RegulonDB

Gene
Name:	ydcI
Synonym(s):	ECK1416, G6737, b1422
Genome position(nucleotides):	1494148 <-- 1495071 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.54
External database links:

ASAP:	ABE-0004746
ECHOBASE:	EB3515
OU-MICROARRAY:	b1422
PortEco:	ydcI
STRING:	511145.b1422
COLOMBOS:	ydcI

Product

Name:

DNA-binding transcriptional repressor YdcI

Synonym(s):

YdcI

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

33.402

Isoelectric point:

8.126

Motif(s):

Type	Positions	Sequence
	101 -> 304	DVVRVGALPTAALGILPSVIGQFHQQQKETTLQVATMSNPMILAGLKTGEIDIGIGRMSDPELMTGLNYELLFLESLKLVVRPNHPLLQENVTLSRVLEWPVVVSPEGTAPRQHSDALVQSQGCKIPSGCIETLSASLSRQLTVEYDYVWFVPSGAVKDDLRHATLVALPVPGHGAGEPIGILTRVDATFSSGCQLMINAIRKS
	11 -> 68	IRLRHLHTFVAVAQQGTLGRAAETLNLSQPALSKTLNELEQLTGARLFERGRQGAQLT
	13 -> 72	LRHLHTFVAVAQQGTLGRAAETLNLSQPALSKTLNELEQLTGARLFERGRQGAQLTLPGE
	28 -> 47	LGRAAETLNLSQPALSKTLN

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 --> 3.1.2.2 - activator
		3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol
	molecular_function	GO:0003677 - DNA binding GO:0003700 - DNA-binding transcription factor activity GO:0043565 - sequence-specific DNA binding GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
	biological_process	GO:0006351 - transcription, DNA-templated GO:0006355 - regulation of transcription, DNA-templated GO:0045892 - negative regulation of transcription, DNA-templated

Note(s):

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

Evidence:

[APPHHH] Assay of protein purified to homogeneity from a heterologous host
[HIFS] Human inference of function from sequence
[IPI] Inferred from physical interaction

Reference(s):

[1] Gao Y., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
[4] Solomon L., et al., 2014

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PFAM:

PFAM:

PRIDE:

PRINTS:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

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	ydcIp4	1495117	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.764. P-value: 5.771e-5 Read more >	[ICWHO]	[5]
promoter	ydcJp10	1495133	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.743. P-value: 9.051e-5 Read more >	[ICWHO]	[5]
promoter	ydcJp11	1495154	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.934. P-value: 6.023e-6 Read more >	[ICWHO]	[5]

Reference(s)
[1] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696
[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] Solomon L., Shah A., Hannagan S., Wilson JW., 2014, Bacterial genus-specific tolerance for YdcI expression., Curr Microbiol 69(5):640-8
[5] 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