RegulonDB

Gene
Name:	ydcR
Synonym(s):	ECK1433, G6750, b1439
Genome position(nucleotides):	1510003 --> 1511409 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.39
External database links:

ASAP:	ABE-0004800
ECHOBASE:	EB3524
OU-MICROARRAY:	b1439
PortEco:	ydcR
STRING:	511145.b1439
COLOMBOS:	ydcR

Product

Name:

fused putative DNA-binding transcriptional regulator/putative aminotransferase YdcR

Synonym(s):

YdcR

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

52.793

Isoelectric point:

8.96

Motif(s):

Type	Positions	Sequence
	1 -> 69	MKKYQQLAEQLREQIASGIWQPGDRLPSLRDQVALSGMSFMTVSHAYQLLESQGYIIARPQSGYYVAPQ
	3 -> 66	KYQQLAEQLREQIASGIWQPGDRLPSLRDQVALSGMSFMTVSHAYQLLESQGYIIARPQSGYYV
	145 -> 445	PGNAELRQAIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALERLRLKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLNQYNVTLIEDDVYSELYFGREKPLPAKAWDRHDGVLHCSSFSKCLVPGFRIGWVAAGKHARKIQRLQLMSTLSTSSPMQLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQALLRYLPAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTHHISIAPGKMFSTGENWSRFFRFNT

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0003824 - catalytic activity GO:0016740 - transferase activity GO:0008483 - transaminase activity GO:0003700 - DNA-binding transcription factor activity GO:0030170 - pyridoxal phosphate binding
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:0009058 - biosynthetic process GO:1901605 - alpha-amino acid metabolic process

Note(s):

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

Evidence:

[HIFS] Human inference of function from sequence
[IHBCE] Inferred by a human based on computational evidence

Reference(s):

[1] Nakata K., et al., 2010
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

ydcR

Operon arrangement:

Transcription unit	Promoter
ydcR	ydcRp

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	ydcSp9	1511453	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.43. P-value: 4.869e-5 Read more >	[ICWHO]	[4]
promoter	ydcSp7	1511515	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.38. P-value: 4.869e-5 Read more >	[ICWHO]	[4]
promoter	TSS_1815	1511596	forward	nd	[RS-EPT-CBR]	[5]

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] Nakata K., Koh MM., Tsuchido T., Matsumura Y., 2010, All genomic mutations in the antimicrobial surfactant-resistant mutant, Escherichia coli OW66, are involved in cell resistance to surfactant., Appl Microbiol Biotechnol 87(5):1895-905
[2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47
[3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50
[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.