinase inhibitor BsuPI
0
1
ybgE ybgE
1
0
ybgJ glsA ybgJ-ybgH
2
2
leuD ilvBHC-leuABCD 3-isopropylmalate dehydratase (small subunit)
5
5
yncD yncD
1
0
yvjB ctpB ctpB
2
1
rocD rocDEF ornithine aminotransferase
3
4
rocF rocDEF arginase
3
4
rocG yweB, ipa-75d rocG glutamate dehydrogenase
2
3
rocA ipa-76d rocABC pyrroline-5 carboxylate dehydrogenase
3
4
rocB ipa-77d rocABC
3
4
ycsA ycsA
0
0
yrhB yrrT-mtn-yrhABC
2
2
yurP yurRQPONML
0
0
yurR yurRQPONML
0
0
yurL yurRQPONML
0
0
yurH pucF yurHG
2
2
carB cpa argCJBD-carAB-argF carbamoyl-phosphate transferase-arginine (subunit B)
3
4
argB argCJBD-carAB-argF N-acetylglutamate 5-phosphotransferase
3
4
yurG pucG yurHG
2
2
argD argCJBD-carAB-argF N-acetylornithine aminotransferase
3
4
argF argCJBD-carAB-argF ornithine carbamoyltransferase
3
4
ilvH ilvN ilvBHC-leuABCD acetolactate synthase (acetohydroxy-acid synthase) (small subunit)
5
5
serA serA phosphoglycerate dehydrogenase
0
0
aroC aroC 3-dehydroquinate dehydratase
0
0
leuB leuC ilvBHC-leuABCD 3-isopropylmalate dehydrogenase
5
5
leuC ilvBHC-leuABCD 3-isopropylmalate dehydratase (large subunit)
5
5
leuA ilvBHC-leuABCD 2-isopropylmalate synthase
5
5
asnO yisO, yucB asnO asparagine synthetase
2
1
asnH yxaN yxbBA-yxnB-asnH-yxaM asparagine synthetase (glutamine-hydrolyzing)
1
0
asnB asn asnB-ytnA asparagine synthetase
0
0
yrhA yrrT-mtn-yrhABC
2
2
hisC aroJ trpEDCFBA-hisC-tyrA-aroE tyrosine/phenylalanine aminotransferase
3
2
yusM yusMLKJ
3
2
pepT pepT peptidase T (tripeptidase)
0
0
nasD nasBC, nirB nasBCDEF assimilatory nitrite reductase (subunit)
7
7
nasE nasBD, nirD nasBCDEF assimilatory nitrite reductase (subunit)
7
7
lysA spoVAABCDEF-lysA diaminopimelate decarboxylase
2
1
lysC ask, aecA lysC aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408)
1
1
ansA ansAB L-asparaginase
2
1
ansB ansAB L-aspartase
2
1
ald spoVN ald L-alanine dehydrogenase
1
1
ureB ureABC urease (beta subunit)
5
5
ureA ureABC urease (gamma subunit)
5
5
asd spoVFAB-asd-dapG-dapA aspartate-semialdehyde dehydrogenase
2
3
gcvPA yqhJ, gcvP gcvT-gcvPA-gcvPB glycine decarboxylase (subunit 1) (glycine cleavage system protein P)
0
0
gcvPB yqhK, gcvP gcvT-gcvPA-gcvPB glycine decarboxylase (subunit 2) (glycine cleavage system protein P)
0
0
ilvD ilvD dihydroxy-acid dehydratase
1
0
ilvA ilvA-ypmP threonine dehydratase
1
0
ilvC ilvBHC-leuABCD ketol-acid reductoisomerase (acetohydroxy-acid isomeroreductase)
5
5
ilvB ilvBHC-leuABCD acetolactate synthase (acetohydroxy-acid synthase) (large subunit)
5
5
nrgB nrgAB nitrogen-regulated PII-like protein
2
2
dapA spoVFAB-asd-dapG-dapA dihydrodipicolinate synthase
2
3
dapG lssD spoVFAB-asd-dapG-dapA aspartokinase I (alpha and beta subunits)
2
3
carA cpa argCJBD-carAB-argF carbamoyl-phosphate transferase-arginine (subunit A)
3
4
ispA ispA intracellular serine protease
4
1
gabT ycnG gabTD 4-aminobutyrate aminotransferase
3
2
gabD ycnH gabTD succinate-semialdehyde dehydrogenase
3
2
proI yqjO proI pyrroline-5-carboxylate reductase
0
0
proG ykeA, yzcA proG pyrroline-5-carboxylate reductase
0
0
pheB pheBA chorismate mutase
0
0
nasB nasBA nasBCDEF assimilatory nitrate reductase (electron transfer subunit)
7
7
nasC narB, nasBB nasBCDEF assimilatory nitrate reductase (catalytic subunit)
7
7
yccC ansZ yccC
2
2
racX pbpE-racX amino acid racemase
2
3
ywrD ywrD
1
1
gudB ypcA gudB glutamate dehydrogenase
1
1
yjcI metI yjcIJ
1
1
yjcJ metC yjcIJ
1
1
metA metB metA homoserine O-succinyltransferase
0
0
metK metE metK S-adenosylmethionine synthetase
0
0
ywaA ipa-0r ywaA
0
0
ywaD ipa-8r ywaD
0
0
yclM yclM
0
0
trpB trpEDCFBA-hisC-tyrA-aroE tryptophan synthase (beta subunit)
3
2
aroA aroG aroA chorismate mutase-isozyme 3
0
0
tyrA trpEDCFBA-hisC-tyrA-aroE prephenate dehydrogenase
3
2
aroE trpEDCFBA-hisC-tyrA-aroE 5-enolpyruvoylshikimate-3-phosphate synthase
3
2
aroK aroI aroK shikimate kinase
0
0
nprE nprE extracellular neutral metalloprotease
5
2
hutU hut urocanase
5
6
hutI hut imidazolone-5-propionate hydrolase
5
6
hutH hut histidase
5
6
hutG hut formiminoglutamate hydrolase
5
6
ysnE ysnE
0
0
bltD bmr2D, bmtD blt-bltD spermine/spermidine acetyltransferase
3
3
yclE yclE
0
0

2.3 Metabolism of nucleotides and nucleic acids
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
upp ipc-35d upp uracil phosphoribosyltransferase
0
0
drm yqkN drm-punA phosphopentomutase
1
2
dra deoR-dra-nupC-pdp deoxyribose-phosphate aldolase
3
3
dgk yaaG dgk-dck deoxyguanosine kinase
0
0
pucA yurF pucABCDE xanthine dehydrogenase
2
1
pucB yurE pucABCDE xanthine dehydrogenase
2
1
pucC yurD pucABCDE xanthine dehydrogenase
2
1
pucD yurC pucABCDE xanthine dehydrogenase
2
1
pucE yurB pucABCDE xanthine dehydrogenase
2
1
pucH yunH pucH allantoinase
2
2
pucL yunL pucRJKLM uricase
3
3
pucM yunM pucRJKLM uricase
3
3
ymaA nrdI nrdIEF-ymaB
2
2
nin comJ nucA-nin
1
2
relA relA-yrvI GTP pyrophosphokinase
1
1
mtn yrrU, mtnN yrrT-mtn-yrhABC methylthioadenosine nucleosidase
2
2
purS yexA purEKBCSQLFMNHD
2
2
purQ purEKBCSQLFMNHD phosphoribosylformylglycinamidine synthetase I
2
2
purT purT phosphoribosylglycinamide formyltransferase 2
1
1
purC purEKBCSQLFMNHD phosphoribosylaminoimidazole succinocarboxamide synthetase
2
2
purB purEKBCSQLFMNHD adenylosuccinate lyase
2
2
purF purB purEKBCSQLFMNHD glutamine phosphoribosylpyrophosphate amidotransferase
2
2
purE purEKBCSQLFMNHD phosphoribosylaminoimidazole carboxylase I
2
2
purD purEKBCSQLFMNHD phosphoribosylglycinamide synthetase
2
2
purK purEKBCSQLFMNHD phosphoribosylaminoimidazole carboxylase II
2
2
purH purJ purEKBCSQLFMNHD inosine-monophosphate cyclohydrolase
2
2
purN purEKBCSQLFMNHD phosphoribosylglycinamide formyltransferase
2
2
purM purEKBCSQLFMNHD phosphoribosylaminoimidazole synthetase
2
2
purL purEKBCSQLFMNHD phosphoribosylformylglycinamidine synthetase II
2
2
nrdE nrdIEF-ymaB ribonucleoside-diphosphate reductase (major subunit)
2
2
nrdF nrdIEF-ymaB ribonucleoside-diphosphate reductase (minor subunit)
2
2
punA pnp, yqkO drm-punA purine nucleoside phosphorylase
1
2
yurI yurI
1
0
xpt xpt-pbuX xanthine phosphoribosyltransferase
2
2
prs gcaD-prs-ctc phosphoribosylpyrophosphate synthetase
2
2
pyrAA pyrRPBCAAABKDFE carbamoyl-phosphate synthetase (glutaminase subunit)
3
5
pyrD pyrDI pyrRPBCAAABKDFE dihydroorotate dehydrogenase (catalytic subunit)
3
5
nucB nucB nuclease
1
1
nucA comI nucA-nin nuclease
1
2
pyrAB pyrRPBCAAABKDFE carbamoyl-phosphate synthetase (catalytic subunit)
3
5
guaD gde, yknA guaD guanine deaminase
2
2
guaC yumD guaC GMP reductase
1
1
guaB guaA guaB inosine-monophosphate dehydrogenase
0
0
guaA guaB guaA GMP synthetase
1
1
yhaM yhaONM
1
1
cdd cdd-era cytidine/deoxycytidine deaminase
3
2
pdp deoR-dra-nupC-pdp pyrimidine-nucleoside phosphorylase
3
3
yirY sbcD-yirY-yisB
1
0
yfkN yfkN
1
1
pyrK pyrDII, ylxD pyrRPBCAAABKDFE dihydroorotate dehydrogenase (electron transfer subunit)
3
5
pyrG ctrA pyrG CTP synthetase
1
1
pyrF pyrRPBCAAABKDFE orotidine 5'-phosphate decarboxylase
3
5
pyrE pyrX pyrRPBCAAABKDFE orotate phosphoribosyltransferase
3
5
pyrC pyrRPBCAAABKDFE dihydroorotase
3
5
pyrB pyrRPBCAAABKDFE aspartate carbamoyltransferase
3
5
ytnL hipO ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
dck yaaF dgk-dck deoxyadenosine/deoxycytidine kinase
0
0
apt yrvE-apt adenine phosphoribosyltransferase
0
0
yabR yabMNOPQ-divIC-yabR
4
3
purA purA adenylosuccinate synthetase
2
2
yabJ purR-yabJ
1
1
ywaC ipa-7d ywaC
1
1

