RegulonDB RegulonDB 10.8: Gene Form
   

ydcI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

trg ydcJ ydcI ydcJp11 ydcJp11 ydcIp ydcIp ydcJp10 ydcJp10 ydcIp4 ydcIp4

Gene      
Name: ydcI    Texpresso search in the literature
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:
G6737-MONOMER
ECOLIWIKI:
b1422
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR005119
INTERPRO:
IPR000847
MODBASE:
P77171
PFAM:
PF00126
PFAM:
PF03466
PRIDE:
P77171
PRINTS:
PR00039
PROSITE:
PS50931
REFSEQ:
NP_415939
SMR:
P77171
UNIPROT:
P77171


Operon      
Name: ydcI         
Operon arrangement:
Transcription unit        Promoter
ydcI


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 ydcIp4 1495117 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ydcJp10 1495133 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ydcJp11 1495154 forward Similarity to the consensus
Read more >
[ICWHO] [5]


Evidence    

 [ICWHO] Inferred computationally without human oversight



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


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