![]() ![]() |
Synonyms: RutR-thymine, RutR-uracil, RutR |
Summary:
RutR regulates genes directly or indirectly involved in the complex pathway of pyrimidine metabolism [1, 3] and also plays a role in regulation of the genes for degradation of purines and genes for maintenance of pH homeostasis [3]. This protein belongs to the TetR family, whose members have an N-terminal DNA-binding domain that contains a helix-turn-helix motif and a C-terminal domain for dimerization and ligand binding []. RutR recognizes and binds a 16-bp (7-2-7) inverted repeat consensus sequence [3, 6], where the central A/T nucleotide in each half-site appears to be the most important for the site [6]. This binding is inhibited when uracil and thymine bind to RutR, although the effect is greater for uracil than for thymine [3]. Read more > |
Transcription factor | ![]() ![]() |
||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
TF conformation(s): |
|
||||||||||||||||||||||||
Evolutionary Family: | TetR/AcrR | ||||||||||||||||||||||||
Connectivity class: | Local Regulator | ||||||||||||||||||||||||
Gene name: | rutR | ||||||||||||||||||||||||
Genome position: | 1074242-1074880 | ||||||||||||||||||||||||
Length: | 639 bp / 212 aa | ||||||||||||||||||||||||
Operon name: | rutR | ||||||||||||||||||||||||
TU(s) encoding the TF: |
|
Regulon |
![]() ![]() |
||||||
---|---|---|---|---|---|---|---|
Regulated gene(s) | carA, carB, fepB, gadW, gadX, gloA, nemA, nemR, pdeR, rutA, rutB, rutC, rutD, rutE, rutF, rutG, rutR | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
nitrogen metabolism (6)
Transcription related (4)
arginine (2)
pyrimidine biosynthesis (2)
repressor (2)
Read more >
|
||||||
Regulated operon(s) | carAB, fepB, gadAXW, nemRA-gloA, pdeR, rutABCDEFG, rutR | ||||||
First gene in the operon(s) | carA, fepB, gadX, gadX, nemR, nemR, pdeR, rutA, rutR | ||||||
Simple and complex regulons | ArcA,NtrC,PhoP,RutR FNR,GadE,GadW,GadX,H-NS,PhoB,RutR Fis,IHF,PepA,PurR,RutR FliZ,RutR Fur,RutR Read more > | ||||||
Simple and complex regulatory phrases | Regulatory phrase (List of promoters regulated by the phrase) |
Transcription factor regulation |
![]() |
---|
Functional conformation | Function | Promoter | Sigma factor | Central Rel-Pos | Distance to first Gene | Genes | Sequence | LeftPos | RightPos | Evidence (Confirmed, Strong, Weak) | References | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
RutR | activator | carAp1 | Sigma70 | -184.0 | -284.0 | carA, carB |
aatgtaaattTTGACCATTTGGTCCACttttttctgc
|
29359 | 29375 | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [3], [4], [5], [6] | |
RutR | repressor | fepBp | Sigma70 | 172.5 | -45.5 | fepB |
gattgtgcgcTTTGTCGAATTTGTCATtacgccctta
|
624548 | 624564 | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [6] | |
RutR | repressor | gadXp | Sigma38 | -824.5 | -853.5 | gadX, gadW |
ggtgttcaacGTTGACTACCTGGGTGGTCAAattggtactt
|
3666654 | 3666674 | [BPP], [GEA] | [3] | |
RutR | repressor | nemRp | Sigma70 | -20.5 | -22.5 | nemR, nemA, gloA |
ttgcttgcacTAGACCGACTGGTCTACtacactccaa
|
1725993 | 1726009 | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] | [6] | |
RutR | repressor | pdeRp | Sigma38 | nd | nd | pdeR | nd | nd | [GEA] | [3] | ||
RutR | repressor | rutAp | Sigma54 | -102.5 | -117.5 | rutA, rutB, rutC, rutD, rutE, rutF, rutG |
atgtgcaactGTTTTGACCGTTTAGTCCActttttacca
|
1074120 | 1074138 | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [3], [5], [6] | |
RutR | repressor | rutRp2 | Sigma70 | 16.5 | -113.5 | rutR |
tggtaaaaagTGGACTAAACGGTCAAAACagttgcacat
|
1074120 | 1074138 | [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] | [3], [5], [6] |
Alignment and PSSM for RutR TFBSs | ![]() |
---|
Aligned TFBS of RutR |
---|
Sequence | |
---|---|
TTGACCATTTGGTCCACTTT | |
TTGACCGTTTAGTCCACTTT | |
TAGACCGACTGGTCTACTAC | |
CCACCCAGGTAGTCAACGTT | |
ATGACAAATTCGACAAAGCG |
Position weight matrix (PWM). RutR matrix-quality result |
---|
A 1 1 1 4 0 1 3 2 0 0 2 0 1 0 2 5 1 0 1 0 C 1 1 0 1 5 4 0 0 1 0 1 0 0 5 2 0 4 0 1 1 G 0 0 4 0 0 0 2 1 1 0 2 5 0 0 0 0 0 2 0 1 T 3 3 0 0 0 0 0 2 3 5 0 0 4 0 1 0 0 3 3 3 |
Consensus |
---|
; consensus.strict ttGaCCaatTgGtCcACttt ; consensus.strict.rc AAAGTGGACCAATTGGTCAA ; consensus.IUPAC ttGaCCrwtTrGtCmACktt ; consensus.IUPAC.rc AAMGTKGACYAAWYGGTCAA ; consensus.regexp ttGaCC[ag][at]tT[ag]GtC[ac]AC[gt]tt ; consensus.regexp.rc AA[AC]GT[GT]GAC[CT]AA[AT][CT]GGTCAA |
Evolutionary conservation of regulatory elements | ![]() |
---|
Reference(s) |
![]() |
---|---|