RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

yccA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	yccA
Synonym(s):	ECK0961, EG11113, b0970
Genome position(nucleotides):	1030759 <-- 1031418 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.21
External database links:

ASAP:	ABE-0003280
ECHOBASE:	EB1104
OU-MICROARRAY:	b0970
PortEco:	yccA
STRING:	511145.b0970
COLOMBOS:	yccA

Product

Name:

modulator of FtsH protease

Synonym(s):

YccA

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

23.363

Isoelectric point:

9.019

Motif(s):

Type	Positions	Sequence
	47 -> 64	LPSPGLILTLVGMYGLMF
	133 -> 153	FLGGMLMAGIVVVLIGMVANI
	19 -> 213	KVLRNTYFLLSLTLAFSAITATASTVLMLPSPGLILTLVGMYGLMFLTYKTANKPTGIISAFAFTGFLGYILGPILNTYLSAGMGDVIAMALGGTALVFFCCSAYVLTTRKDMSFLGGMLMAGIVVVLIGMVANIFLQLPALHLAISAVFILISSGAILFETSNIIHGGETNYIRATVSLYVSLYNIFVSLLSIL
	74 -> 94	TGIISAFAFTGFLGYILGPIL
	196 -> 216	VSLYVSLYNIFVSLLSILGFA

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
		4 - transport --> 4.9.B - Putative uncharacterized transport protein
		6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)
	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane
	biological_process	GO:0043066 - negative regulation of apoptotic process GO:0030162 - regulation of proteolysis

Note(s):

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

Evidence:

[IMP] Inferred from mutant phenotype

Reference(s):

[1] Chae HJ., et al., 2003
[2] Kihara A., et al., 1998
[3] Schumann W. 1999
[4] Shimohata N., et al., 2002

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

MINT:

PANTHER:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

yccA

Operon arrangement:

Transcription unit	Promoter
yccA	yccAp

Transcriptional Regulation
	Display Regulation
Activated by:	CpxR

RNA cis-regulatory element

Attenuation:	Transcriptional

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	TSS_1295 (cluster)	1030888	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1030887 to 1030888, where the highest frequency is at position 1030110. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_1296	1030891	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1297	1031154	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1298	1031167	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1299	1031229	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1300	1031236	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1301 (cluster)	1031262	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1031261 to 1031262, where the highest frequency is at position 1030485. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_1302	1031273	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1303	1031275	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1304 (cluster)	1031345	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1031344 to 1031345, where the highest frequency is at position 1030567. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_1305 (cluster)	1031450	reverse	For this promoter, there is a cluster of 7 transcription start sites,in the interval 1031444 to 1031450, where the highest frequency is at position 1030669. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[5]
promoter	TSS_1306	1031454	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1307	1031546	reverse	nd	[RS-EPT-CBR]	[5]

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

Reference(s)
[1] Chae HJ., Ke N., Kim HR., Chen S., Godzik A., Dickman M., Reed JC., 2003, Evolutionarily conserved cytoprotection provided by Bax Inhibitor-1 homologs from animals, plants, and yeast., Gene 323:101-13
[2] Kihara A., Akiyama Y., Ito K., 1998, Different pathways for protein degradation by the FtsH/HflKC membrane-embedded protease complex: an implication from the interference by a mutant form of a new substrate protein, YccA., J Mol Biol 279(1):175-88
[3] Schumann W., 1999, FtsH--a single-chain charonin?, FEMS Microbiol Rev 23(1):1-11
[4] Shimohata N., Chiba S., Saikawa N., Ito K., Akiyama Y., 2002, The Cpx stress response system of Escherichia coli senses plasma membrane proteins and controls HtpX, a membrane protease with a cytosolic active site., Genes Cells 7(7):653-62
[5] 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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