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Synonyms: CytR-cytidine, CytR |
Summary:
CytR, "Cytidine Regulator," is a transcription factor required for transport and utilization of ribonucleosides and deoxyribonucleosides [4, 18, 19, 20, 21, 22, 26] The repressor CytR and the activator CRP, two dimeric proteins, interact to form a complex repressor nucleoprotein in the intergenic region. When only CRP is bound to this promoter, it functions as an activator, and then, when CytR binds to DNA and to CRP, the activation is repressed because CytR masks an activating region of CRP that otherwise would contact the RNA polymerase to activate transcription [29, 30, 30, 31, 32, 33, 34] The CytR protein cannot act alone; the synergistic DNA binding is increased by direct interaction with CRP [13, 15, 35] However, footprinting analyses showed that the dimers of CytR are flanked or "sandwiched" by two dimers of CRP [1, 11, 25, 30] At times CytR also repositions CRP to alternative DNA-binding sites that are not functional for activation [29] Gavigan et al. Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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Evolutionary Family: | GalR/LacI | ||||||||||||||||||
Sensing class: | Sensing external and internal signals | ||||||||||||||||||
Connectivity class: | Local Regulator | ||||||||||||||||||
Gene name: | cytR | ||||||||||||||||||
Genome position: | 4123431-4124456 | ||||||||||||||||||
Length: | 1026 bp / 341 aa | ||||||||||||||||||
Operon name: | cytR | ||||||||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | cdd, cytR, deoA, deoB, deoC, deoD, nupC, nupG, ppiA, rpoH, tsx, udp, ycdZ | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
nucleotide and nucleoside conversions (9)
Transcription related (2)
Porters (Uni-, Sym- and Antiporters) (2)
membrane (2)
activator (1)
Read more >
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Regulated operon(s) | cdd, cytR, deoCABD, mutY-yggX-mltC-nupG, nupC, ppiA, rpoH, tsx, udp, ycdZ | ||||||
First gene in the operon(s) | cdd, cytR, deoC, nupC, nupG, ppiA, rpoH, tsx, udp, ycdZ | ||||||
Simple and complex regulons | CRP,CytR CRP,CytR,DeoR CRP,CytR,DeoR,Fis,ModE CRP,CytR,DnaA CRP,CytR,Nac Read more > | ||||||
Simple and complex regulatory phrases | Regulatory phrase (List of promoters regulated by the phrase) |
Transcription factor regulation |
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Functional conformation | Function | Promoter | Sigma factor | Central Rel-Pos | Distance to first Gene | Genes | Sequence![]() |
LeftPos | RightPos | Evidence (Confirmed, Strong, Weak) | References | |
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CytR | repressor | cddp | Sigma70 | -82.5 | -107.5 | cdd |
tgcgatgcgtCGCGCATTTTTGATGTAtgtttcacgc
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2231729 | 2231745 | [GEA], [APIORCISFBSCS], [BPP] | [2], [3], [4] | |
CytR | repressor | cddp | Sigma70 | -64.0 | -89.0 | cdd |
tttgatgtatGTTTCACGCGTTGCATAAttaatgagat
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2231747 | 2231764 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [2], [3], [4], [5] | |
CytR | repressor | cytRp | Sigma70 | -59.0 | -112.0 | cytR |
atcgaaaaatTCAATATTCATCACACTTTTCATGaaaattctgt
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4124557 | 4124580 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [6], [7] | |
CytR | repressor | cytRp | Sigma70 | -43.0 | -96.0 | cytR |
atcacactttTCATGAAAATTCTGTAACcgttttcacg
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4124544 | 4124561 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [6], [7], [8] | |
CytR | repressor | cytRp | Sigma70 | -22.0 | -75.0 | cytR |
ttctgtaaccGTTTTCACGCGCTATCTGCTAAaaatgttgcc