2.4 Metabolism of lipids
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
mmgC yqiN mmgABCDE-yqiQ acyl-CoA dehydrogenase
2
2
mmgB yqiM mmgABCDE-yqiQ 3-hydroxybutyryl-CoA dehydrogenase
2
2
mmgA yqiL mmgABCDE-yqiQ acetyl-CoA acetyltransferase
2
2
yngJ yngJIHGFE
1
1
yngF yngJIHGFE
1
1
yngG yngJIHGFE
1
1
cypC ybdT cypC fatty acid beta-hydroxylating cytochrome P450
0
0
pssA pss pssA-ybfM-psd phosphatidylserine synthase
2
3
accC yqhX accBC-yqhY acetyl-CoA carboxylase subunit (biotin carboxylase subunit)
0
0
yhfL yhfL
2
2
bkdAB bfmBAB, bfmB1b, bkd ptb-bcd-buk-lpdV-bkdAABB branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase beta subunit)
4
4
yqjQ yqjPQ-dsdA-coaA-yqjT
0
0
bkdAA bfmBAA, bfmB1a, bkd ptb-bcd-buk-lpdV-bkdAABB branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase alpha subunit)
4
4
yngI yngJIHGFE
1
1
ycsD ycsD
0
0
accA accA acetyl CoA carboxylase (alpha subunit)
0
0
accB fabE, yqhW accBC-yqhY acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit)
0
0
scoA yxjD yxjC-scoAB-yxjF succinyl CoA:3-oxoacid CoA-transferase (subunit A)
2
2
bkdB bfmBB, bfmB2, bkd ptb-bcd-buk-lpdV-bkdAABB branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase)
4
4
ydbM ydbM
1
1
yusL yusMLKJ
3
2
yusK yusMLKJ
3
2
yusJ yusMLKJ
3
2
acdA ywjF-acdA-rpoE acyl-CoA dehydrogenase
2
3
lcfA lcfA-ysiAB-etfBA long chain acyl-CoA synthetase
3
3
psd pssA-ybfM-psd phosphatidylserine decarboxylase; 32 kDa precursor processed into a 29 kDa protein
2
3
ptb yqiS, bkd ptb-bcd-buk-lpdV-bkdAABB phosphate butyryltransferase
4
4
fabHB yhfB fabHB beta-ketoacyl-acyl carrier protein synthase III
1
1
fabHA yjaX fabHAF beta-ketoacyl-acyl carrier protein synthase III
2
2
des yocE des fatty acid desaturase
2
2
scoB yxjE yxjC-scoAB-yxjF succinyl CoA:3-oxoacid CoA-transferase (subunit B)
2
2
ysiB lcfA-ysiAB-etfBA
3
3
lip lipA lip lipase
0
0
plsX ylpD fapR-plsX-fabDG
2
2
lipB yfiP lipB esterase
0
0
glpQ ybeD glpTQ glycerophosphoryl diester phosphodiesterase
3
4
lpdV yqiV, bkd ptb-bcd-buk-lpdV-bkdAABB branched-chain alpha-keto acid dehydrogenase E3 subunit (dihydrolipoamide dehydrogenase)
4
4
yhdO yhdNO
2
2
buk yqiU, bkd ptb-bcd-buk-lpdV-bkdAABB branched-chain fatty-acid kinase (butyrate kinase)
4
4
fabD ylpE fapR-plsX-fabDG malonyl CoA-acyl carrier protein transacylase
2
2
fabG ylpF fapR-plsX-fabDG beta-ketoacyl-acyl carrier protein reductase
2
2
fabF yjaY fabHAF beta-ketoacyl-acyl carrier protein synthase II
2
2
fabL yfhR, ygaA yfhQ-fabL-sspE enoyl-acyl carrier protein reductase
5
5
fabI yjbW fabI enoyl-acyl carrier protein reductase
1
1
yybR yybR
0
0
yfjR yfjR
0
0
bcd bkd, yqiT ptb-bcd-buk-lpdV-bkdAABB leucine dehydrogenase
4
4

2.5 Metabolism of coenzymes and prosthetic groups
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ybcP ybcQ, skfB skf
4
2
yngH yngJIHGFE
1
1
hemL hemK hemAXCDBL glutamate-1-semialdehyde 2,1-aminotransferase
2
3
hemX hemAXCDBL membrane-bound protein
2
3
hemY hemG hemEHY protoporphyrinogen IX and coproporphyrinogen III oxidase
0
0
menD menBEC 2-oxoglutarate decarboxylase and 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
1
3
menE menBEC O-succinylbenzoic acid-CoA ligase
1
3
menF icsM, entC menBEC menaquinone-specific isochorismate synthase
1
3
menA ywaB, ipa-6d menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase
0
0
menB menBEC dihydroxynapthoic acid synthetase
1
3
menC ytfD menBEC O-succinylbenzoate-CoA synthase
1
3
ribR ytnK ytmIJKLMNO-ytnIJ-ribR-ytnLM riboflavin kinase
4
3
ribT ribD ypuE-ribDEAHT reductase
1
1
ribH ypuE-ribDEAHT riboflavin synthase (beta subunit)
1
1
ribA ypuE-ribDEAHT GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase
1
1
ribE ribB ypuE-ribDEAHT riboflavin synthase (alpha subunit)
1
1
ribD ribG ypuE-ribDEAHT riboflavin-specific deaminase
1
1
mtrA mtrAB GTP cyclohydrolase I
1
1
yhxA yhxA-glpP
0
0
bioW bioWAFDBI-ytbQ 6-carboxyhexanoate-CoA ligase
1
1
coaA yqjS yqjPQ-dsdA-coaA-yqjT pantothenate kinase
0
0
nadA nadBCA quinolinate synthetase
2
2
nasF nasBE nasBCDEF uroporphyrin-III C-methyltransferase
7
7
hemH hemF hemEHY ferrochelatase
0
0
hemN yqeR lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV coproporphyrinogen III oxidase
3
6
hemB hemAXCDBL delta-aminolevulinic acid dehydratase (porphobilinogen synthase)
2
3
hemC hemAXCDBL porphobilinogen deaminase (hydroxymethylbilane synthase)
2
3
hemA hemAXCDBL glutamyl-tRNA reductase
2
3
hemD hemAXCDBL uroporphyrinogen III cosynthase
2
3
hemE hemEHY uroporphyrinogen III decarboxylase
0
0
hemZ yhaW, yhaV hemZ coproporphyrinogen III oxidase
4
1
sul pabBAC-sul-folBK-yazB-yacF-lysS dihydropteroate synthase
2
2
moaB moaB molybdopterin precursor biosynthesis protein B
0
0
moaA narA, narAB moaA
0
0
nifS nifS-yrxA
2
2
yjbV tenAI-goxB-thiSGF-yjbV
1
0
bioB bioWAFDBI-ytbQ biotin synthetase
1
1
bioA bioWAFDBI-ytbQ adenosylmethionine-8-amino-7-oxononanoate aminotransferase
1
1
bioF bioWAFDBI-ytbQ 8-amino-7-oxononanoate synthase
1
1
bioD bioWAFDBI-ytbQ dethiobiotin synthetase
1
1
bioI bioWAFDBI-ytbQ cytochrome P450 enzyme
1
1
pabC pabBAC-sul-folBK-yazB-yacF-lysS aminodeoxychorismate lyase
2
2
pabB pab pabBAC-sul-folBK-yazB-yacF-lysS para-aminobenzoate synthase (subunit A)
2
2
pabA trpG, trpX pabBAC-sul-folBK-yazB-yacF-lysS anthranilate synthase (subunit II)
2
2
folD yqiA nusB-folD methenyltetrahydrofolate cyclohydrolase
1
1
folC valS-folC folyl-polyglutamate synthetase
2
2
folB folA, yacE pabBAC-sul-folBK-yazB-yacF-lysS dihydroneopterin aldolase
2
2
folK pabBAC-sul-folBK-yazB-yacF-lysS 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase
2
2
dhbF dhbACEBF
2
2
dhbE entE dhbACEBF 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E)
2
2
dhbB dhbACEBF isochorismatase
2
2
dhbC dhbACEBF isochorismate synthase
2
2
dhbA entA dhbACEBF 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
2
2
thiS yjbS tenAI-goxB-thiSGF-yjbV
1
0
thiM thiK, ipa-25d, ywbJ ywbI-thiME hydroxyethylthiazole kinase
1
1
thiG yjbT tenAI-goxB-thiSGF-yjbV
1
0
thiF yjbU tenAI-goxB-thiSGF-yjbV
1
0
thiE thiC, ipa-26d, ywbK ywbI-thiME thiamine-phosphate pyrophosphorylase
1
1
thiD ywdB, ipa-52r thiD phosphomethylpyrimidine kinase
0
0
ylnD cysHP-sat-cysC-ylnDEF
1
1
ylnF cysHP-sat-cysC-ylnDEF
1
1
nadB nadBCA L-aspartate oxidase
2
2
nadE outB, tscBGH, gsp-81 nadE NH3-dependent NAD+ synthetase
2
2
nadC yrxB nadBCA nicotinate-nucleotide pyrophosphorylase
2
2
yueK pncB yueK
0
0

