RegulonDB RegulonDB 10.9: Gene Form
   

yhcD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yhcD yhcA yhcF3\' insH10 TSS_3550 TSS_3550

Gene      
Name: yhcD    Texpresso search in the literature
Synonym(s): ECK3206, G7670, b3216
Genome position(nucleotides): 3362807 --> 3365188 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
45.51
External database links:  
ASAP:
ABE-0010554
ECHOBASE:
EB2661
ECOLIHUB:
yhcD
ECOO157CYC:
Z1536
ECOO157CYC:
Z5222
ECOO157CYC:
Z4968
ECOO157CYC:
Z0022
ECOO157CYC:
Z2203
ECOO157CYC:
Z4967
OU-MICROARRAY:
b3216
STRING:
511145.b3216
COLOMBOS: yhcD


Product      
Name: putative fimbrial usher protein YhcD
Synonym(s): YhcD
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 86.289
Isoelectric point: 4.584
Motif(s):
 
Type Positions Sequence
22 -> 793 DGIEIAAVDFDRETLKSLGVDPNISHYFSRSARFLPGEYSLIVSVNGEKKGNIATRFDENGDICLDQAFLQQAGLKIPSEEKNGCYDYILSYPGTTITPLPNQEALDIIVSPQAIIPIGLDLTNAATGGTAALLNYSLMSSRAEFSNGSSDYSQAALEGGININDWMLRSHQFLTQTNGTFSNQNSSTYLQRTFTDLKTLMRAGEVNLNNSVLEGASIYGIEIAPDNALQTSGSGVQVTGIANTSQARVEIRQQGVLIHSILVPAGAFTIPDVPVRNGNSDLNVTVVETDGSSHNYIVPSTLFNQHVESFQGYRFAIGRVDDDYDESPWVISASSGWNLTRWSAMNGGVIVAENYQAASIRSSLVPLPDLTVSSQISTSQDTKDSLQGQKYRLDANYNLPFSLGLTTSLTRSDRHYRELSEAIDDDYTDPTKSTYALGLNWSNSILGGFNISGYKTYSYDGDNDSSNLNINWNKAFKHATVSVNWQHQLSASENNEDDGDLFYVNISIPFGRSNTATLYTRHDDHKTHYGTGVMGVVSDEMSYYVNAERDHDERETSLNGSISSNLHYTQVSLAAGASGSDSRTYNGTMSGGIAVHDQGVTFSPWTINDTFAIAKMDNNIAGVRITSQAGPVWTDFRGNAVIPSIQPWRTSGVEIDTASLPKNVDIGNGTKMIKQGRGAVGKVGFSAITQRRALLNITLSDGKKLPRGVAIEDSEGNYLTTSVDDGVVFLNNIKPDMVLDIKDEQQSCRIHLTFPEDAPKDVFYETATGECQ
1 -> 21 MLKKTLLAYTIGFAFSPPANA
715 -> 777 LLNITLSDGKKLPRGVAIEDSEGNYLTTSVDDGVVFLNNIKPDMVLDIKDEQQSCRIHLTFPE
31 -> 159 FDRETLKSLGVDPNISHYFSRSARFLPGEYSLIVSVNGEKKGNIATRFDENGDICLDQAFLQQAGLKIPSEEKNGCYDYILSYPGTTITPLPNQEALDIIVSPQAIIPIGLDLTNAATGGTAALLNYSL
176 -> 706 AALEGGININDWMLRSHQFLTQTNGTFSNQNSSTYLQRTFTDLKTLMRAGEVNLNNSVLEGASIYGIEIAPDNALQTSGSGVQVTGIANTSQARVEIRQQGVLIHSILVPAGAFTIPDVPVRNGNSDLNVTVVETDGSSHNYIVPSTLFNQHVESFQGYRFAIGRVDDDYDESPWVISASSGWNLTRWSAMNGGVIVAENYQAASIRSSLVPLPDLTVSSQISTSQDTKDSLQGQKYRLDANYNLPFSLGLTTSLTRSDRHYRELSEAIDDDYTDPTKSTYALGLNWSNSILGGFNISGYKTYSYDGDNDSSNLNINWNKAFKHATVSVNWQHQLSASENNEDDGDLFYVNISIPFGRSNTATLYTRHDDHKTHYGTGVMGVVSDEMSYYVNAERDHDERETSLNGSISSNLHYTQVSLAAGASGSDSRTYNGTMSGGIAVHDQGVTFSPWTINDTFAIAKMDNNIAGVRITSQAGPVWTDFRGNAVIPSIQPWRTSGVEIDTASLPKNVDIGNGTKMIKQGRGAVGKVGF

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0016021 - integral component of membrane
molecular_function GO:0015473 - fimbrial usher porin activity
biological_process GO:0009297 - pilus assembly
GO:0055085 - transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Korea CG., et al., 2010
[2] Korea CG., et al., 2011
[3] Wurpel DJ., et al., 2013
External database links:  
DIP:
DIP-12277N
ECOCYC:
G7670-MONOMER
ECOLIWIKI:
b3216
ECOO157CYC:
Z0022-MONOMER
ECOO157CYC:
Z5222-MONOMER
ECOO157CYC:
Z4968-MONOMER
ECOO157CYC:
Z4967-MONOMER
ECOO157CYC:
Z2203-MONOMER
ECOO157CYC:
Z1536-MONOMER
INTERPRO:
IPR042186
INTERPRO:
IPR043142
INTERPRO:
IPR000015
INTERPRO:
IPR018030
INTERPRO:
IPR025885
INTERPRO:
IPR037224
INTERPRO:
IPR025949
PANTHER:
PTHR30451
PFAM:
PF13954
PFAM:
PF00577
PFAM:
PF13953
PRIDE:
P45420
PROSITE:
PS01151
REFSEQ:
NP_417683
SMR:
P45420
UNIPROT:
P45420


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_3550 3364436 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] Korea CG., Badouraly R., Prevost MC., Ghigo JM., Beloin C., 2010, Escherichia coli K-12 possesses multiple cryptic but functional chaperone-usher fimbriae with distinct surface specificities., Environ Microbiol 12(7):1957-77

 [2] Korea CG., Ghigo JM., Beloin C., 2011, The sweet connection: Solving the riddle of multiple sugar-binding fimbrial adhesins in Escherichia coli: Multiple E. coli fimbriae form a versatile arsenal of sugar-binding lectins potentially involved in surface-colonisation and tissue tropism., Bioessays 33(4):300-11

 [3] Wurpel DJ., Beatson SA., Totsika M., Petty NK., Schembri MA., 2013, Chaperone-usher fimbriae of Escherichia coli., PLoS One 8(1):e52835

 [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.


RegulonDB