Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes
-- version 3.2 --

Regulon of CodY in Bacillus pumilus SAFR-032

Properties
Regulator type: Transcription factor
TF locus tag: BPUM_1515
Regulator family: CodY
Regulation mode:
Biological process: Amino acid metabolism
Effector: Guanosine triphosphate; Branched-chain amino acids
Regulog: CodY - Bacillales
Statistics of regulated genes:
- Genes 88
- Operons 47
Visualization:
Allows to visualize regulon content in the context of metabolic pathways
Built upon 445 sites [see more]
Member of regulog collections
Regulated operons
Locus Tag Name Function

Position: -136
Score: 4.4
Sequence: TTTTTTTAGAAAAAT
Locus tag: BPUM_1603
Name: tdh
Funciton: L-threonine 3-dehydrogenase (EC 1.1.1.103)
Locus tag: BPUM_1604
Name: kbl
Funciton: 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
tdh
L-threonine 3-dehydrogenase (EC 1.1.1.103)
kbl
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)

Position: -366
Score: 4
Sequence: TATTTTCGGTAAATA
Locus tag: BPUM_0319
Name: srfAA
Funciton: Surfactin synthetase subunit 1
Locus tag: BPUM_0320
Name: srfAB
Funciton: Surfactin synthetase subunit 2
Locus tag: BPUM_0321
Name: srfAC
Funciton: Bacitracin synthetase 3 (BA3)( EC:5.1.1.11,EC:5.1.1.13 )
Locus tag: BPUM_0322
Name: srfAA
Funciton: Surfactin synthetase subunit 1
Locus tag: BPUM_0323
Name: srfAA
Funciton: Surfactin synthetase subunit 1
Locus tag: BPUM_0324
Name: srfAD
Funciton: Surfactin synthetase thioesterase subunit (EC 3.1.2.-)
srfAA
Surfactin synthetase subunit 1
srfAB
Surfactin synthetase subunit 2
srfAC
Bacitracin synthetase 3 (BA3)( EC:5.1.1.11,EC:5.1.1.13 )
srfAA
Surfactin synthetase subunit 1
srfAA
Surfactin synthetase subunit 1
srfAD
Surfactin synthetase thioesterase subunit (EC 3.1.2.-)

Position: -252
Score: 5
Sequence: AATTTTCTAAAAATA
Position: -230
Score: 4.4
Sequence: AATAGTATGAAAATA
Locus tag: BPUM_0421
Name: gltO
Funciton: Proton/sodium-glutamate symport protein
gltO
Proton/sodium-glutamate symport protein

Position: -77
Score: 4.6
Sequence: AGTTTTTTAAAAATT
Locus tag: BPUM_2616
Name: acsA
Funciton: Acetyl-coenzyme A synthetase (EC 6.2.1.1)
acsA
Acetyl-coenzyme A synthetase (EC 6.2.1.1)

Position: -27
Score: 4.4
Sequence: AAATTACAAAAAATT
Locus tag: BPUM_1877
Name: yoyD
Funciton: Hypothetical protein
Locus tag: BPUM_1878
Name: yodF
Funciton: SSS family solute:sodium (Na+) symporter
yoyD
Hypothetical protein
yodF
SSS family solute:sodium (Na+) symporter

Position: -83
Score: 4.7
Sequence: AATTGTGAGAAAATT
Position: -52
Score: 4.6
Sequence: ATTTTTCTGAGAATT
Locus tag: BPUM_1699
Name: citB
Funciton: Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
citB
Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)

Position: -206
Score: 4.7
Sequence: ATTATTCAGAAAATA
Locus tag: BPUM_2579
Name: ackA
Funciton: Acetate kinase (EC 2.7.2.1)
ackA
Acetate kinase (EC 2.7.2.1)

Position: -62
Score: 4.9
Sequence: TTTTTTCAGAAAATT
Locus tag: BPUM_1860
Name: yocS
Funciton: Sodium-dependent transporter
yocS
Sodium-dependent transporter

Position: -52
Score: 5
Sequence: ATTATTCTGAAAATT
Locus tag: BPUM_0276
Name: ycgA
Funciton: Putative integral inner membrane protein
ycgA
Putative integral inner membrane protein

