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Protein

Uncharacterized HTH-type transcriptional regulator YbdO

Gene

ybdO

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at transcript leveli

Functioni

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi27 – 4620H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6332-MONOMER.
ECOL316407:JW0596-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Uncharacterized HTH-type transcriptional regulator YbdO
Gene namesi
Name:ybdO
Ordered Locus Names:b0603, JW0596
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13534. ybdO.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 300300Uncharacterized HTH-type transcriptional regulator YbdOPRO_0000105778Add
BLAST

Proteomic databases

PaxDbiP77746.
PRIDEiP77746.

Expressioni

Inductioni

Induced by LeuO, a monocistronic operon (PubMed:19429622). Maximally induced in early stationary phase, repressed by H-NS via 2 binding sites in the upstream and coding region; H-NS may bind both regions to form a bridge which then prevents transcription (PubMed:26789284).2 Publications

Interactioni

Protein-protein interaction databases

BioGridi4260901. 8 interactions.
IntActiP77746. 5 interactions.
STRINGi511145.b0603.

Structurei

3D structure databases

ProteinModelPortaliP77746.
SMRiP77746. Positions 17-67.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini10 – 6758HTH lysR-typePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 HTH lysR-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105DQS. Bacteria.
ENOG410XQ6Z. LUCA.
HOGENOMiHOG000117868.
OMAiQLYLMYN.
OrthoDBiEOG6XM78X.
PhylomeDBiP77746.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR005119. LysR_subst-bd.
IPR000847. Tscrpt_reg_HTH_LysR.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00126. HTH_1. 1 hit.
PF03466. LysR_substrate. 1 hit.
[Graphical view]
PRINTSiPR00039. HTHLYSR.
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS50931. HTH_LYSR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P77746-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MANLYDLKKF DLNLLVIFEC IYQHLSISKA AESLYITPSA VSQSLQRLRA
60 70 80 90 100
QFNDPLFIRS GKGIAPTTTG LNLHHHLEKN LRGLEQTINI VNKSELKKNF
110 120 130 140 150
IIYGPQLISC SNNSMLIRCL RQDSSVEIEC HDILMSAENA EELLVHRKAD
160 170 180 190 200
LVITQMPVIS RSVICMPLHT IRNTLICSNR HPRITDNSTY EQIMAEEFTQ
210 220 230 240 250
LISKSAGVDD IQMEIDERFM NRKISFRGSS LLTIINSIAV TDLLGIVPYE
260 270 280 290 300
LYNSYRDFLN LKEIKLEHPL PSIKLYISYN KSSLNNLVFS RFIDRLNESF
Length:300
Mass (Da):34,397
Last modified:February 1, 1997 - v1
Checksum:i1A5ECC6F28123D4F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82598 Genomic DNA. Translation: AAB40804.1.
U00096 Genomic DNA. Translation: AAC73704.1.
AP009048 Genomic DNA. Translation: BAA35233.1.
PIRiA64794.
RefSeqiNP_415136.1. NC_000913.3.
WP_000002474.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73704; AAC73704; b0603.
BAA35233; BAA35233; BAA35233.
GeneIDi945216.
KEGGiecj:JW0596.
eco:b0603.
PATRICi32116384. VBIEscCol129921_0632.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82598 Genomic DNA. Translation: AAB40804.1.
U00096 Genomic DNA. Translation: AAC73704.1.
AP009048 Genomic DNA. Translation: BAA35233.1.
PIRiA64794.
RefSeqiNP_415136.1. NC_000913.3.
WP_000002474.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP77746.
SMRiP77746. Positions 17-67.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260901. 8 interactions.
IntActiP77746. 5 interactions.
STRINGi511145.b0603.

Proteomic databases

PaxDbiP77746.
PRIDEiP77746.

Protocols and materials databases

DNASUi945216.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73704; AAC73704; b0603.
BAA35233; BAA35233; BAA35233.
GeneIDi945216.
KEGGiecj:JW0596.
eco:b0603.
PATRICi32116384. VBIEscCol129921_0632.

Organism-specific databases

EchoBASEiEB3305.
EcoGeneiEG13534. ybdO.

Phylogenomic databases

eggNOGiENOG4105DQS. Bacteria.
ENOG410XQ6Z. LUCA.
HOGENOMiHOG000117868.
OMAiQLYLMYN.
OrthoDBiEOG6XM78X.
PhylomeDBiP77746.

Enzyme and pathway databases

BioCyciEcoCyc:G6332-MONOMER.
ECOL316407:JW0596-MONOMER.

Miscellaneous databases

PROiP77746.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR005119. LysR_subst-bd.
IPR000847. Tscrpt_reg_HTH_LysR.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00126. HTH_1. 1 hit.
PF03466. LysR_substrate. 1 hit.
[Graphical view]
PRINTSiPR00039. HTHLYSR.
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS50931. HTH_LYSR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux."
    Shimada T., Yamamoto K., Ishihama A.
    J. Bacteriol. 191:4562-4571(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: OPERON STRUCTURE, INDUCTION.
    Strain: K12 / BW25113.
  6. "H-NS facilitates sequence diversification of horizontally transferred DNAs during their integration in host chromosomes."
    Higashi K., Tobe T., Kanai A., Uyar E., Ishikawa S., Suzuki Y., Ogasawara N., Kurokawa K., Oshima T.
    PLoS Genet. 12:E1005796-E1005796(2016) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Entry informationi

Entry nameiYBDO_ECOLI
AccessioniPrimary (citable) accession number: P77746
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: February 1, 1997
Last modified: July 6, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The protein is quite variable across different genetic subgroups, probably due to its binding and repression by H-NS (PubMed:26789284).1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.