2.6 Metabolism of phosphate
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
xpaC xpaC-yaaN
1
1
ybfM pssA-ybfM-psd
2
3
ppaC yybQ ppaC inorganic pyrophosphatase
0
0
phoA phoAIV phoA alkaline phosphatase A
3
2
phoB phoAIII phoB-ydhF alkaline phosphatase III
3
4
phoD ycbS phoD phosphodiesterase/alkaline phosphatase D
2
2

2.7 Metabolism of sulfur
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yvgQ cysI yvgRQ
2
2
yvgR cysJ yvgRQ
2
2
sat ylnB cysHP-sat-cysC-ylnDEF sulfate adenylyltransferase
1
1
ssuD ygcA, yzeC ssuBACD-ygaN aliphatic sulfonate monooxygenase
3
2
yitB yitBA-yisZ
1
1
yitA yitBA-yisZ
1
1
yisZ yitBA-yisZ
1
1

3 Information pathways

3.1 DNA replication
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
rnhC ysgB rnhC ribonuclease HIII
0
0
ligA lig, yerG pcrBA-ligA-yerH DNA ligase
1
1
pcrA yerF pcrBA-ligA-yerH ATP-dependent DNA helicase
1
1
ssb yyaF-rpsF-ssb-rpsR single-strand DNA-binding protein
1
2
dnaA dnaH, dnaJ, dnaK dnaAN
2
10
dnaC dnaC replicative DNA helicase
0
0
dnaE dnaE DNA polymerase III (alpha subunit)
1
1
dnaG dnaE yqxD-dnaG-sigA DNA primase
4
7
dnaN dnaG, dnaK dnaAN DNA polymerase III (beta subunit)
2
10
ypcP ypcP
0
0
ywpH ywpH-glcR
1
2

3.2 DNA restriction/modification and repair
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ypvA ypvA
0
0
ung ipa-57d, ywdG ung uracil-DNA glycosylase
0
0
yqjH yqjHI
0
0
yqjW yqjWX
1
2
yozK yozLK-yobH
1
2
uvrX yolE yolD-uvrX UV-damage repair protein
1
2
uvrC uvrB uvrC excinuclease ABC (subunit C)
1
1
uvrB dinA, uvrA uvrBA excinuclease ABC (subunit B)
1
1
uvrA uvrBA excinuclease ABC (subunit A)
1
1
exoA exoA-ccpB
1
0
radC ysxA radC DNA repair protein
2
2
radA sms, yacJ ctsR-mcsAB-clpC-radA-yacK DNA repair protein homolog
3
3
adaA adaAB methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family)
2
1
adaB adaAB O6-methylguanine-DNA methyltransferase
2
1
yqfS nfo yqfSU
1
1
ydiO ydiOP
1
1
dinB dinB nuclease inhibitor
1
1
ydiP ydiOP
1
1
ydiS ydiRS-ydjA
0
0
yhaZ yhaZ
1
1
yxlJ yxlJ-yxzF
0
0
ywqL ywqL
0
0
yobH yozLK-yobH
1
2
mutL mutSL
0
0
mutS mutSL
0
0
ogt dat kinE-ogt O6-methylguanine DNA alkyltransferase
1
1
alkA alkA DNA-3-methyladenine glycosylase
2
2
yfjP yfjPO
0
0
yfhQ yfhQ-fabL-sspE
5
5

3.3 DNA recombination
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yrvE yrvE-apt
0
0
addB addBA ATP-dependent deoxyribonuclease (subunit B)
2
3
addA recE5 addBA ATP-dependent deoxyribonuclease (subunit A)
2
3
sbcD yixA sbcD-yirY-yisB exonuclease SbcD homolog
1
0
recN ahrC-recN
0
0
recA recE recA multifunctional SOS repair regulator
3
6
recF yaaA-recF-yaaB-gyrB
1
2
recU recG, prfA, yppB, jopB recU-ponA
0
0
ywqA ywqA
0
0
ruvA ruvAB Holliday junction DNA helicase
1
1
ruvB ruvAB Holliday junction DNA helicase
1
1

3.4 DNA packaging and segregation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
smc ylqA rnc-smc-ftsY chromosome segregation SMC protein homolog
3
3
topA topI topA DNA topoisomerase I
0
0
hbs dbpA hbs non-specific DNA-binding protein HBsu; signal recognition particle-like (SRP) component
4
4
gyrB novA yaaA-recF-yaaB-gyrB DNA gyrase (subunit B)
1
2
gyrA nalA gyrA DNA gyrase (subunit A)
1
1
parE grlB parEC subunit of DNA topoisomerase IV
1
1
parC grlA parEC subunit of DNA topoisomerase IV
1
1

3.5 RNA synthesis

3.5.1 Initiation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yvyD yviI yvyD
2
2
spoIVCB cisB, sigK spoIVCB-spoIIIC RNA polymerase sporulation-specific sigma factor (sigma-K) (N-terminal half)
4
7
sigA rpoD, crsA yqxD-dnaG-sigA RNA polymerase major sigma-43 factor (sigma-A)
4
7
sigB rpoF rsbRSTUVW-sigB-rsbX RNA polymerase sigma-37 factor (sigma-B)
2
2
sigE spoIIGB spoIIGA-sigE-sigG RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
6
7
sigD flaB fla-che RNA polymerase sigma-28 factor (sigma-D)
2
3
sigG spoIIIG spoIIGA-sigE-sigG RNA polymerase sporulation-specific sigma factor (sigma-G)
6
7
sigF spoIIAC dacF-spoIIAAB-sigF RNA polymerase sporulation-specific sigma factor (sigma-F)
5
7
sigH spo0H sigH RNA polymerase sigma-30 factor (sigma-H)
2
2
sigM yhdM sigM-yhdLK RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-M)
2
2
sigW ybbL sigW-ybbM RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-W)
2
2
sigV sigV-yrhM RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-V)
0
0
sigY yxlB sigY-yxlCDEFG RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-Y)
1
1
sigX ypuM sigX-rsiX RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-X)
3
2
sigI ykoZ sigI-rsgI RNA polymerase sigma factor
1
1
sigL sigL RNA polymerase sigma-54 factor (sigma-L)
1
1
ylaC ylaABCD
3
2
spoIIIC sigK, spoIVD, spoIVE spoIVCB-spoIIIC RNA polymerase sporulation-specific sigma factor (sigma-K) (C-terminal half)
4
7