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4124521 | 4124542 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [6], [7] | |
CytR | repressor | deoCp2 | Sigma70 | -87.5 | -132.5 | deoC, deoA, deoB, deoD |
tgaattatttGAACCAGATCGCATTACAGTGAtgcaaacttg
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4617180 | 4617201 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [1], [9], [10], [11], [12], [13], [14], [15], [16], [17] | |
CytR | repressor | deoCp2 | Sigma70 | -70.5 | -115.5 | deoC, deoA, deoB, deoD |
gcattacagtGATGCAAACTTGTAAGTagatttcctt
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4617200 | 4617216 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [1], [9], [10], [11], [12], [13], [14], [15], [16], [17] | |
CytR | repressor | deoCp2 | Sigma70 | -61.0 | -106.0 | deoC, deoA, deoB, deoD |
gtgatgcaaaCTTGTAAGTAGATTTCCTTAattgtgatgt
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4617208 | 4617227 | [GEA], [BPP], [SM] | [1], [9], [10], [11], [12], [13], [14], [15], [16], [17] | |
CytR | repressor | nupCp | Sigma70 | nd | nd | nupC | nd | nd | [TAS], [BPP] | [18] | ||
CytR | repressor | nupGp | Sigma70 | -76.5 | -139.5 | nupG |
cacatcacaaTTTCGTTTTGCAAATtgggaatgtt
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3105568 | 3105582 | [APIORCISFBSCS], [BPP] | [19] | |
CytR | repressor | nupGp | Sigma70 | -61.0 | -124.0 | nupG |
cgttttgcaaATTGGGAATGTTTGCAATTatttgccaca
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3105581 | 3105599 | [APIORCISFBSCS], [BPP] | [19] | |
CytR | repressor | nupGp | Sigma70 | -53.0 | -116.0 | nupG |
aaattgggaaTGTTTGCAATTATTTGCCACaggtaacaaa
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3105589 | 3105608 | [APIORCISFBSCS], [BPP] | [19] | |
CytR | repressor | ppiAp2 | Sigma70 | -83.0 | -181.0 | ppiA |
gtgatctgttTAAATGTTTTATTGCAATcggttgctaa
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3492470 | 3492487 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [20] | |
CytR | repressor | ppiAp2 | Sigma70 | -64.5 | -162.5 | ppiA |
tattgcaatcGGTTGCTAAATTGCATTttaagaggtg
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3492452 | 3492468 | [GEA], [APIORCISFBSCS], [BPP] | [20] | |
CytR | repressor | ppiAp3 | Sigma70 | -48.0 | -181.0 | ppiA |
gtgatctgttTAAATGTTTTATTGCAATcggttgctaa
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3492470 | 3492487 | [BPP], [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [20] | |
CytR | repressor | ppiAp3 | Sigma70 | -29.5 | -162.5 | ppiA |
tattgcaatcGGTTGCTAAATTGCATTttaagaggtg
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3492452 | 3492468 | [GEA], [APIORCISFBSCS], [BPP] | [20] | |
CytR | repressor | ppiAp4 | Sigma70 | -29.0 | -181.0 | ppiA |
gtgatctgttTAAATGTTTTATTGCAATcggttgctaa
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3492470 | 3492487 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC] | [20] | |
CytR | repressor | ppiAp4 | Sigma70 | -10.5 | -162.5 | ppiA |
tattgcaatcGGTTGCTAAATTGCATTttaagaggtg
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3492452 | 3492468 | [GEA], [APIORCISFBSCS], [BPP] | [20] | |
CytR | repressor | rpoHp3 | Sigma24 | -52.0 | -139.0 | rpoH |
tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg
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3600913 | 3600932 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | rpoHp3 | Sigma24 | -33.5 | -120.5 | rpoH |
ttattcacaaGCTTGCATTGAACTTGTggataaaatc
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3600896 | 3600912 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | rpoHp4 | Sigma70 | -59.0 | -139.0 | rpoH |
tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg
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3600913 | 3600932 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | rpoHp4 | Sigma70 | -40.5 | -120.5 | rpoH |
