RegulonDB RegulonDB 10.9: Gene Form
   

yncD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yncD yncE mcbR MarA yncDp11 yncDp11 yncEp yncEp

Gene      
Name: yncD    Texpresso search in the literature
Synonym(s): ECK1445, G6762, b1451
Genome position(nucleotides): 1520963 <-- 1523065 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.07
External database links:  
ASAP:
 ABE-0004839
ECHOBASE:
 EB3536
ECOLIHUB:
 yncD
OU-MICROARRAY:
 b1451
STRING:
 511145.b1451
COLOMBOS: yncD


Product      
Name: putative TonB-dependent outer membrane receptor
Synonym(s): YncD
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 77.261
Isoelectric point: 5.13
Motif(s):
 
Type Positions Sequence
40 -> 151 ELDTPAAVSVVDGEEMRLATPRINLSESLTGVPGLQVQNRQNYAQDLQLSIRGFGSRSTYGIRGIRLYVDGIPATMPDGQGQTSNIDLSSVQNVEVLRGPFSALYGNASGGV
1 -> 23 MKIFSVRQTVLPALLVLSPVVFA
24 -> 700 ADEQTMIVSAAPQVVSELDTPAAVSVVDGEEMRLATPRINLSESLTGVPGLQVQNRQNYAQDLQLSIRGFGSRSTYGIRGIRLYVDGIPATMPDGQGQTSNIDLSSVQNVEVLRGPFSALYGNASGGVMNVTTQTGQQPPTIEASSYYGSFGSWRYGLKATGATGDGTQPGDVDYTVSTTRFTTHGYRDHSGAQKNLANAKLGVRIDEASKLSLIFNSVDIKADDPGGLTKAEWKANPQQAPRAEQYDTRKTIKQTQAGLRYERSLSSRDDMSVMMYAGERETTQYQSIPMAPQLNPSHAGGVITLQRHYQGIDSRWTHRGELGVPVTFTTGLNYENMSENRKGYNNFRLNSGMPEYGQKGELRRDERNLMWNIDPYLQTQWQLSEKLSLDAGVRYSSVWFDSNDHYVTPGNGDDSGDASYHKWLPAGSLKYAMTDAWNIYLAAGRGFETPTINELSYRADGQSGMNLGLKPSTNDTIEIGSKTRIGDGLLSLALFQTDTDDEIVVDSSSGGRTTYKNAGKTRRQGAELAWDQRFAGDFRVNASWTWLDATYRSNVCNEQDCNGNRMPGIARNMGFASIGYVPEDGWYAGTEARYMGDIMADDENTAKAPSYTLVGLFTGYKYNYHNLTVDLFGRVDNLFDKEYVGSVIVNESNGRYYEPSPGRNYGVGMNIAWRFE
248 -> 695 DPGGLTKAEWKANPQQAPRAEQYDTRKTIKQTQAGLRYERSLSSRDDMSVMMYAGERETTQYQSIPMAPQLNPSHAGGVITLQRHYQGIDSRWTHRGELGVPVTFTTGLNYENMSENRKGYNNFRLNSGMPEYGQKGELRRDERNLMWNIDPYLQTQWQLSEKLSLDAGVRYSSVWFDSNDHYVTPGNGDDSGDASYHKWLPAGSLKYAMTDAWNIYLAAGRGFETPTINELSYRADGQSGMNLGLKPSTNDTIEIGSKTRIGDGLLSLALFQTDTDDEIVVDSSSGGRTTYKNAGKTRRQGAELAWDQRFAGDFRVNASWTWLDATYRSNVCNEQDCNGNRMPGIARNMGFASIGYVPEDGWYAGTEARYMGDIMADDENTAKAPSYTLVGLFTGYKYNYHNLTVDLFGRVDNLFDKEYVGSVIVNESNGRYYEPSPGRNYGVGMNI
680 -> 700 YYEPSPGRNYGVGMNIAWRFE

 
Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.1 - Channel-type Transporters --> 4.1.B - Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:0016021 - integral component of membrane
GO:0031230 - intrinsic component of cell outer membrane
GO:0045203 - integral component of cell outer membrane
molecular_function GO:0038023 - signaling receptor activity
GO:0015344 - siderophore uptake transmembrane transporter activity
biological_process GO:0015891 - siderophore transport
GO:0044718 - siderophore transmembrane transport
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Zhai Y., et al., 2002
External database links:  
DIP:
 DIP-12750N
ECOCYC:
 G6762-MONOMER
ECOLIWIKI:
 b1451
INTERPRO:
 IPR010105
INTERPRO:
 IPR039426
INTERPRO:
 IPR000531
INTERPRO:
 IPR012910
INTERPRO:
 IPR036942
INTERPRO:
 IPR037066
MODBASE:
 P76115
PANTHER:
 PTHR30069
PDB:
 6v81
PFAM:
 PF00593
PFAM:
 PF07715
PRIDE:
 P76115
PROSITE:
 PS00430
REFSEQ:
 NP_415968
UNIPROT:
 P76115


Operon      
Name: yncD         
Operon arrangement:
Transcription unit        Promoter
yncD


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 yncDp11 1523276 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Zhai Y., Saier MH., 2002, The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes., Protein Sci 11(9):2196-207

 [2] 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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