3.5.2 Regulation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
abrB cpsX abrB transcriptional regulator
3
4
ydgG ydgGH
1
1
cheY cheB fla-che two-component response regulator
2
3
cheB cheL fla-che methyl-accepting chemotaxis proteins (MCP)-glutamate methylesterase and two-component response regulator-like
2
3
yacF pabBAC-sul-folBK-yazB-yacF-lysS
2
2
gltR yrdL gltR transcriptional regulator (LysR family)
2
3
gltC gltC transcriptional regulator (LysR family)
2
2
ccpB yyaG exoA-ccpB putative transcriptional regulator (LacI family)
1
0
ccpC ykuM ykuJK-ykzF-ykuL-ccpC transcriptional regulator (LysR family)
3
3
ybbB yzbC ybbB
1
1
bmrR bmrU-bmr-bmrR transcriptional regulator (MerR family)
4
4
pucR yunI pucRJKLM transcriptional regulator
3
3
treR yfxA trePAR transcriptional regulator (GntR family)
3
4
ydfI ydfHI
0
0
ycnC ycnCB
0
0
ycnK ycnK
1
0
dctR ydbG dctSRP two-component response regulator
3
2
padR yfiO padR transcriptional regulator
0
0
lmrA lin-2, yccB lmrAB transcriptional regulator
2
2
fnr narK-fnr transcriptional regulator (FNR/CRP family)
4
4
yvrH yvrI-yvrHa
1
0
yrhI fatR yrhIJ
3
0
tnrA scgR tnrA transcriptional regulator
1
1
glnR glnRA transcriptional regulator
3
5
yneI yoxH ccdA-yneIJ
1
3
yvhJ yvhJ
0
0
ccpA graR, alsA ccpA-motPS transcriptional regulator (Lacl family)
0
0
araR araC, yvbS araR transcriptional regulator (LacI family)
2
2
fruR fruRKA transcriptional regulator (DeoR family)
1
0
yxdJ yxdJK
0
0
acoR yfjG, yzcB acoR-sspH transcriptional regulator
2
2
mtrB TRAP mtrAB tryptophan operon RNA-binding attenuation protein (TRAP)
1
1
mta ywnD mta transcriptional regulator (MerR family)
2
2
yhjM ntdR ntdR
0
1
perR ygaG perR transcriptional regulator (Fur family)
2
3
yycF yycFGHIJ-yyxA
0
0
purR yabI purR-yabJ transcriptional regulator
1
1
ywhA thrZ-ywhA
2
4
rocR rocR transcriptional regulator (NtrC/NifA family)
2
2
lexA dinR lexA transcriptional regulator
1
3
citR citR transcriptional regulator (LysR family)
1
1
citT yflQ citST-yflP two-component response regulator
0
0
degU sacU, iep degSU two-component response regulator
1
1
ywtF ywtF
0
0
licR celR licR transcriptional regulator
1
1
licT licT-bglS transcriptional antiterminator (BglG family)
4
3
ctsR yacG ctsR-mcsAB-clpC-radA-yacK transcriptional regulator
3
3
hxlR yckH hxlR
0
0
yrhM sigV-yrhM
0
0
spoVT yabL spoVT transcriptional regulator
2
1
arfM ywiD arfM probable transcriptional regulator
3
2
ycbL ycbLM
0
0
comQ comQX transcriptional regulator
1
1
ycbG ycbCDEFGHJ
0
0
comK comK competence transcription factor (CTF)
7
6
comA srfB, comAA comA-yuxO two-component response regulator
1
1
lytT lytT two-component response regulator
0
0
lytR lytR membrane-bound protein
3
2
yofA yofA
0
0
glcR ywpI ywpH-glcR transcriptional regulator (DeoR family)
1
2
kdgR kdgRKAT transcriptional regulator (LacI family)
3
2
resD ypxD resABCDE two-component response regulator
3
4
iolR iolRS transcriptional regulator (DeoR family)
2
3
rsiX ypuN sigX-rsiX
3
2
ytrA ytrABCDEF
2
1
yvbA sdpR sdpRI
3
2
ansR ansR transcriptional regulator (Xre family)
1
0
yrxA nadR nifS-yrxA
2
2
abh ylxT, yzaA abh transcriptional regulator
2
2
splA ykxI splAB transcriptional regulator
2
2
lrpC ydaI lrpC transcriptional regulator (Lrp/AsnC family)
2
2
cggR yvbQ cggR-gapA-pgk-tpiA-pgm-eno transcriptional regulator
2
3
ysiA lcfA-ysiAB-etfBA
3
3
rbsR rbsRKDACB transcriptional regulator (LacI family)
3
4
yfmP yfmPO
1
1
yceK yceK
0
0
gntR gntRKPZ transcriptional regulator (GntR family)
4
5
yocG desR yocFG
0
0
ywfK ipa-89d, cysL ywfK
2
2
gabR ycnF gabR transcriptional regulator (GntR/MocR family)
2
1
ytlI ytlI
3
3
fur yqkL fur transcriptional regulator (Fur family)
2
2
hrcA yqxE, yqeS lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV transcriptional regulator
3
6
yydK yydK
0
0
yczG yczG
0
0
ypoP ypoP
0
0
exuR yjmH uxaC-yjmBCD-uxuA-yjmF-exuTR-uxaBA transcriptional regulator (LacI family)
4
4
phoP phoPR two-component response regulator
6
11
yufM malR yufM
0
0
pyrR pyrRPBCAAABKDFE transcriptional attenuator and uracil phosphoribosyltransferase activity (minor)
3
5
spo0A spo0C, spo0G, spoIIL, sof-1 spo0A two-component response regulator
3
6
glpP yhxA-glpP transcription antiterminator
0
0
spo0F spo0F two-component response regulator
3
4
senS senS transcriptional regulator
2
0
codY codV-clpQY-codY transcriptional regulator
1
1
yccH yccH
0
0
yhcB yhbIJ-yhcABCDEFGHI
1
0
yhcF yhbIJ-yhcABCDEFGHI
1
0
nhaX yheK nhaX
1
0
sinR sin, flaD sinIR transcriptional regulator
4
7
gerE gerE transcriptional regulator
2
1
deoR yxxC deoR-dra-nupC-pdp transcriptional regulator
3
3
yybE yybEDC
0
0
yhbI yhbIJ-yhcABCDEFGHI
1
0
sacT ipa-47d sacT transcriptional antiterminator
0
0
sacY ipa-13r, sacS sacXY transcriptional antiterminator
4
4
xylR xylR transcriptional regulator
0
0
xre xre transcriptional regulator
1
2
yxaD yxaD
0
0
yxaF yxaF
0
0
bkdR yqiR bkdR transcriptional regulator (sigma-L-dependent)
0
0
yfiK yfiJK
0
0
yfiF yfiF
0
0
yfiV yfiV
0
0
yfiR yfiSR
0
0
tenI tenAI-goxB-thiSGF-yjbV transcriptional regulator
1
0
tenA tenAI-goxB-thiSGF-yjbV transcriptional regulator
1
0
ywbI ipa-24d ywbI-thiME
1
1
hutP hutP1 hut transcriptional regulator
5
6
kipR ycsO ycsFGI-kipIAR-ycsK transcriptional regulator (IclR family)
3
0
azlB yrdG azlBCD-brnQ-yrdK transcriptional regulator (Lrp/AsnC family)
1
0
mtlR ydaA mtlR transcriptional regulator
0
0
arsR yqcJ arsR-yqcK-arsBC transcriptional regulator (ArsR family)
2
2
gutR gutR transcriptional regulator
0
0
cssR yvqA cssRS two-component response regulator
2
3
spoIIID usd-spoIIID-mbl-flhOP transcriptional regulator
1
1
hpr catA, scoC hpr transcriptional regulator (MarR family)
3
0
ahrC ahrC-recN transcriptional regulator
0
0

3.5.3 Elongation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
rpoB rpoB RNA polymerase (beta subunit)
1
1
rpoE ywjF-acdA-rpoE RNA polymerase (delta subunit)
2
3

3.5.4 Termination
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
nusB yqhZ nusB-folD
1
1
nusA ylxS-nusA-ylxRQ-infB-ylxP-rbfA
1
1

3.6 RNA modification
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yacO gltX-cysES-yazC-yacOP
2
2
trmU yrrA cymR-yrvO-trmU tRNA (5-methylaminomethyl-2-thiouridylate) methyltransferase
1
1
rnc rncS rnc-smc-ftsY ribonuclease III
3
3
deaD yxiN yxiM-deaD ATP-dependent RNA helicase
0
0
rnmV yabF rnmV-ksgA ribonuclease M5
0
0
ysgA ysgA
0
0
yfmL yfmL
0
0
yfjO yfjPO
0
0
yugI yugI
0
0

3.7 Protein synthesis

3.7.1 Ribosomal proteins
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
rpsF yyaF-rpsF-ssb-rpsR ribosomal protein S6 (BS9)
1
2
rpsD rpsD ribosomal protein S4 (BS4)
1
1
rpsR yyaF-rpsF-ssb-rpsR ribosomal protein S18
1
2
rpsP rpsP-ylqC ribosomal protein S16 (BS17)
0
0
yfjL yztA yfjML
0
0
rplT infC-rpmI-rplT-ysdA ribosomal protein L20
2
2
rplI yybST-rplI ribosomal protein L9
0
0
rpmI infC-rpmI-rplT-ysdA ribosomal protein L35
2
2
rpmH rpmH ribosomal protein L34
1
2
rpmA rpmA ribosomal protein L27 (BL24)
0
0
rpmE rpmE ribosomal protein L31
0
0
ylxQ ymxC ylxS-nusA-ylxRQ-infB-ylxP-rbfA
1
1

