RegulonDB

Gene
Name:	ydcL
Synonym(s):	ECK1424, G6742, b1431
Genome position(nucleotides):	1502457 --> 1503125 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	44.69
External database links:

ASAP:	ABE-0004775
ECHOBASE:	EB3518
OU-MICROARRAY:	b1431
PortEco:	ydcL
STRING:	511145.b1431
COLOMBOS:	ydcL

Product

Name:

DUF3313 domain-containing lipoprotein YdcL

Synonym(s):

YdcL

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

periplasmic space,inner membrane

Molecular weight:

24.427

Isoelectric point:

8.609

Motif(s):

Type	Positions	Sequence
	21 -> 222	CASKITQPDKYSGFLNNYSDLKETTSATGKPVLRWVDPSFDQSKYDSIVWNPITYYPVPKPSTQVGQKVLDKILNYTNTEMKEAIAQRKPLVTTAGPRSLIFRGAITGVDTSKEGLQFYEVVPVALVVAGTQMATGHRTMDTRLYFEGELIDAATNKPVIKVVRQGEGKDLNNESTPMAFENIKQVIDDMATDATMFDVNKK
	1 -> 20	MRTTSFAKVAALCGLLALSG
	30 -> 213	KYSGFLNNYSDLKETTSATGKPVLRWVDPSFDQSKYDSIVWNPITYYPVPKPSTQVGQKVLDKILNYTNTEMKEAIAQRKPLVTTAGPRSLIFRGAITGVDTSKEGLQFYEVVPVALVVAGTQMATGHRTMDTRLYFEGELIDAATNKPVIKVVRQGEGKDLNNESTPMAFENIKQVIDDMATD

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0030288 - outer membrane-bounded periplasmic space GO:0005886 - plasma membrane

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

UNIPROT:

Operon

Name:

ydcL

Operon arrangement:

Transcription unit	Promoter

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	ydcLp7	1502323	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.095. P-value: 3.792e-5 Read more >	[ICWHO]	[1]
promoter	ydcLp4	1502345	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.54. P-value: 4.233e-5 Read more >	[ICWHO]	[1]
promoter	ydcLp1	1502369	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 2.814. P-value: 6.252e-5 Read more >	[ICWHO]	[1]
promoter	ydcLp6	1502445	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.89. P-value: 1.441e-6 Read more >	[ICWHO]	[1]
promoter	ydcLp5	1502446	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.286. P-value: 9.611e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1812	1503657	forward	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.