RegulonDB

Gene
Name:	ynfC
Synonym(s):	ECK1580, G6843, b1585
Genome position(nucleotides):	1656747 <-- 1657457 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	43.74
External database links:

ASAP:	ABE-0005288
ECHOBASE:	EB3602
OU-MICROARRAY:	b1585
PortEco:	ynfC
STRING:	511145.b1585
COLOMBOS:	ynfC

Product

Name:

UPF0257 family lipoprotein YnfC

Synonym(s):

YnfC

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

26.507

Isoelectric point:

4.38

Motif(s):

Type	Positions	Sequence
	17 -> 236	CDRTEVTLSFTPEMASFSNEFDFDPLRGPVKDFTQTLMDEQGEVTKRVSGTLSEEGCFDSLELLDLENNTVVALVLDANYYRDAETLEKRVRLQGKCQLAELPSAGVSWETDDNGFVIKASSKQMQMEYRYDDQGYPLGKTTKSNDKTLSVSATPSTDPIKKLDYTAVTLLNNQRVGNVKQSCEYDSHANPVDCQLIIVDEGVKPAVERVYTIKNTIDYY
	1 -> 236	MKYKLLPCLLAIFLTGCDRTEVTLSFTPEMASFSNEFDFDPLRGPVKDFTQTLMDEQGEVTKRVSGTLSEEGCFDSLELLDLENNTVVALVLDANYYRDAETLEKRVRLQGKCQLAELPSAGVSWETDDNGFVIKASSKQMQMEYRYDDQGYPLGKTTKSNDKTLSVSATPSTDPIKKLDYTAVTLLNNQRVGNVKQSCEYDSHANPVDCQLIIVDEGVKPAVERVYTIKNTIDYY

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane

Note(s):

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

Reference(s):

[1] Berven FS., et al., 2004
[2] Brokx SJ., et al., 2004
[3] Gonnet P., et al., 2004

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PRODOM:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ynfC

Operon arrangement:

Transcription unit	Promoter
ynfC

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	ynfDp6	1657414	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.445. P-value: 3.431e-5 Read more >	[ICWHO]	[4]
promoter	TSS_1872	1657482	reverse	nd	[RS-EPT-CBR]	[5]
promoter	TSS_1873	1657539	forward	nd	[RS-EPT-CBR]	[5]
promoter	ynfCp9	1657547	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.905. P-value: 4.918e-5 Read more >	[ICWHO]	[4]

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] Berven FS., Flikka K., Jensen HB., Eidhammer I., 2004, BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria., Nucleic Acids Res 32(Web Server issue):W394-9
[2] Brokx SJ., Ellison M., Locke T., Bottorff D., Frost L., Weiner JH., 2004, Genome-wide analysis of lipoprotein expression in Escherichia coli MG1655., J Bacteriol 186(10):3254-8
[3] Gonnet P., Rudd KE., Lisacek F., 2004, Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12., Proteomics 4(6):1597-613
[4] 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
[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.