3.7.2 Aminoacyl-tRNA synthetases
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
gltX gltX-cysES-yazC-yacOP glutamyl-tRNA synthetase
2
2
glyS yqfK glyQS glycyl-tRNA synthetase (beta subunit)
4
4
glyQ yqfJ glyQS glycyl-tRNA synthetase (alpha subunit)
4
4
pheT pheT phenylalanyl-tRNA synthetase (beta subunit)
0
0
cysS snpA gltX-cysES-yazC-yacOP cysteinyl-tRNA synthetase
2
2
thrZ thrS2 thrZ-ywhA threonyl-tRNA synthetase
2
4
pheS pheST phenylalanyl-tRNA synthetase (alpha subunit)
3
3
argS argS arginyl-tRNA synthetase
0
0
serS serS seryl-tRNA synthetase
1
1
leuS leuS leucyl-tRNA synthetase
1
1
lysS pabBAC-sul-folBK-yazB-yacF-lysS lysyl-tRNA synthetase
2
2
valS valS-folC valyl-tRNA synthetase
2
2
thrS thrS threonyl-tRNA synthetase
2
2
metS metG metS methionyl-tRNA synthetase
0
0
trpS trpS tryptophanyl-tRNA synthetase
1
1
tyrS tyrS tyrosyl-tRNA synthetase
3
3
tyrZ ipa-9r, tyrS1, tyrT tyrZ tyrosyl-tRNA synthetase
2
2

3.7.3 Initiation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
rbfA ymxE, ylxO ylxS-nusA-ylxRQ-infB-ylxP-rbfA ribosome-binding factor A
1
1
infC infC-rpmI-rplT-ysdA initiation factor IF-3
2
2
infB ylxS-nusA-ylxRQ-infB-ylxP-rbfA initiation factor IF-2
1
1
ykrS mtnS, mtnA mtnKA
1
1

3.7.4 Elongation
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
lepA yqxB, yqeQ lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV GTP-binding protein
3
6

3.7.5 Termination
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
prfB secA-prfB peptide chain release factor 2
1
1

3.8 Protein modification
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ytjP ytjP
0
0
ppiB cypBS ppiB peptidyl-prolyl isomerase
1
1
yoaA yoxCB-yoaA
1
1
sppA yteI sppA-yteJ signal peptide peptidase
1
1
yppQ yppQ
0
0
yflG yflG-yflH
1
1
dppA dciAA dppABCDE D-alanyl-aminopeptidase
3
3
yqeT lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV
3
6
yfkJ yfkJIH
2
2
ytxM ytfB menBEC
1
3
yxaL yxaK yxaJL
1
0
mlpA ymxG mlpA mitochondrial processing peptidase-like
0
0
amhX amhX amidohydrolase
1
1
prkA prkA serine protein kinase
1
1

3.9 Protein folding
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
tig yzzH tig trigger factor (prolyl isomerase)
0
0
groEL groESL class I heat-shock protein (chaperonin)
2
2
groES groESL class I heat-shock protein (chaperonin)
2
2
bdbA yolI sunT-bdbA-yolJ-bdbB thiol-disulfide oxidoreductase
2
0
bdbB yolK sunT-bdbA-yolJ-bdbB thiol-disulfide oxidoreductase
2
0
bdbC yvgU bdbDC thiol-disulfide oxidoreductase
2
0
bdbD yvgV bdbDC thiol-disulfide oxidoreductase
2
0
dnaK lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV class I heat-shock protein (molecular chaperone)
3
6

4 Other functions

4.1 Adaptation to atypical conditions
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
cspB cspB major cold-shock protein
2
2
ywtB ywsC-ywtABC
0
0
mcsA yacH ctsR-mcsAB-clpC-radA-yacK
3
3
mcsB yacI ctsR-mcsAB-clpC-radA-yacK
3
3
yvfE epsN eps
2
3
yvtA yvtB, htrB yvtA
1
0
yveR epsH eps
2
3
yveQ epsG eps
2
3
yveK epsA eps
2
3
yveN epsD eps
2
3
yveL epsB eps
2
3
yveM epsC eps
2
3
yfiQ yfiQ
0
0
htpG yxbB htpG class III heat-shock protein (molecular chaperone)
1
2
lonB ysxF lonB Lon-like ATP-dependent protease
1
1
htrA ykdA htrA serine protease Do (heat-shock protein)
3
2
degQ sacQ degQ
3
2
degR prtR degR
2
1
ywtA ywsC-ywtABC
0
0
yqhA yqhA
1
1
yyxA yycK yycFGHIJ-yyxA
0
0
yxkI yxkI
0
0
mrgA mrgA metalloregulation DNA-binding stress protein
2
2
ypjQ ypjQ
0
0
pspA ydjF pspA-ydjGHI phage shock protein A homolog
1
1
ypqP ypqP
0
0
clpX clpX ATP-dependent Clp protease ATP-binding subunit (class III heat-shock protein)
2
1
clpP yvdN clpP ATP-dependent Clp protease proteolytic subunit (class III heat-shock protein)
3
3
clpC mecB ctsR-mcsAB-clpC-radA-yacK class III stress response-related ATPase
3
3
clpE ykvH clpE ATP-dependent Clp protease-like (class III stress gene)
2
7
gsiB gsiB general stress protein
1
1
lonA lon lonA-ysxC class III heat-shock ATP-dependent Lon protease
2
2
csbB yfhN csbB stress response protein
2
2
yocK yocK
1
1
clpY hslU, codX codV-clpQY-codY two-component ATP-dependent protease (N-terminal serine protease)
1
1
clpQ hslV, codW codV-clpQY-codY two-component ATP-dependent protease (N-terminal serine protease)
1
1
ytxJ csb40 ytxGHJ
2
2
ytxH csb40 ytxGHJ
2
2
ytxG csb40 ytxGHJ
2
2
ywsC ywsC-ywtABC
0
0
dnaJ lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV heat-shock protein
3
6
yraA yraA
1
0
dps ytkB dps DNA-protecting protein
1
2
ctc gcaD-prs-ctc general stress protein
2
2
gspA ipa-12d, ywaG gspA general stress protein
1
1
grpE lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV heat-shock protein
3
6
ydaG yzzA ydaDEFG
1
2
rsbS ycxS rsbRSTUVW-sigB-rsbX antagonist of RsbT
2
2
rsbR ycxR rsbRSTUVW-sigB-rsbX
2
2
rsbW rsbRSTUVW-sigB-rsbX switch protein/serine kinase and anti-sigma factor (inhibitory sigma-B binding protein)
2
2
rsbV rsbRSTUVW-sigB-rsbX anti-anti-sigma factor (antagonist of RsbW)
2
2
rsbU rsbRSTUVW-sigB-rsbX serine phosphatase
2
2
rsbT ycxT rsbRSTUVW-sigB-rsbX switch protein/serine-threonine kinase
2
2
rsbX rsbRSTUVW-sigB-rsbX serine phosphatase
2
2

4.2 Detoxification
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ksgA rnmV-ksgA dimethyladenosine transferase
0
0
tetL tetLB tetracycline resistance leader peptide
1
1
bmrU bmrU-bmr-bmrR multidrug resistance protein
4
4
ahpF ndh ahpCF alkyl hydroperoxide reductase (large subunit) and NADH dehydrogenase
2
2
yxeK yxeKLMNOPQ
3
2
yaaN xpaC-yaaN
1
1
yaaD yaaDE
0
0
tmrB tmrB ATP-binding membrane protein
0
0
yndN fosB yndN
1
1
cah cah cephalosporin C deacetylase
0
0
yrhJ yrhIJ
3
0
ycsF ycsFGI-kipIAR-ycsK
3
0
yvdP cotQ yvdP
1
0
ybfO ybfO
1
1
ydbD dctB-ydbD
1
1
ycbJ ycbCDEFGHJ
0
0
ycbR ycbR
0
0
ytmO ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
ybxI ybdS ybxI
0
0
yfnC yfnC
0
0
mmr mmr methylenomycin A resistance protein
0
0
yisY yisY
1
0
yceC yceCDEFGH
2
2
yceF yceCDEFGH
2
2
yceE yceCDEFGH
2
2
yceD yceCDEFGH
2
2
yceH yceCDEFGH
2
2
tpx ytgI tpx thiol peroxidase
0
0
ydhU ydhU
1
1
yflM yflMK
0
0
ykzA yzzE, ohrB ohrB
1
1
nap nap carboxylesterase NA
0
0
katX yxlI katX major catalase in spores
3
2
katA kat-19 katA vegetative catalase 1
1
1
katE katB katE-yxiS catalase 2
1
2
ytnJ ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
ydjP yeaA-ydjP-ydjO
1
1
ahpC perR ahpCF alkyl hydroperoxide reductase (small subunit)
2
2
yxeI yxeIJ
0
0
arsC yqcM arsR-yqcK-arsBC arsenate reductase
2
2
mrpC yufV mrpABCDEFG
0
0
mrpB yufU mrpABCDEFG
0
0
mrpE mrpABCDEFG
0
0
mrpD yufD mrpABCDEFG
0
0
mrpG yufB mrpABCDEFG
0
0
mrpF yufC mrpABCDEFG probable efflux system for Na+ and cholate
0
0
yaaJ yaaJ-scr
1
2
ywcH ipa-44d nfrA-ywcH
2
2
thdF thdF-gidAB-yyaA
1
2