Position: -116
Score: 5
Sequence: AATTTTCAGAATAAT
Locus tag: BPUM_0275
Name: amhX
Funciton: Amidohydrolase amhX (EC 3.5.1.-)
amhX
Amidohydrolase amhX (EC 3.5.1.-)

Position: -227
Score: 4.4
Sequence: TTTATTAAGAAAATT
Locus tag: BPUM_3562
Name: metE2
Funciton: Methionine synthase II (cobalamin-independent)
metE2
Methionine synthase II (cobalamin-independent)

Position: -44
Score: 4.5
Sequence: AATTAACAGAATATT
Locus tag: BPUM_2605
Name: braB
Funciton: Branched-chain amino acid transport system carrier protein
braB
Branched-chain amino acid transport system carrier protein

Position: -44
Score: 4.5
Sequence: AAAATTCTTAAAATT
Locus tag: BPUM_0501
Name: gltP
Funciton: Proton/glutamate symport protein @ Proton/aspartate symport protein
gltP
Proton/glutamate symport protein @ Proton/aspartate symport protein

Position: -210
Score: 4.3
Sequence: AAATGTCTGATTATT
Locus tag: BPUM_2556
Name: citZ
Funciton: Citrate synthase (si) (EC 2.3.3.1)
Locus tag: BPUM_2555
Name: icd
Funciton: Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
Locus tag: BPUM_2554
Name: mdh
Funciton: Malate dehydrogenase (EC 1.1.1.37)
citZ
Citrate synthase (si) (EC 2.3.3.1)
icd
Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
mdh
Malate dehydrogenase (EC 1.1.1.37)

Position: -201
Score: 4.5
Sequence: AATTTATTGACAATT
Position: -134
Score: 4.5
Sequence: AATTTTCCGAAATTT
Locus tag: BPUM_2504
Name: yslB
Funciton: Predicted hydrocarbon binding protein (V4R domain)
yslB
Predicted hydrocarbon binding protein (V4R domain)

Position: -161
Score: 4.5
Sequence: AAATTTCGGAAAATT
Position: -94
Score: 4.5
Sequence: AATTGTCAATAAATT
Locus tag: BPUM_2503
Name: sdhC
Funciton: Succinate dehydrogenase, cytochrome b subunit
Locus tag: BPUM_2502
Name: sdhA
Funciton: Succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1)
Locus tag: BPUM_2501
Name: sdhB
Funciton: Succinate dehydrogenase iron-sulfur protein (EC 1.3.99.1)
sdhC
Succinate dehydrogenase, cytochrome b subunit
sdhA
Succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1)
sdhB
Succinate dehydrogenase iron-sulfur protein (EC 1.3.99.1)

Position: -226
Score: 4.4
Sequence: AATTGTCAGATTAAT
Locus tag: BPUM_3500
Name: ybgE
Funciton: Branched-chain amino acid aminotransferase (EC 2.6.1.42)
ybgE
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Position: -233
Score: 4.5
Sequence: ATTTTTTTAAAAATA
Locus tag: BPUM_2823
Name: nupN
Funciton: Guanosine ABC transport system, substrate-binding component
Locus tag: BPUM_2824
Name: nupO
Funciton: Guanosine ABC transport system, ATP-binding protein
Locus tag: BPUM_2825
Name: nupP
Funciton: Guanosine ABC transport system, permease component Ia (FIG025991) / Unspecified monosaccharide ABC transport system, permease component Ib (FIG143636)
Locus tag: BPUM_2826
Name: nupQ
Funciton: Guanosine ABC transport system, permease component 2
nupN
Guanosine ABC transport system, substrate-binding component
nupO
Guanosine ABC transport system, ATP-binding protein
nupP
Guanosine ABC transport system, permease component Ia (FIG025991) / Unspecified monosaccharide ABC transport system, permease component Ib (FIG143636)
nupQ
Guanosine ABC transport system, permease component 2

Position: -196
Score: 5
Sequence: AATTTTCAGATTATT
Locus tag: BPUM_0906
Name: yhdT
Funciton: Hemolysins and related proteins containing CBS domains
yhdT
Hemolysins and related proteins containing CBS domains

