RegulonDB

Gene
Name:	yedD
Synonym(s):	ECK1927, EG11659, b1928
Genome position(nucleotides):	2007677 <-- 2008090 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	57.0
External database links:

ASAP:	ABE-0006416
ECHOBASE:	EB1611
OU-MICROARRAY:	b1928
PortEco:	yedD
STRING:	511145.b1928
COLOMBOS:	yedD

Product

Name:

lipoprotein YedD

Synonym(s):

YedD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

14.983

Isoelectric point:

4.596

Motif(s):

Type	Positions	Sequence
	16 -> 137	CAEVENYNNVVKTPAPDWLAGYWQTKGPQRALVSPEAIGSLIVTKEGDTLDCRQWQRVIAVPGKLTLMSDDLTNVTVKRELYEVERDGNTIEYDGMTMERVDRPTAECAAALDKAPLPTPLP
	25 -> 129	VVKTPAPDWLAGYWQTKGPQRALVSPEAIGSLIVTKEGDTLDCRQWQRVIAVPGKLTLMSDDLTNVTVKRELYEVERDGNTIEYDGMTMERVDRPTAECAAALDK
	1 -> 15	MKKLAIAGALLLLAG

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] Paradis-Bleau C., et al., 2014

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

MINT:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

yedD

Operon arrangement:

Transcription unit	Promoter
yedD

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_2267 (cluster)	2008115	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2008114 to 2008115, where the highest frequency is at position 2006138. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_2268	2008117	reverse	nd	[RS-EPT-CBR]	[2]
promoter	yedEp8	2008155	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.073. P-value: 5.771e-5 Read more >	[ICWHO]	[3]
promoter	TSS_2269	2008240	forward	nd	[RS-EPT-CBR]	[2]
promoter	yedDp5	2008261	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.88. P-value: 2.060e-5 Read more >	[ICWHO]	[3]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056
[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.
[3] 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