4.3 Antibiotic production
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
albA ywiA sboAX-albABCDEFG
4
1
albB ywhR sboAX-albABCDEFG
4
1
albD ywhP sboAX-albABCDEFG
4
1
sboX sboAX-albABCDEFG bacteriocin-like product
4
1
sboA sbo sboAX-albABCDEFG subtilosin A
4
1
sunA yolG sunA sublancin 168 lantibiotic antimicrobial precursor peptide
2
0
albC ywhQ sboAX-albABCDEFG
4
1
albE ywhO sboAX-albABCDEFG
4
1
albG ywhM sboAX-albABCDEFG
4
1
albF ywhN sboAX-albABCDEFG
4
1
srfAA comL srfAA-srfAB-comS-srfAC-srfAD surfactin synthetase
4
5
srfAC comL srfAA-srfAB-comS-srfAC-srfAD surfactin synthetase
4
5
srfAB comL srfAA-srfAB-comS-srfAC-srfAD surfactin synthetase
4
5
srfAD comL srfAA-srfAB-comS-srfAC-srfAD surfactin synthetase
4
5

4.4 Phage-related functions
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
xtmB ykxG xtmAB-xkdEFGHIJKM PBSX defective prophage terminase (large subunit)
1
0
xtmA ykxF xtmAB-xkdEFGHIJKM PBSX defective prophage terminase (small subunit)
1
0
yjbJ yjbJ
1
1
xkdC ykxC xkdBCD-xtrA
1
2
yndL yndL
1
1
yobO yobO
1
1
xtrA xkdBCD-xtrA
1
2
codV codV-clpQY-codY site-specific integrase/recombinase
1
1
xkdB ykxB xkdBCD-xtrA
1
2
xkdA ykxA xkdA
1
1
xkdG xtmAB-xkdEFGHIJKM
1
0
xkdF xtmAB-xkdEFGHIJKM
1
0
xkdE xtmAB-xkdEFGHIJKM
1
0
xkdD ykxD xkdBCD-xtrA
1
2
xkdK xtmAB-xkdEFGHIJKM
1
0
xkdJ xtmAB-xkdEFGHIJKM
1
0
xkdI xtmAB-xkdEFGHIJKM
1
0
xkdH xtmAB-xkdEFGHIJKM
1
0
xkdM xtmAB-xkdEFGHIJKM
1
0

4.5 Transposon and IS
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
yneB yneAB-ynzC
2
5

4.6 Miscellaneous
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
mmgE yqiP mmgABCDE-yqiQ
2
2
yplQ yplQ
0
0
yyaF yyaF-rpsF-ssb-rpsR
1
2
era bex, yqfH cdd-era GTP-binding protein
3
2
yrvO cymR-yrvO-trmU
1
1
veg veg
1
1
yqhB yqhB
1
1
yvrE yvrE
1
1
ycbU ycbU
0
0
yqxC yqiF yqxC
0
0
sbp murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp small basic protein
3
5
ysxC lonA-ysxC
2
2
yuaG yuaH yuaFGI
1
1
pcrB yerE pcrBA-ligA-yerH PcrB homolog
1
1
csbA csbA putative membrane protein
2
2
csfB yaaM csfB
1
0
sapB sapB
0
0
ctaG ctaBCDEFG
1
1
eag ykvC eag small membrane protein
0
0
yugS yugS
0
0

5 Similar to unknown proteins

5.1 From B. subtilis
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ywsB ywsB
0
0
ydgB ydgBA-cotP
2
2
ydgA ydgBA-cotP
2
2
yacK ctsR-mcsAB-clpC-radA-yacK
3
3
ywlG ipc-33d ywlFG
1
1
ywlB ipc-28d ywlB
0
0
yyaC yyaC
1
1
yyaB yyaB
0
0
yyaD yyaD
1
1
yyaK yyaK
0
0
ysdA infC-rpmI-rplT-ysdA
2
2
yxbD yxaR yxbCD
1
0
yxbF yxaT yxbF
0
0
yxbC yxaQ yxbCD
1
0
yvdQ yvdQ
1
1
ybbM rsiW sigW-ybbM
2
2
ybbA feuABC-ybbA
2
2
ynxB ynaA ynxB
0
0
ydfO ydfO
1
1
yflP citST-yflP
0
0
yuiI yuiI
1
1
ywmF ywmF-csbD
1
1
ywmC ywmC
0
0
yoxA yoxA-dacC
2
2
yteJ sppA-yteJ
1
1
yteA yzwB yteA
1
1
ybaK ybxH ybaK-cwlD
3
3
yxeQ yxeKLMNOPQ
3
2
yxeL yxeKLMNOPQ
3
2
yczE yczE
0
0
yczH yczH
0
0
yrkC yrkC
1
1
yunB yunB
1
1
ywnB ywnB
0
0
ywnF ywnF
0
0
yneJ yoxI ccdA-yneIJ
1
3
yneK yoxJ yneK
0
0
yneF yoxG yneEF
0
0
yneE yoxF yneEF
0
0
yhgC yixC yhgC
0
0
yvfF epsO eps
2
3
yrvD yrvD
1
1
yqjL yqjL
3
2
yqjY yqjYZ-yqkABC
0
0
yqjZ yqjYZ-yqkABC
0
0
yqjP yqjPQ-dsdA-coaA-yqjT
0
0
yqjT yqjPQ-dsdA-coaA-yqjT
0
0
ylpC fapR fapR-plsX-fabDG
2
2
yxxF yxxF
0
0
yttP yttP
1
0
yerH pcrBA-ligA-yerH
1
1
yhjE yhjE-sipV
1
1
yhjD yhjD
1
1
yazB pabBAC-sul-folBK-yazB-yacF-lysS
2
2
yhjR yhjR
2
1
ywoF ywoF
0
0
yqkA yqjYZ-yqkABC
0
0
yqkD yqkD
0
0
yodH yodHI
1
1
yfiH yfiGHI
0
0
yozO yozO
1
1
yycP yycOPQ
0
0
ytoI ytoI
0
0
yxiD yxiD-yxxD-yxxE
0
0
yxiB yxiB
0
0
ypiP ypiP
0
0
ylaJ ylaJ
1
0
ydcC ydcC
1
1
ycsE ycsE
0
0
ywzA ywzA
0
0
yqzF yqzF
0
0
ytfI ytfIJ
1
1
ytfJ ytfIJ
1
1
ytpB ytpB
0
0
ysdB ysdB
1
1
yweA ipa-74d yweA
0
0
ykuK ykuJK-ykzF-ykuL-ccpC
3
3
ykuL ykuJK-ykzF-ykuL-ccpC
3
3
ykuG ykuFG
2
2
yphA csfD yphA-seaA
1
0
yphP yphP
0
0
yqhP yqhQP
2
2
yqhQ yqhQP
2
2
yqhY accBC-yqhY
0
0
ypzA ypzA
1
1
ydbS ydbST
1
1
ydbT ydbST
1
1
yqiW yqiW
0
0
yvqH yvqH
1
0
ykvI ykvI
1
1
ykvP ykvPQ
1
0
ywjG ywjG
0
0
ybyB ybyB
0
0
ywdL ipa-62r, gerQ ywdL
1
1
ytrI ytrHI
1
1
ypjB ypjB
2
1
yqfZ yqfZY
2
1
yqfU yqfSU
1
1
yqfA yqeZ-yqfA-yqfB
1
1
yqfC yqfCD
2
1
yshE yshE
0
0
yshB yshB
0
0
yxjN yxjN
0
0
yxjH yxjH
0
0
yxjG yxjG
0
0
yxjC yxjC-scoAB-yxjF
2
2
yvgO yvgO
1
0
ylbC ylbBC
1
1
ylbE ylbDE
1
1
ylbD ylbDE
1
1
ylbJ ylbJ
2
1
ylbO gerR gerR
1
0
yfnF yfnHGFED
2
3
yfnD yfnHGFED
2
3
ycdB ycdB
0
0
ywkC racA racA
2
0
yhdJ yhdJ
0
0
ycxA ycxA
0
0
ycxC ycxCB
0
0
ytcG ytcG
0
0
yitE yitE
1
0
ytmI ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
ypmP ilvA-ypmP
1
0
yvaW sdpA sdp
3
0
yvaX sdpB sdp
3
0
yvaY sdpC sdp
3
0
ywfL ipa-90d ywfL
0
0
ysnF ysnF
1
0
ytbQ bioWAFDBI-ytbQ
1
1
yoaR yoaR
1
1
yjcA yjcA
1
1
yjcC spoVIF yjcB-yjcZ-spoVIF
2
4
ywpE ywpE
0
0
yqhV yqgE yqhV-spoIIIAABCDEFGH
3
3
yxlG sigY-yxlCDEFG
1
1
yllA yllA
0
0
ydhF phoB-ydhF
3
4
yflE yflE
0
0
yflN citM-yflN
3
4
yflH yflG-yflH
1
1
yuaI yuaFGI
1
1
yugN pgi-yugMN
0
0
yjzC yjzC
0
0
yjbF yjbF
0
0
yjbC yjbCD
7
8
yczJ yczJ
0
0
ywgA ywgA
0
0
yolD yolD-uvrX
1
2
yqeZ yqeZ-yqfA-yqfB
1
1
ywmD ywmD
0
0
yfkA yfkABC
0
0
yfkB yfkABC
0
0
yfkD yfkED
1
0
yfkH yfkJIH
2
2
ycgG ycgFG
2
1
ycgF ycgFG
2
1
ysxE spoVID-ysxE
1
1
yhcQ yhcQ
1
1
yhcN yhcN
2
2
ytnM ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
yisB sbcD-yirY-yisB
1
0
yuzA yuzA
1
1
ynzD ynzD
0
0
yfhH yfhGH
0
0
ytxK ythI ytxK
0
0
ytxC ytxC
1
1
yslB yslB
0
0
ylxF fla-che
2
3
ylxL fla-che
2
3
ydjG pspA-ydjGHI
1
1
ydjI pspA-ydjGHI
1
1
ydjH pspA-ydjGHI
1
1
yfjE yfjABCDEF
0
0
yybS yybST-rplI
0
0
yhbF yzdB yhbF
0
0
ypuI ypuGHI
0
0
ypuA ypuA
0
0
ypuF ypuF
0
0
yxaG yxaGH
1
1
yknX yknWXYZ
2
2
yknW yknWXYZ
2
2
yfiI yfiGHI
0
0
yfiE yfiDE
0
0
yycJ yycFGHIJ-yyxA
0
0
yycI yycFGHIJ-yyxA
0
0
yycH yycFGHIJ-yyxA
0
0
yfiT yfiT
0
0
ywcE ipa-41r ywcE
0
0
yheC yheCD
1
0
yheD yheCD
1
0
yckC yckC
0
0
ywbO ipa-30d ywbO
0
0
ykrT mtnK mtnKA
1
1
yvlD yvlABCD
2
2
yvlC yvlABCD
2
2
yvlB yvlABCD
2
2
yuxK yugD pbpD-yuxK
1
1
yuxH comB, yufA yuxH
2
2
ypbS ypbS
0
0
ypbR mrgC mrgC
1
0
yrrD yrrD
1
1
yrrS yrrRS
2
1
yfjD yfjABCDEF
0
0
yybT yybST-rplI
0
0
ynzC yneAB-ynzC
2
5
yabP spoVUA yabMNOPQ-divIC-yabR
4
3
yabQ spoVUB yabMNOPQ-divIC-yabR
4
3
yfhG yfhGH
0
0
yfhP yfhP
2
3
yfhS yfhS
1
1
yfjM yfjML
0
0
yukF yukF
0
0
ytkD ytkD
2
2