Position: -153
Score: 5
Sequence: AATAATCTGAAAATT
Locus tag: BPUM_0905
Name: cueR
Funciton: Transcriptional regulator, MerR family
cueR
Transcriptional regulator, MerR family

Position: -36
Score: 5
Sequence: AATTTTTAGAAAATA
Locus tag: BPUM_0503
Name: yaaC
Funciton: Conserved hypothetical protein
yaaC
Conserved hypothetical protein

Position: -231
Score: 4.5
Sequence: AAATTTCAGAATAAT
Position: -33
Score: 4.3
Sequence: AATATTCTAAAAACA
Locus tag: BPUM_0543
Name: gabP
Funciton: Gamma-aminobutyrate (GABA) permease
gabP
Gamma-aminobutyrate (GABA) permease

Position: -185
Score: 4.8
Sequence: AATATTTTGAAAATA
Locus tag: BPUM_2888
Name: hom
Funciton: Homoserine dehydrogenase (EC 1.1.1.3)
Locus tag: BPUM_2887
Name: thrC
Funciton: Threonine synthase (EC 4.2.3.1)
Locus tag: BPUM_2886
Name: thrB
Funciton: Homoserine kinase (EC 2.7.1.39)
hom
Homoserine dehydrogenase (EC 1.1.1.3)
thrC
Threonine synthase (EC 4.2.3.1)
thrB
Homoserine kinase (EC 2.7.1.39)

Position: -43
Score: 5
Sequence: AATTTTCTGAATATA
Locus tag: BPUM_3043
Name: opuCA
Funciton: Osmotically activated L-carnitine/choline ABC transporter, ATP-binding protein OpuCA
Locus tag: BPUM_3042
Name: opuCB
Funciton: Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCB
Locus tag: BPUM_3041
Name: opuCC
Funciton: Osmotically activated L-carnitine/choline ABC transporter, substrate-binding protein OpuCC
Locus tag: BPUM_3040
Name: opuCD
Funciton: Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCD
opuCA
Osmotically activated L-carnitine/choline ABC transporter, ATP-binding protein OpuCA
opuCB
Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCB
opuCC
Osmotically activated L-carnitine/choline ABC transporter, substrate-binding protein OpuCC
opuCD
Osmotically activated L-carnitine/choline ABC transporter, permease protein OpuCD

Position: -182
Score: 4.9
Sequence: AATTTTCTGATAAAT
Locus tag: BPUM_0644
Name: gatC
Funciton: Aspartyl-tRNA(Asn) amidotransferase subunit C (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit C (EC 6.3.5.7)
Locus tag: BPUM_0645
Name: gatA
Funciton: Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Locus tag: BPUM_0646
Name: gatB
Funciton: Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)
gatC
Aspartyl-tRNA(Asn) amidotransferase subunit C (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit C (EC 6.3.5.7)
gatA
Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
gatB
Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)

Position: -222
Score: 5
Sequence: AATTTTTAGACAATT
Locus tag: BPUM_0978
Name: comK
Funciton: Competence transcription factor
comK
Competence transcription factor

Position: -166
Score: 4.7
Sequence: AATTGTCTAATAATT
Position: -54
Score: 4.6
Sequence: AAGTGTCTGAAAATT
Locus tag: BPUM_2473
Name: dat
Funciton: Branched-chain amino acid aminotransferase (EC 2.6.1.42)
dat
Branched-chain amino acid aminotransferase (EC 2.6.1.42)

Position: -183
Score: 4.6
Sequence: AATTCTCAGAAAAAT
Position: -152
Score: 4.7
Sequence: AATTTTCTCACAATT
Locus tag: BPUM_1698
Name: sspO
Funciton: Small, acid-soluble spore protein O
Locus tag: BPUM_1697
Name: sspP
Funciton: Small, acid-soluble spore protein P
sspO
Small, acid-soluble spore protein O
sspP
Small, acid-soluble spore protein P

