RegulonDB RegulonDB 10.9: Gene Form
   

fimD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fimD fimC fimF terminator anti-terminator TSS_5141 TSS_5141 TSS_5140 TSS_5140 TSS_5139 TSS_5139 TSS_5138 TSS_5138 TSS_5137 TSS_5137

Gene      
Name: fimD    Texpresso search in the literature
Synonym(s): ECK4308, EG10311, b4317, fimD_1, fimD_2
Genome position(nucleotides): 4545096 --> 4547732 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.62


Product      
Name: type I fimbriae usher protein
Synonym(s): FimD, FimD usher, FimD_1, FimD_2
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 96.482
Isoelectric point: 7.117
Motif(s):
 
Type Positions Sequence
352 -> 402 DGSTQIFTVPYSSVPLLQREGHTRYSITAGEYRSGNAQQEKTRFFQSTLLH
658 -> 670 GGDGNSGSTGYAT
799 -> 863 LMTLTHNNKPLPFGAMVTSESSQSSGIVADNGQVYLSGMPLAGKVQVKWGEEENAHCVANYQLPP
811 -> 811 F
723 -> 742 APGAKDAKVENQTGVRTDWR

 

Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.5 - pilus
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0016021 - integral component of membrane
molecular_function GO:0005515 - protein binding
GO:0015473 - fimbrial usher porin activity
biological_process GO:0009297 - pilus assembly
GO:0055085 - transmembrane transport
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
Reference(s): [1] Nishiyama M., et al., 2008
[2] Palomino C., et al., 2011
[3] Phan G., et al., 2011
External database links:  
DIP:
DIP-9612N
ECOCYC:
EG10311-MONOMER
ECOLIWIKI:
b4317
INTERPRO:
IPR025949
INTERPRO:
IPR025885
INTERPRO:
IPR000015
INTERPRO:
IPR037224
INTERPRO:
IPR042186
INTERPRO:
IPR043142
INTERPRO:
IPR018030
MINT:
P30130
PANTHER:
PTHR30451
PDB:
6E15
PDB:
6E14
PDB:
4J3O
PDB:
3RFZ
PDB:
3OHN
PDB:
3BWU
PDB:
1ZE3
PDB:
1ZDX
PDB:
1ZDV
PFAM:
PF00577
PFAM:
PF13954
PFAM:
PF13953
PRIDE:
P30130
PRODB:
PRO_000022619
PROSITE:
PS01151
REFSEQ:
NP_418737
SMR:
P30130
UNIPROT:
P30130


Operon      
Name: fimAICDFGH         
Operon arrangement:
Transcription unit        Promoter
fimAICDFGH


Transcriptional Regulation      
Display Regulation             
Activated by: H-NS, IHF, Lrp, QseB


RNA cis-regulatory element    
Attenuation: Transcriptional


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_5137 4544668 forward nd [RS-EPT-CBR] [4]
  promoter TSS_5138 4544808 forward nd [RS-EPT-CBR] [4]
  promoter TSS_5139 4545062 forward nd [RS-EPT-CBR] [4]
  promoter TSS_5140 4545183 forward nd [RS-EPT-CBR] [4]
  promoter TSS_5141 4547980 forward nd [RS-EPT-CBR] [4]


Evidence    

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



Reference(s)    

 [1] Nishiyama M., Ishikawa T., Rechsteiner H., Glockshuber R., 2008, Reconstitution of pilus assembly reveals a bacterial outer membrane catalyst., Science 320(5874):376-9

 [2] Palomino C., Marin E., Fernandez LA., 2011, The fimbrial usher FimD follows the SurA-BamB pathway for its assembly in the outer membrane of Escherichia coli., J Bacteriol 193(19):5222-30

 [3] Phan G., Remaut H., Wang T., Allen WJ., Pirker KF., Lebedev A., Henderson NS., Geibel S., Volkan E., Yan J., Kunze MB., Pinkner JS., Ford B., Kay CW., Li H., Hultgren SJ., Thanassi DG., Waksman G., 2011, Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate., Nature 474(7349):49-53

 [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.


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