5.2 From other organisms
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ymxH ymxH
0
0
yacN yacLMN
1
1
yacM yacLMN
1
1
yacL yacLMN
1
1
yyaL yyaL
0
0
yyaO yyaO
0
0
yyaS yyaTS
0
0
yyaT yyaTS
0
0
yngK yotA yngK
1
1
yvjA yvjA-cccB
0
0
yxbB yxaP yxbBA-yxnB-asnH-yxaM
1
0
ybdE skfH skf
4
2
ydfK ydfK
2
1
ydfS ydfS
1
1
ydfR ydfR
1
1
yhfN yzoA yhfN
0
0
yacP gltX-cysES-yazC-yacOP
2
2
ycnE ycnED
0
0
ytwI ytwI
0
0
ysaA ysaA
0
0
yviA degV, sacU yviA
0
0
ykrU mtnU mtnU
1
1
ykrZ mtnZ, mtnD mtnWXBD
1
2
ykrX mtnX mtnWXBD
1
2
ykrY mtnY, mtnB mtnWXBD
1
2
yxeH yxeFGH
0
0
ypgR ypgR
0
0
yaaA yaaA-recF-yaaB-gyrB
1
2
ylqC rpsP-ylqC
0
0
ytvI ytvI
1
1
yrvI relA-yrvI
1
1
yqjK yqjK
0
0
yhjK ntdB ntdABC-glcP
2
1
yhjJ ntdC ntdABC-glcP
2
1
yazC gltX-cysES-yazC-yacOP
2
2
yqcK arsR-yqcK-arsBC
2
2
yxiE bglPH-yxiE
3
3
ybgG ybgG
0
0
yxiO yxiO
0
0
yveS epsI eps
2
3
ytqI ytqI
0
0
ydcE ydcE
0
0
ydcA ydcA
1
1
ysbB ysbB
0
0
yqgZ yqgZ
1
1
yulF yulF
0
0
ywhH ywhH
0
0
ycsI ycsFGI-kipIAR-ycsK
3
0
ycsK ycsFGI-kipIAR-ycsK
3
0
yqzB ccpN ccpN-yqfL
1
0
yesJ yeeN, yfxC, yfxD cotJABC-yesJK
2
2
yesF yeeM, yfxB yesEF
0
0
yrzC cymR cymR-yrvO-trmU
1
1
ykgA ykgAB
1
1
ykgB ykgAB
1
1
ycbH ycbCDEFGHJ
0
0
yxkF yxkF-msmX
1
1
yxkD yxkD
0
0
yxkH yxkH
0
0
yxkO yxkO
1
1
ytsP ytsP
0
0
yitD yitCD
2
2
yfkM yfkM
1
1
ywdJ ipa-60d ywdIJK
1
1
ywdK ipa-61d ywdIJK
1
1
yqxD yqfM yqxD-dnaG-sigA
4
7
yqxL yqhC yqxL
2
2
yqfL ccpN-yqfL
1
0
yxjB yxjB
0
0
ytaG ytaG
0
0
yfnB yfnB
0
0
ywkB ywkAB
2
2
ytcJ ytcJ
0
0
ytmQ ytmQ
0
0
yitC yitCD
2
2
ywfI ipa-87r ywfI
0
0
yhaX yhaX
1
1
yhaN yhaONM
1
1
yhaO yhaONM
1
1
yoaG yoaG
1
1
yoaN oxdD yoaN
2
1
yllB yllB-ylxA-ftsL-pbpB
0
0
yflL yflL
0
0
yflK yflMK
0
0
yjbE yjbE
1
0
yjbD spx, spxA yjbCD
7
8
yqeU lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV
3
6
yqeV lepA-hemN-hrcA-grpE-dnaKJ-yqeTUV
3
6
yuiC yuiC
1
1
yklA ohrA yklA
2
2
yfkC yfkABC
0
0
ycgA ycgA
0
0
yciB yciABC
2
4
yciA yciABC
2
4
ywjB ywjB
0
0
ypnP ypnP
0
0
ykmA ohrR ykmA
0
0
yfhB yfhB
0
0
ylnE cysHP-sat-cysC-ylnDEF
1
1
ylxA yllC yllB-ylxA-ftsL-pbpB
0
0
ylxM ylxM-ffh
1
1
ylxR ymxB ylxS-nusA-ylxRQ-infB-ylxP-rbfA
1
1
ylxP ymxD ylxS-nusA-ylxRQ-infB-ylxP-rbfA
1
1
ylxW murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp
3
5
ylxX murE-mraY-murD-spoVE-murG-murB-divIB-ylxWX-sbp
3
5
yfjN yfjN
0
0
yybD yybEDC
0
0
yybG yybG
0
0
yhbH yzdC yhbH
2
1
ytiP pbuO ytiP
1
1
ypuH ypuGHI
0
0
ypuG ypuGHI
0
0
yxaH yxaGH
1
1
yxaI yxaI
0
0
yxaA yxaAB
0
0
yxaB yxaAB
0
0
yxaC yxaC
0
0
yknZ yknWXYZ
2
2
yfiD yfiDE
0
0
yfiA glvR malA-yfiA-malP
3
2
yycN yycN
0
0
yfiX yfiWX
0
0
ywbC ipa-18r ywbC
0
0
ywbN ipa-29d ywbLMN
3
3
ywbL ipa-27d ywbLMN
3
3
ywbM ipa-28d ywbLMN
3
3
yuxO srfB, comAB comA-yuxO
1
1
ylxS ymxA ylxS-nusA-ylxRQ-infB-ylxP-rbfA
1
1
ytzA pfkA-pyk-ytzA
0
0
ysnB ysnB
0
0
yfjF yfjABCDEF
0
0
yfhC yfhC
1
1
yabN yabMNOPQ-divIC-yabR
4
3
yabO yabMNOPQ-divIC-yabR
4
3
yhdE nsrR yhdE
0
0
ytkL ytkL
1
1