Position: -131
Score: 4.5
Sequence: TATTTTCTAACTATT
Locus tag: BPUM_0158
Name: murQ
Funciton: N-acetylmuramic acid 6-phosphate etherase (EC 4.2.-.-)
Locus tag: BPUM_0157
Name: murR
Funciton: Transcriptional regulator of muropeptide rescue pathway operon, RpiR family
Locus tag: BPUM_0156
Name: ybbF
Funciton: PTS system, IIB component (EC 2.7.1.69) / PTS system, IIC component (EC 2.7.1.69)
Locus tag: BPUM_0155
Name: amiE
Funciton: Amidase of hydrolyzes the N-acetylmuramyl- L-Ala bond of MurNAc peptides
Locus tag: BPUM_0154
Name: nagZ
Funciton: Beta--N-acetylglucosaminidase
Locus tag: BPUM_0153
Name: ybbC
Funciton: Hypothetical protein
murQ
N-acetylmuramic acid 6-phosphate etherase (EC 4.2.-.-)
murR
Transcriptional regulator of muropeptide rescue pathway operon, RpiR family
ybbF
PTS system, IIB component (EC 2.7.1.69) / PTS system, IIC component (EC 2.7.1.69)
amiE
Amidase of hydrolyzes the N-acetylmuramyl- L-Ala bond of MurNAc peptides
nagZ
Beta--N-acetylglucosaminidase
ybbC
Hypothetical protein

Position: -111
Score: 4.4
Sequence: ATTATTCGGAAAATT
Locus tag: BPUM_2154
Name: spo0A
Funciton: Stage 0 sporulation two-component response regulator (Spo0A)
spo0A
Stage 0 sporulation two-component response regulator (Spo0A)

Position: -55
Score: 5
Sequence: ATTTTTTAGAAAATT
Locus tag: BPUM_1184
Name: dppA
Funciton: D-aminopeptidase (EC 3.4.11.-)
Locus tag: BPUM_1185
Name: dppB
Funciton: Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
Locus tag: BPUM_1186
Name: dppC
Funciton: Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
Locus tag: BPUM_1187
Name: dppD
Funciton: Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
Locus tag: BPUM_1188
Name: dppE
Funciton: Dipeptide-binding ABC transporter, periplasmic substrate-binding component (TC 3.A.1.5.2)
dppA
D-aminopeptidase (EC 3.4.11.-)
dppB
Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
dppC
Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)
dppD
Dipeptide transport ATP-binding protein DppD (TC 3.A.1.5.2)
dppE
Dipeptide-binding ABC transporter, periplasmic substrate-binding component (TC 3.A.1.5.2)

Position: -231
Score: 4.9
Sequence: ATTTATCAGAAAATT
Locus tag: BPUM_0643
Name: opuE
Funciton: Sodium/proline symporter
opuE
Sodium/proline symporter

Position: -38
Score: 4.4
Sequence: AATATACAGAAAAGT
Locus tag: BPUM_1071
Name: oppB
Funciton: Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Locus tag: BPUM_1072
Name: oppC
Funciton: Oligopeptide transport system permease protein OppC (TC 3.A.1.5.1)
Locus tag: BPUM_1073
Name: oppD
Funciton: Oligopeptide transport ATP-binding protein OppD (TC 3.A.1.5.1)
Locus tag: BPUM_1074
Name: oppF
Funciton: Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
oppB
Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
oppC
Oligopeptide transport system permease protein OppC (TC 3.A.1.5.1)
oppD
Oligopeptide transport ATP-binding protein OppD (TC 3.A.1.5.1)
oppF
Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)

Position: -140
Score: 4.4
Sequence: AATTTTCTGTATTTT
Locus tag: BPUM_1118
Name: ycjH
Funciton: Putative acetyl esterase YjcH (EC 3.1.1.-)
Locus tag: BPUM_1117
Name: yjcG
Funciton: RNA ligase/cyclic nucleotide phosphodiesterase
Locus tag: BPUM_1116
Name: yjcF
Funciton: GNAT family acetyltransferase YjcF
ycjH
Putative acetyl esterase YjcH (EC 3.1.1.-)
yjcG
RNA ligase/cyclic nucleotide phosphodiesterase
yjcF
GNAT family acetyltransferase YjcF

Position: -64
Score: 4.8
Sequence: TATTTTTTGAATATT
Locus tag: BPUM_1911
Name: ilvA
Funciton: Threonine dehydratase biosynthetic (EC 4.3.1.19)
ilvA
Threonine dehydratase biosynthetic (EC 4.3.1.19)

