RegulonDB

Gene
Name:	ydcF
Synonym(s):	ECK1407, EG12110, b1414
Genome position(nucleotides):	1487235 --> 1488035 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.19
External database links:

ASAP:	ABE-0004722
ECHOBASE:	EB2033
OU-MICROARRAY:	b1414
PortEco:	ydcF
STRING:	511145.b1414
COLOMBOS:	ydcF

Product

Name:

DUF218 domain-containing protein YdcF

Synonym(s):

YdcF

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane,cytosol

Molecular weight:

29.706

Isoelectric point:

5.741

Motif(s):

Type	Positions	Sequence
	40 -> 173	VILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDA
	217 -> 266	PRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESRSLR
	97 -> 97	A

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0005829 - cytosol GO:0005886 - plasma membrane

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PDB:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ydcF

Operon arrangement:

Transcription unit	Promoter

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	ydcFp3	1487202	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.706. P-value: 8.872e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1801	1487204	forward	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1802	1487218	forward	nd	[RS-EPT-CBR]	[2]
promoter	ydcFp4	1487231	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 6.346. P-value: 1.225e-5 Read more >	[ICWHO]	[1]

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.