6 No similarity
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
ybcO skfA skf
4
2
ybcT skfD skf
4
2
ybcS skfC skf
4
2
ypeQ ypeQ
0
0
yxcD yxcED
0
0
yxcE yxcED
0
0
yorC yorBC
1
1
yxbA yxaO yxbBA-yxnB-asnH-yxaM
1
0
yflT yflT
0
0
yjdB yjdB
1
1
yjdH yjdH
1
0
yhfM yhfM
1
1
ywmE ywmE
1
1
yoxB yoxCB-yoaA
1
1
yoxC yoxCB-yoaA
1
1
ywtC ywsC-ywtABC
0
0
yteV cse60 yteV
1
1
yxeC yxeC
0
0
yxeD yxeD
1
1
yxeE yxeE
1
1
yxeF yxeFGH
0
0
yxeG yxeFGH
0
0
ywqO ywqO
0
0
yxeJ yxeIJ
0
0
ydaS ydaTS
1
2
ydaT ydaTS
1
2
yaaB yaaA-recF-yaaB-gyrB
1
2
ywnJ ywnJ
3
3
ylqB ylqB
1
1
yneA yneAB-ynzC
2
5
yvfB epsK eps
2
3
yvfA epsK eps
2
3
yqjX yqjWX
1
2
yqjU yqjVU
0
0
yrdK azlBCD-brnQ-yrdK
1
0
yvfG yvfG
0
0
yfjC yfjABCDEF
0
0
yxxG wapA-yxxG
3
3
yxxE yxiD-yxxD-yxxE
0
0
yxxD yxiD-yxxD-yxxE
0
0
yndA yndA
1
0
yqkC yqjYZ-yqkABC
0
0
yqkE yqkE
0
0
yodI yodHI
1
1
yozL yozLK-yobH
1
2
yozM yozM
1
2
yycS yycS
0
0
yozQ yozQ
1
1
yycQ yycOPQ
0
0
yxiT yxiT
0
0
yxiS katE-yxiS
1
2
ybgB ybgB
1
1
yscB yscB
1
1
yfiW yfiWX
0
0
ylaA ylaABCD
3
2
ylaB ylaABCD
3
2
ylaD ylaABCD
3
2
yqzH yqzH
1
2
yqzE comGABCDEFG-yqzE
3
3
yqzG yqzG
1
1
yeaA ydjQ yeaA-ydjP-ydjO
1
1
yesK cotJABC-yesJK
2
2
yesE yeeL yesEF
0
0
yurQ yurRQPONML
0
0
yurS sspG-yurS
2
3
ykuJ ykuJK-ykzF-ykuL-ccpC
3
3
ykuO ykuNOP
2
3
yvrI yvrI-yvrHa
1
0
yxzE yxzE
2
2
yxzF yxlJ-yxzF
0
0
ydbN ydbN
1
1
yrhC yrrT-mtn-yrhABC
2
2
yhzC yhzC
0
0
antE antE
1
1
ytaP ytaP
0
0
yotK yotK
1
1
ytaB ytaB
0
0
ykvR ykvR
1
1
ypkP ypkP
0
0
ypmT ypmT
0
0
yxxB yxeR-yxxB
0
0
ywjC ywjC
1
1
yttA yttA
1
1
yoaW G4 yoaW
2
1
yycO yycOPQ
0
0
ywdA ipa-51d sacPA-ywdA
3
3
ywdI ipa-59d ywdIJK
1
1
yqxA yqeP spoIIP-yqxA
2
1
yqxM yqhD yqxM-sipW-tasA
3
3
yycC yycCB
1
1
ygaN ssuBACD-ygaN
3
2
yqfQ yqfQ
1
0
yqfB yqeZ-yqfA-yqfB
1
1
yxjI yxjJI
2
1
ybdO ybdO
1
1
yxjJ yxjJI
2
1
yjgB yjgB
1
1
ybxH csgA-ybxH
2
1
yhjC yhjCB
1
2
yfnE yfnHGFED
2
3
ycdA ycdA
0
0
ywkF ywkF
0
0
ycxB ycxCB
0
0
yxkC yxkC
2
2
ytmB ytmB
0
0
yvaZ sdpI sdpRI
3
2
ypqA ypqA
2
2
yhcO yhcOP
2
2
yfmQ yfmQ
0
0
yfmK yfmK
0
0
yfmH yfmH
0
0
ydiR ydiRS-ydjA
0
0
yfmG yfmG
0
0
ybdD skfG skf
4
2
yceG yceCDEFGH
2
2
yqkB yqjYZ-yqkABC
0
0
yhaG trpP yhaG
2
2
yoaF yoaF
1
1
ysxD ysxD
0
0
ytlB ytlABCD
1
1
ytlA ytlABCD
1
1
yjcB yjcB-yjcZ-spoVIF
2
4
yjcN yjcN
1
0
yjcP yjcPQ
1
1
yqdB yqcR, txpA txpA
1
1
yxlC sigY-yxlCDEFG
1
1
yxlE sigY-yxlCDEFG
1
1
yxlD sigY-yxlCDEFG
1
1
ydhK ydhK
1
1
yuaF yuaFGI
1
1
yydF yydFGHIJ
1
0
yydG yydFGHIJ
1
0
yydJ yydFGHIJ
1
0
yydH yydFGHIJ
1
0
yxnB yxbBA-yxnB-asnH-yxaM
1
0
yczI yczI
0
0
yjbX cotO yjbX
1
1
yolC yolC
1
2
yobJ yobJ
1
1
ykzB ykzB-ykoL
3
4
ykzF ykuJK-ykzF-ykuL-ccpC
3
3
ycnL ycnL
0
0
yfkI yfkJIH
2
2
ycgI ycgI
0
0
ycgB ycgB
0
0
csbD ywmG ywmF-csbD sigma-B-controlled gene
1
1
csbX csbX-bofC sigma-B-transcribed gene
4
3
yhcP yhcOP
2
2
yhcI yhbIJ-yhcABCDEFGHI
1
0
yhcM yhcM
1
0
yhcC yhbIJ-yhcABCDEFGHI
1
0
yhcD yhbIJ-yhcABCDEFGHI
1
0
yhcE yhbIJ-yhcABCDEFGHI
1
0
ytnI ytmIJKLMNO-ytnIJ-ribR-ytnLM
4
3
yczA rtpA rtpA-ycbK
3
3
yuzC yuzC
1
1
ywrE ywrE
1
1
ywrJ ywrJ
1
0
ykyB ykyB
0
0
ytxO ytbB cotSA-cotS-ytxO
1
1
ydjA ydiRS-ydjA
0
0
ydjC ydjC
0
0
ydjM yzvA ydjM
0
0
ydjO yeaA-ydjP-ydjO
1
1
yfjA yfjABCDEF
0
0
yybP yybP
0
0
yybI yybHI
1
1
yybK yybNMLKJ
1
0
yugE mtnE yugE
0
0
yfjT yfjT
0
0
yybC yybEDC
0
0
ymaB nrdIEF-ymaB
2
2
yjcQ yjcPQ
1
1
yhbJ yhbIJ-yhcABCDEFGHI
1
0
yorB yorBC
1
1
ypuB ypuBC
1
1
ypuC ypuBC
1
1
ypuD ypuD
1
1
ypuE ypuE-ribDEAHT
1
1
yhdK sigM-yhdLK
2
2
yxaJ yxaJL
1
0
yhdL sigM-yhdLK
2
2
yycD yycD
1
1
yckD yckD
1
1
ywbB ipa-17d ywbB
0
0
ythQ ythPQ
1
1
ythC ythC
0
0
ykrI rsgI sigI-rsgI
1
1
yvlA yvlABCD
2
2
ysfE ysfE
0
0
ykoL ykzB-ykoL
3
4
yrrT yrrT-mtn-yrhABC
2
2
ysnD ysnD
2
1
ydjJ ydjJ
0
0
yfjB yfjABCDEF
0
0
yybH yybHI
1
1
yybM yybNMLKJ
1
0
yybN yybNMLKJ
1
0
ydaE ydaDEFG
1
2
yfhL yfhKLM
2
2
yfhO yfhO
0
0
yfhE yfhFED
1
0
yfhD yfhFED
1
0
yugM pgi-yugMN
0
0
yjfB yjfB
1
1
yjfA yjfA
1
0

Category not assigned
Gene Synonym Operon Description Num. of regulatory elements Num. of binding sequences
rtpLP rtpA-ycbK rtpA leader peptide
3
3
csfC S transcription unit csfC
1
1
ytrH ytrHI
1
1
bsrB BS203 RNA bsrB small cytoplasmic RNA
1
1
yjcZ yjcB-yjcZ-spoVIF
2
4