RegulonDB RegulonDB 11.2: Gene Form
   

ihfB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycaI rpsA ihfB IHF IHF IHF IHF IHF IHF RseX terminator anti-terminator anti-anti-terminator terminator anti-terminator anti-anti-terminator ycaIp7 ycaIp7 ycaIp8 ycaIp8 ycaIp6 ycaIp6 TSS_1188 TSS_1188 ihfBp2 ihfBp2 ihfBp ihfBp TSS_1187 (cluster) TSS_1187 (cluster) TSS_1186 (cluster) TSS_1186 (cluster) TSS_1185 (cluster) TSS_1185 (cluster) TSS_1184 TSS_1184 TSS_1183 TSS_1183 TSS_1182 (cluster) TSS_1182 (cluster) TSS_1181 TSS_1181

Gene      
Name: ihfB    Texpresso search in the literature
Synonym(s): ECK0903, EG10441, b0912, himD, hip
Genome position(nucleotides): 963828 --> 964112
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.12
External database links:  
ASAP:
 ABE-0003107
CGSC:
 637
ECHOBASE:
 EB0436
ECOLIHUB:
 ihfB
OU-MICROARRAY:
 b0912
STRING:
 511145.b0912
COLOMBOS: ihfB


Product      
Name: integration host factor subunit β
Synonym(s): HimD, Hip, IhfB, integration host factor (IHF), beta; subunit; site-specific recombination
Sequence: Get amino acid sequence Fasta Format
Cellular location: bacterial nucleoid,cytosol
Molecular weight: 10.651
Isoelectric point: 9.897
Motif(s):
 
Type Positions Sequence Comment
1 -> 91 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRAN
9 -> 9 R UniProt: In Ref. 6; AA sequence..
44 -> 44 E UniProt: Altered DNA-binding specificity..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.3 - DNA recombination
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins
  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:1990177 - IHF-DNA complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0005694 - chromosome
molecular_function GO:0003677 - DNA binding
GO:0043565 - sequence-specific DNA binding
biological_process GO:0006310 - DNA recombination
GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0006417 - regulation of translation
GO:0000746 - conjugation
Note(s): Note(s): ...[more].
Reference(s): [1] Aviv M., et al., 1994
[2] Dai Y., et al., 2017
[3] Goosen N., et al., 1995
External database links:  
ALPHAFOLD:
 P0A6Y1
DIP:
 DIP-41099N
ECOCYC:
 PD00348
ECOLIWIKI:
 b0912
INTERPRO:
 IPR020816
INTERPRO:
 IPR000119
INTERPRO:
 IPR010992
INTERPRO:
 IPR005685
MODBASE:
 P0A6Y1
PANTHER:
 PTHR33175
PDB:
 5J0N
PDB:
 2IIF
PDB:
 2IIE
PDB:
 2HT0
PDB:
 1OWG
PDB:
 1OWF
PDB:
 1IHF
PDB:
 1OUZ
PFAM:
 PF00216
PRIDE:
 P0A6Y1
PRINTS:
 PR01727
PRODB:
 PRO_000022999
PROSITE:
 PS00045
REFSEQ:
 NP_415432
SMART:
 SM00411
SMR:
 P0A6Y1
UNIPROT:
 P0A6Y1


Operon      
Name: cmk-rpsA-ihfB         
Operon arrangement:
Transcription unit        Promoter
cmk-rpsA
rpsA-ihfB
rpsA-ihfB
ihfB
ihfB


Transcriptional Regulation      
Display Regulation             
Repressed by: IHF


RNA cis-regulatory element    
Attenuation: Transcriptional


Regulation by small RNA    
  Display Regulation
small RNA rseX


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 TSS_1181 962373 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1182 (cluster) 962813 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1183 962831 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1184 962837 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1185 (cluster) 963236 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1186 (cluster) 963240 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1187 (cluster) 963362 forward nd [RS-EPT-CBR] [4]
  promoter TSS_1188 964101 forward nd [RS-EPT-CBR] [4]
  promoter ycaIp6 964105 forward nd [COMP-AINF] [5]
  promoter ycaIp8 964108 forward nd [COMP-AINF] [5]
  promoter ycaIp7 964238 forward nd [COMP-AINF] [5]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Aviv M., Giladi H., Schreiber G., Oppenheim AB., Glaser G., 1994, Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation., Mol Microbiol 14(5):1021-31

 [2] Dai Y., Shortreed MR., Scalf M., Frey BL., Cesnik AJ., Solntsev S., Schaffer LV., Smith LM., 2017, Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database., J Proteome Res 16(11):4156-4165

 [3] Goosen N., van de Putte P., 1995, The regulation of transcription initiation by integration host factor., Mol Microbiol 16(1):1-7

 [4] 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.

 [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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