Position: -103
Score: 4.6
Sequence: AAATTTCAGAAATTT
Locus tag: BPUM_1672
Name: lutA
Funciton: Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit
Locus tag: BPUM_1673
Name: lutB
Funciton: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit
Locus tag: BPUM_1674
Name: lutC
Funciton: Predicted L-lactate dehydrogenase, hypothetical protein subunit
lutA
Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit
lutB
Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit
lutC
Predicted L-lactate dehydrogenase, hypothetical protein subunit

Position: -109
Score: 4.6
Sequence: GATTTTTTGAAAATT
Locus tag: BPUM_3062
Name: lutR
Funciton: Transcriptional regulator of L-lactate utilization, GntR family
lutR
Transcriptional regulator of L-lactate utilization, GntR family

Position: -43
Score: 4.6
Sequence: TATTTTTTGAAAAGT
Locus tag: BPUM_3302
Name: spoIIQ
Funciton: Stage II sporulation protein related to metaloproteases (SpoIIQ)
spoIIQ
Stage II sporulation protein related to metaloproteases (SpoIIQ)

Position: -83
Score: 4.5
Sequence: AATAAACAGAAAATT
Locus tag: BPUM_1922
Name: ilvD
Funciton: Dihydroxy-acid dehydratase (EC 4.2.1.9)
ilvD
Dihydroxy-acid dehydratase (EC 4.2.1.9)

Position: -45
Score: 4.5
Sequence: AATTATCAGATATTT
Locus tag: BPUM_2039
Name: serA
Funciton: D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
serA
D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

Position: -93
Score: 4.6
Sequence: AATTTTTAAAAAACT
Locus tag: BPUM_2617
Name: acuA
Funciton: Acetyltransferase AcuA, acetyl-CoA synthetase inhibitor
Locus tag: BPUM_2618
Name: acuB
Funciton: Component of the acetoin degradation regulation pathway
Locus tag: BPUM_2619
Name: acuC
Funciton: NAD-independent protein deacetylase AcuC
acuA
Acetyltransferase AcuA, acetyl-CoA synthetase inhibitor
acuB
Component of the acetoin degradation regulation pathway
acuC
NAD-independent protein deacetylase AcuC

Position: -80
Score: 4.7
Sequence: AATTTTCTGAAATAT
Locus tag: BPUM_0697
Name: yfmB
Funciton: Hypothetical protein
yfmB
Hypothetical protein

Position: -187
Score: 4.5
Sequence: AATTTTAAATAAATT
Locus tag: BPUM_0343
Name: yclF
Funciton: POT family proton (H+)-dependent oligopeptide transporter
yclF
POT family proton (H+)-dependent oligopeptide transporter

Position: -273
Score: 4.6
Sequence: TTTTTTCTGAAAAAT
Position: -140
Score: 4.4
Sequence: TTTTTTCAAACAATT
Locus tag: BPUM_0965
Name: gltT
Funciton: Proton/sodium-glutamate symport protein
gltT
Proton/sodium-glutamate symport protein

Position: -158
Score: 4.6
Sequence: AATAGTTTGAATATT
Locus tag: BPUM_2600
Name: ytcI
Funciton: Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
ytcI
Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases

Position: -297
Score: 4.4
Sequence: AAAATACAGAAAATT
Position: -287
Score: 4.1
Sequence: AAATTTCAATTAATT
Locus tag: BPUM_1119
Name: metI
Funciton: Cystathionine gamma-synthase (EC 2.5.1.48)
Locus tag: BPUM_1120
Name: metC
Funciton: Cystathionine beta-lyase (EC 4.4.1.8)
metI
Cystathionine gamma-synthase (EC 2.5.1.48)
metC
Cystathionine beta-lyase (EC 4.4.1.8)

Position: -58
Score: 4.2
Sequence: AAGATTCTAACAATT
Locus tag: BPUM_0954
Name: yhaA
Funciton: N-acyl-L-amino acid amidohydrolase (EC 3.5.1.14)
yhaA
N-acyl-L-amino acid amidohydrolase (EC 3.5.1.14)
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