RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

ycgR gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ycgR
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
ECOLIHUB:	ycgR
OU-MICROARRAY:	b1194
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:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ycgR

Operon arrangement:

Transcription unit	Promoter
ycgR	ycgRp

Transcriptional Regulation
	Display Regulation
Activated by:	FlhDC

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

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	ldcAp9	1243197	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 9.705. P-value: 1.228e-6 Read more >	[ICWHO]	[5]
promoter	TSS_1520	1243371	forward	nd	[RS-EPT-CBR]	[6]
promoter	ymgEp7	1244555	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 5.539. P-value: 4.968e-5 Read more >	[ICWHO]	[5]
promoter	ymgEp6	1244579	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.395. P-value: 3.607e-5 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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