RegulonDB

Gene
Name:	ybdN
Synonym(s):	ECK0596, G6331, b0602
Genome position(nucleotides):	635349 <-- 636569 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.58
External database links:

ASAP:	ABE-0002073
ECHOBASE:	EB3304
ECOLIHUB:	ybdN
OU-MICROARRAY:	b0602
STRING:	511145.b0602
COLOMBOS:	ybdN

Product

Name:

putative PAPS reductase/DUF3440 domain-containing protein YbdN

Synonym(s):

YbdN

Sequence:

Get amino acid sequence Fasta Format

Molecular weight:

47.827

Isoelectric point:

7.878

Motif(s):

Type	Positions	Sequence
	237 -> 343	GVPLRHMRICEPFGPEQRQGLWLYHVIEPDRWAAMCARVSGVKSGGIYAGHDNHFYGHRKILKPEHLDWQEYALLLLNSMPEKTAEHYRNKIAIYLHWYQKKGIEVP
	352 -> 384	AKDIPSWRRICKVLLNNDYWCRALSFSPTKSKN
	30 -> 234	VCVSFSGGKDSGLMLHLTAELARQMGKKICVLFIDWEAQFSCTINYVQSLRELYTDVIEEFYWVALPLTTQNSLSQYQPEWQCWEPDVEWVRQPPQDAITDPDFFCFYQPGMTFEQFVREFAEWFSQKRPAAMMIGIRADESYNRFVAIASLNKQRFADDKPWTTAAPGGHSWYIYPIYDWKVADIWTWYANHQSLCNPLYNLMY

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	molecular_function	GO:0003824 - catalytic activity GO:0000976 - transcription regulatory region sequence-specific DNA binding

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

ybdN

Operon arrangement:

Transcription unit	Promoter
ybdN	ybdNp

Transcriptional Regulation
	Display Regulation
Activated by:	CysB, FNR, ArcA

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	ybdMp2	635555		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.336. P-value: 1.960e-5 Read more >	[ICWHO]	[1]
	promoter	TSS_729	637288		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.