RegulonDB RegulonDB 10.8: Gene Form
   

ycgR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycgR emtA ymgE terminator ymgEp6 ymgEp6 ycgRp ycgRp ymgEp7 ymgEp7 TSS_1520 TSS_1520 ldcAp9 ldcAp9

Gene      
Name: ycgR    Texpresso search in the literature
Synonym(s): ECK1182, G6623, b1194
Genome position(nucleotides): 1243793 <-- 1244527 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.75
External database links:  
ASAP:
ABE-0004009
ECHOBASE:
EB3658
OU-MICROARRAY:
b1194
PortEco:
ycgR
STRING:
511145.b1194
COLOMBOS: ycgR


Product      
Name: flagellar brake protein YcgR
Synonym(s): YcgR, molecular brake that regulates flagellar motility in response to c-di-GMP
Sequence: Get amino acid sequence Fasta Format
Cellular location: cell projection
Molecular weight: 27.857
Isoelectric point: 9.385
Motif(s):
 
Type Positions Sequence
42 -> 42 K
81 -> 81 K
112 -> 230 QRRRYFRISAPLHPPYFCQTKLADNSTLRFRLYDLSLGGMGALLETAKPAELQEGMRFAQIEVNMGQWGVFHFDAQLISISERKVIDGKNETITTPRLSFRFLNVSPTVERQLQRIIFS
118 -> 118 R
8 -> 109 FLKQNPLAVLGVLRDLHKAAIPLRLSWNGGQLISKLLAITPDKLVLDFGSQAEDNIAVLKAQHITITAETQGAKVEFTVEQLQQSEYLQLPAFITVPPPTLW

 

Classification:
Multifun Terms (GenProtEC)  
  3 - regulation
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
Gene Ontology Terms (GO)  
cellular_component GO:0009288 - bacterial-type flagellum
GO:0009425 - bacterial-type flagellum basal body
molecular_function GO:0005515 - protein binding
GO:0000166 - nucleotide binding
GO:0035438 - cyclic-di-GMP binding
biological_process GO:0051270 - regulation of cellular component movement
GO:0071945 - regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed
GO:0071973 - bacterial-type flagellum-dependent cell motility
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IGI] Inferred from genetic interaction
Reference(s): [1] Chong H., et al., 2014
[2] Kim EA., et al., 2015
[3] Ko M., et al., 2000
[4] Ryjenkov DA., et al., 2006
External database links:  
DIP:
DIP-11561N
ECOCYC:
G6623-MONOMER
ECOLIWIKI:
b1194
INTERPRO:
IPR009875
INTERPRO:
IPR009926
INTERPRO:
IPR023787
PDB:
5Y6G
PDB:
5Y6H
PDB:
5Y6F
PFAM:
PF07238
PFAM:
PF07317
PRIDE:
P76010
REFSEQ:
NP_415712
SMR:
P76010
UNIPROT:
P76010


Operon      
Name: ycgR         
Operon arrangement:
Transcription unit        Promoter
ycgR


Transcriptional Regulation      
Display Regulation             
Activated by: FlhDC


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter ldcAp9 1243197 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_1520 1243371 forward nd [RS-EPT-CBR] [6]
  promoter ymgEp7 1244555 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ymgEp6 1244579 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Chong H., Geng H., Zhang H., Song H., Huang L., Jiang R., 2014, Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP)., Biotechnol Bioeng 111(4):700-8

 [2] Kim EA., Blair DF., 2015, Function of the Histone-Like Protein H-NS in Motility of Escherichia coli: Multiple Regulatory Roles Rather than Direct Action at the Flagellar Motor., J Bacteriol 197(19):3110-20

 [3] Ko M., Park C., 2000, Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli., J Mol Biol 303(3):371-82

 [4] Ryjenkov DA., Simm R., Romling U., Gomelsky M., 2006, The PilZ domain is a receptor for the second messenger c-di-GMP. The PilZ domain protein YcgR controls motility in enterobacteria., J Biol Chem 281(41):30310-4

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


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