RegulonDB RegulonDB 10.6.3: Gene Form
   

nimR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nimT nimR yeaL yoaI NimR NimR NimR terminator anti-terminator anti-anti-terminator yeaOp3 yeaOp3 yeaOp4 yeaOp4 nimTp nimTp yeaMp1 yeaMp1 yeaNp9 yeaNp9 nimRp nimRp yeaMp6 yeaMp6 yeaNp4 yeaNp4 yeaLp yeaLp

Gene      
Name: nimR    Texpresso search in the literature
Synonym(s): ECK1788, G6976, b1790, yeaM
Genome position(nucleotides): 1874755 <-- 1875576 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.88
External database links:  
ASAP:
ABE-0005956
ECHOBASE:
EB3272
ECOCYC:
G6976
ECOLIHUB:
yeaM
OU-MICROARRAY:
b1790
REGULONDB:
b1790
STRING:
511145.b1790
M3D: nimR
COLOMBOS: nimR
PortEco: b1790


Product      
Name: DNA-binding transcriptional repressor NimR
Synonym(s): NimR, YeaM
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 30.553
Isoelectric point: 9.077
Motif(s):
 
Type Positions Sequence
22 -> 96 FCIHAGTDELTSPVHQHRKGQLILALHGAITCTVENALWMVPPQYAVWIPGGVEHSNQVTANAELCFLFIEPSAV
180 -> 257 WAGFFAMSERNLARLIVKETGLSFRQWRQQLQLIMALQGLVKGDTVQKVAHTLGYDSTTAFITMFKKGLGQTPGRYIA
225 -> 248 VQKVAHTLGYDSTTAFITMFKKGL
178 -> 199 GQWAGFFAMSERNLARLIVKET
158 -> 258 PKIRTMVEMMAKGPVEWGALGQWAGFFAMSERNLARLIVKETGLSFRQWRQQLQLIMALQGLVKGDTVQKVAHTLGYDSTTAFITMFKKGLGQTPGRYIAR

 

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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[APPHINH] Assay of protein purified to homogeneity from its native host
[IEP] Inferred from expression pattern
Reference(s): [1] Ogasawara H., et al., 2015
[2] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G6976-MONOMER
ECOLIWIKI:
b1790
INTERPRO:
IPR014710
INTERPRO:
IPR018062
INTERPRO:
IPR018060
INTERPRO:
IPR011051
INTERPRO:
IPR009057
INTERPRO:
IPR003313
MODBASE:
P76241
PFAM:
PF12833
PFAM:
PF02311
PRIDE:
P76241
PROSITE:
PS01124
PROSITE:
PS00041
PROTEINMODELPORTAL:
P76241
REFSEQ:
NP_416304
SMART:
SM00342
SMR:
P76241
UNIPROT:
P76241


Operon      
Name: nimR         
Operon arrangement:
Transcription unit        Promoter
yeaM


Transcriptional Regulation      
Display Regulation             
Repressed by: NimR


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 yeaNp4 1875463 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yeaMp6 1875598 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yeaMp1 1875648 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yeaNp9 1875648 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yeaOp4 1876777 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yeaOp3 1876822 forward Similarity to the consensus
Read more >
[ICWHO] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Ogasawara H., Ohe S., Ishihama A., 2015, Role of transcription factor NimR (YeaM) in sensitivity control of Escherichia coli to 2-nitroimidazole., FEMS Microbiol Lett 362(1):1-8

 [2] 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

 [3] 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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