RegulonDB RegulonDB 11.1: Gene Form
   

opgD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

opgD ydcJ ydcH unknown anti-terminator anti-anti-terminator rimLp rimLp TSS_1808 TSS_1808 TSS_1807 TSS_1807 TSS_1806 TSS_1806 opgDp9 opgDp9 opgDp7 opgDp7 opgDp8 opgDp8 opgDp4 opgDp4

Gene      
Name: opgD    Texpresso search in the literature
Synonym(s): ECK1418, EG12859, b1424, mdoD, ydcG, yzzZ
Genome position(nucleotides): 1496856 --> 1498511
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.79
External database links:  
ASAP:
 ABE-0004754
ECHOBASE:
 EB2701
ECOLIHUB:
 mdoD
OU-MICROARRAY:
 b1424
STRING:
 511145.b1424
COLOMBOS: opgD


Product      
Name: glucans biosynthesis protein D
Synonym(s): MdoD, OpgD, YdcG, YzzZ
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 62.758
Isoelectric point: 6.249
Motif(s):
 
Type Positions Sequence Comment
1 -> 32 MDRRRFIKGSMAMAAVCGTSGIASLFSQAAFA
33 -> 551 ADSDIADGQTQRFDFSILQSMAHDLAQTAWRGAPRPLPDTLATMTPQAYNSIQYDAEKSLWHNVENRQLDAQFFHMGMGFRRRVRMFSVDPATHLAREIHFRPELFKYNDAGVDTKQLEGQSDLGFAGFRVFKAPELARRDVVSFLGASYFRAVDDTYQYGLSARGLAIDTYTDSKEEFPDFTAFWFDTVKPGATTFTVYALLDSASITGAYKFTIHCEKSQVIMDVENHLYARKDIKQLGIAPMTSMFSCGTNERRMCDTIHPQIHDSDRLSMWRGNGEWICRPLNNPQKLQFNAYTDNNPKGFGLLQLDRDFSHYQDIMGWYNKRPSLWVEPRNKWGKGTIGLMEIPTTGETLDNIVCFWQPEKAVKAGDEFAFQYRLYWSAQPPVHCPLARVMATRTGMGGFSEGWAPGEHYPEKWARRFAVDFVGGDLKAAAPKGIEPVITLSSGEAKQIEILYIEPIDGYRIQFDWYPTSDSTDPVDMRMYLRCQGDAISETWLYQYFPPAPDKRQYVDDRVMS UniProt: Glucans biosynthesis protein D.
45 -> 534 FDFSILQSMAHDLAQTAWRGAPRPLPDTLATMTPQAYNSIQYDAEKSLWHNVENRQLDAQFFHMGMGFRRRVRMFSVDPATHLAREIHFRPELFKYNDAGVDTKQLEGQSDLGFAGFRVFKAPELARRDVVSFLGASYFRAVDDTYQYGLSARGLAIDTYTDSKEEFPDFTAFWFDTVKPGATTFTVYALLDSASITGAYKFTIHCEKSQVIMDVENHLYARKDIKQLGIAPMTSMFSCGTNERRMCDTIHPQIHDSDRLSMWRGNGEWICRPLNNPQKLQFNAYTDNNPKGFGLLQLDRDFSHYQDIMGWYNKRPSLWVEPRNKWGKGTIGLMEIPTTGETLDNIVCFWQPEKAVKAGDEFAFQYRLYWSAQPPVHCPLARVMATRTGMGGFSEGWAPGEHYPEKWARRFAVDFVGGDLKAAAPKGIEPVITLSSGEAKQIEILYIEPIDGYRIQFDWYPTSDSTDPVDMRMYLRCQGDAISETWLYQY

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0003824 - catalytic activity
GO:0030246 - carbohydrate binding
biological_process GO:0016051 - carbohydrate biosynthetic process
GO:0005975 - carbohydrate metabolic process
GO:0009250 - glucan biosynthetic process
GO:0051274 - beta-glucan biosynthetic process
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Lequette Y., et al., 2004
External database links:  
ALPHAFOLD:
 P40120
ECOCYC:
 EG12859-MONOMER
ECOLIWIKI:
 b1424
INTERPRO:
 IPR014756
INTERPRO:
 IPR019546
INTERPRO:
 IPR014438
INTERPRO:
 IPR023724
INTERPRO:
 IPR013783
INTERPRO:
 IPR011013
INTERPRO:
 IPR014718
INTERPRO:
 IPR006311
INTERPRO:
 IPR007444
PANTHER:
 PTHR30504
PFAM:
 PF04349
PRIDE:
 P40120
PRODB:
 PRO_000023179
PROSITE:
 PS51318
REFSEQ:
 NP_415941
UNIPROT:
 P40120


Operon      
Name: opgD         
Operon arrangement:
Transcription unit        Promoter
opgD


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 opgDp4 1496645 forward nd [COMP-AINF] [2]
  promoter opgDp8 1496655 forward nd [COMP-AINF] [2]
  promoter opgDp7 1496682 forward nd [COMP-AINF] [2]
  promoter opgDp9 1496776 forward nd [COMP-AINF] [2]
  promoter TSS_1806 1497690 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1807 1497713 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1808 1497832 forward nd [RS-EPT-CBR] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Lequette Y., Odberg-Ferragut C., Bohin JP., Lacroix JM., 2004, Identification of mdoD, an mdoG paralog which encodes a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures., J Bacteriol 186(12):3695-702

 [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

 [3] 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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