RegulonDB

Gene
Name:	ydcC
Synonym(s):	ECK1454, EG11526, b1460
Genome position(nucleotides):	1531816 --> 1532952 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	41.78
External database links:

ASAP:	ABE-0004872
ECHOBASE:	EB1488
ECOO157CYC:	Z2253
ECOO157CYC:	Z0857
ECOO157CYC:	Z2254
ECOO157CYC:	Z0700
ECOO157CYC:	Z0854
OU-MICROARRAY:	b1460
PortEco:	ydcC
STRING:	511145.b1460
COLOMBOS:	ydcC

Product

Name:

H repeat-associated putative transposase YdcC

Synonym(s):

YdcC

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

43.079

Isoelectric point:

7.424

Motif(s):

Type	Positions	Sequence
	102 -> 343	DKDVIAIDGKTLRHSYDKSRRRGAIHVISAFSTMHSLVIGQIKTDEKSNEITAIPELLNMLDIKGKIITTDAMGCQKDIAEKIQKQGGDYLFAVKGNQGRLNKAFEEKFPLKELNNPAHDSYAMSEKSHGREEIRLHIVCDVPDELIDFTFEWKGLKKLCVAVSFRSIIAEQKKELEMTVRYYISSADLTAEKFATAIRNHWHVENKLHWRLDVVMNEDDCKIRRGNAAELFSGIRHIAINI
	9 -> 94	HISIIPDYRQAWKMEHKLSDILLLTICAVISGAEGWEDIEDFGETHPDFLKQYGDFENGIPVHDTIARVVSCISPAKFHECFINWM

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0004803 - transposase activity
	biological_process	GO:0006313 - transposition, DNA-mediated

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

ECOO157CYC:

ECOO157CYC:

ECOO157CYC:

ECOO157CYC:

ECOO157CYC:

INTERPRO:

INTERPRO:

PFAM:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ydcC

Operon arrangement:

Transcription unit	Promoter

RNA cis-regulatory element

Attenuation:	Translational

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	pptAp7	1532858	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.695. P-value: 7.636e-5 Read more >	[ICWHO]	[1]
promoter	pptAp6	1532867	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.0. P-value: 4.586e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1826	1533030	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.