ttattcacaaGCTTGCATTGAACTTGTggataaaatc
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3600896 | 3600912 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | rpoHp5 | Sigma70 | -73.5 | -139.0 | rpoH |
tgtcacatttTGTGCGTAATTTATTCACAAgcttgcattg
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3600913 | 3600932 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | rpoHp5 | Sigma70 | -54.5 | -120.5 | rpoH |
ttattcacaaGCTTGCATTGAACTTGTggataaaatc
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3600896 | 3600912 | [GEA], [APIORCISFBSCS], [BPP] | [21] | |
CytR | repressor | tsxp2 | Sigma70 | -68.5 | -146.5 | tsx |
tgtgtaaacgTGAACGCAATCGATTACGTAAatgatagaac
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432150 | 432170 | [GEA], [IC], [APIORCISFBSCS], [BPP], [IC], [SM] | [22] | |
CytR | repressor | tsxp2 | Sigma70 | -57.5 | -135.5 | tsx |
aacgcaatcgATTACGTAAATGATAGAACtgtgaaacga
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432140 | 432158 | [GEA], [IC], [BPP], [IC], [IHBCE] | [22], [23] | |
CytR | repressor | tsxp2 | Sigma70 | -31.5 | -109.5 | tsx |
atagaactgtGAAACGAAACATATTTTTGTGAGCAATgatttttata
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432110 | 432136 | [GEA], [IC], [BPP], [IC], [SM] | [22] | |
CytR | repressor | udpP | Sigma70 | -87.0 | -127.0 | udp |
atttatgtgaTTTGCATCACTTTTGGTGGGtaaatttatg
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4016295 | 4016314 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [24], [25], [26] | |
CytR | repressor | udpP | Sigma70 | -70.5 | -110.5 | udp |
acttttggtgGGTAAATTTATGCAACGcatttgcgtc
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4016313 | 4016329 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [24], [25], [26], [27] | |
CytR | repressor | udpP | Sigma70 | -61.0 | -101.0 | udp |
tgggtaaattTATGCAACGCATTTGCGTCAtggtgatgag
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4016321 | 4016340 | [GEA], [APIORCISFBSCS], [BPP], [SM] | [24], [25], [26], [27] | |
CytR | repressor | ycdZp4 | Sigma70 | -22.0 | -66.0 | ycdZ |
gtcactcataACTGCAACGGATAATTTGTTGTTGCATAAaatgtgtgct
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1100216 | 1100244 | [AIBSCS] | [28] |
Alignment and PSSM for CytR TFBSs | ![]() |
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Aligned TFBS of CytR |
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Sequence | |
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CATTGCTCACAAAAATATGTTTC | |
AACCGATTGCAATAAAACATTTA | |
ACCAGATCGCATTACAGTGATGC | |
AATCGGTTGCTAAATTGCATTTT | |
CCCAATTTGCAAAACGAAATTGT | |
AAACGGTTACAGAATTTTCATGA | |
AATTGCAAACATTCCCAATTTGC | |
CATTTTATGCAACAACAAATTAT | |
ACAAGCTTGCATTGAACTTGTGG | |
AATGCGTTGCATAAATTTACCCA | |
CATTTTTAGCAGATAGCGCGTGA | |
CAGTTCTATCATTTACGTAATCG | |
ATCTACTTACAAGTTTGCATCAC | |
AAGCTTGTGAATAAATTACGCAC | |
CATACATCAAAAATGCGCGACGC | |
ACCCACCAAAAGTGATGCAAATC | |
TGTTTCACGCGTTGCATAATTAA |
Position weight matrix (PWM). CytR matrix-quality result |
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A 10 11 2 4 3 3 3 4 6 3 15 7 8 9 9 4 5 5 9 5 1 4 5 C 6 4 5 5 2 7 1 4 0 14 0 0 1 1 4 4 2 5 3 1 4 2 7 G 0 1 2 1 7 3 1 0 10 0 1 3 1 3 1 2 6 1 3 3 0 7 2 T 1 1 8 7 5 4 12 9 1 0 1 7 7 4 3 7 4 6 2 8 12 4 3 |
Consensus |
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; consensus.strict aatcgcttGCAaaaatgcattgc ; consensus.strict.rc GCAATGCATTTTTGCAAGCGATT ; consensus.IUPAC mmyygctyRCAwwamyrhawygm ; consensus.IUPAC.rc KCRWTDYRKTWWTGYRAGCRRKK ; consensus.regexp [ac][ac][ct][ct]gct[ct][AG]CA[at][at]a[ac][ct][ag][act]a[at][ct]g[ac] ; consensus.regexp.rc [GT]C[AG][AT]T[AGT][CT][AG][GT]T[AT][AT]TG[CT][AG]AGC[AG][AG][GT][GT] |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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