RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

ygcG gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ygcG
Synonym(s):	ECK2772, G7444, b2778
Genome position(nucleotides):	2905711 --> 2906583 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	41.12
External database links:

ASAP:	ABE-0009108
ECHOBASE:	EB2850
ECOLIHUB:	ygcG
OU-MICROARRAY:	b2778
STRING:	511145.b2778
COLOMBOS:	ygcG

Product

Name:

protein YgcG

Synonym(s):

YgcG

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

32.206

Isoelectric point:

7.424

Motif(s):

Type	Positions	Sequence
	17 -> 290	AQPTIVPQLQQQVTDLTSSLNSQEKKELTHKLESIFNNTQVQIAVLIVPTTKDETIEQYATRVFDNWRLGDAKRNDGILIVVAWSDRTVRIQVGYGLEEKVTDALAGDIIRSNMIPAFKQQKLAKGLELAINALNNQLTSQHQYPTNPSESESASSSDHYYFAIFWVFAVMFFPFWFFHQGSNFCRACKSGVCISAIYLLDLFLFSDKIFSIAVFSFFFTFTIFMVFTCLCVLQKRASGRSYHSDNSGSAGGSDSGGFSGGGGSSGGGGASGRW
	29 -> 152	VTDLTSSLNSQEKKELTHKLESIFNNTQVQIAVLIVPTTKDETIEQYATRVFDNWRLGDAKRNDGILIVVAWSDRTVRIQVGYGLEEKVTDALAGDIIRSNMIPAFKQQKLAKGLELAINALNN
	1 -> 16	MRYFILMFTFVCSFVA
	175 -> 195	HYYFAIFWVFAVMFFPFWFFH
	264 -> 288	GSAGGSDSGGFSGGGGSSGGGGASG

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane

Note(s):

Note(s): ...[more].

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ygcG

Operon arrangement:

Transcription unit	Promoter
ygcG

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	ygcGp7	2905605	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.23. P-value: 9.470e-7 Read more >	[ICWHO]	[1]
promoter	queEp7	2905606	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.894. P-value: 3.918e-6 Read more >	[ICWHO]	[1]
promoter	ygcGp6	2905666	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.646. P-value: 6.773e-5 Read more >	[ICWHO]	[1]
promoter	TSS_3055	2907117	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3056	2907189	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3057 (cluster)	2907196	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2907195 to 2907196, where the highest frequency is at position 2905217. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3058 (cluster)	2907241	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2907240 to 2907241, where the highest frequency is at position 2905262. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3059	2907580	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3060	2907627	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3061	2907633	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3062	2907661	forward	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3063	2907662	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3064 (cluster)	2907665	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2907664 to 2907665, where the highest frequency is at position 2905686. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3065	2907682	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3066	2907694	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3067	2907716	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3068	2907923	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3069	2907932	reverse	nd	[RS-EPT-CBR]	[2]

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] 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
[2] 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.

Reference(s)

[1] 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

[2] 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.

RegulonDB