RegulonDB RegulonDB 11.1: Gene Form
   

lptD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lptD surA djlA impp3 impp3 djlAp3 djlAp3 TSS_113 TSS_113 TSS_112 TSS_112 impp2 impp2 impp1 impp1 TSS_109 TSS_109 TSS_108 (cluster) TSS_108 (cluster) TSS_107 TSS_107 TSS_106 TSS_106 TSS_105 TSS_105 TSS_104 TSS_104 TSS_103 (cluster) TSS_103 (cluster) TSS_102 (cluster) TSS_102 (cluster) TSS_101 TSS_101 TSS_100 TSS_100 TSS_99 TSS_99 TSS_98 TSS_98 TSS_97 TSS_97 TSS_96 (cluster) TSS_96 (cluster) TSS_95 TSS_95 TSS_94 TSS_94 TSS_93 TSS_93 TSS_92 TSS_92 TSS_91 TSS_91 TSS_90 TSS_90

Gene      
Name: lptD    Texpresso search in the literature
Synonym(s): ECK0055, EG11569, b0054, imp, ostA, yabG
Genome position(nucleotides): 54755 <-- 57109
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.38
External database links:  
ASAP:
 ABE-0000183
CGSC:
 36754
ECHOBASE:
 EB1529
ECOLIHUB:
 lptD
OU-MICROARRAY:
 b0054
STRING:
 511145.b0054
COLOMBOS: lptD


Product      
Name: lipopolysaccharide assembly protein LptD
Synonym(s): Imp, LptD, OstA, YabG
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 89.671
Isoelectric point: 4.724
Motif(s):
 
Type Positions Sequence Comment
1 -> 24 MKKRIPTLLATMIATALYSQQGLA
25 -> 784 ADLASQCMLGVPSYDRPLVQGDTNDLPVTINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQVAEIWNARFKVGPVPIFYSPYLQLPVGDKRRSGFLIPNAKYTTTNYFEFYLPYYWNIAPNMDATITPHYMHRRGNIMWENEFRYLSQAGAGLMELDYLPSDKVYEDEHPNDDSSRRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKLLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGISQVGAVASWPIADRWSIVGAYYYDTNANKQADSMLGVQYSSCCYAIRVGYERKLNGWDNDKQHAVYDNAIGFNIELRGLSSNYGLGTQEMLRSNILPYQNTL UniProt: LPS-assembly protein LptD.
53 -> 194 TINADHAKGDYPDDAVFTGSVDIMQGNSRLQADEVQLHQKEAPGQPEPVRTVDALGNVHYDDNQVILKGPKGWANLNTKDTNVWEGDYQMVGRQGRGKADLMKQRGENRYTILDNGSFTSCLPGSDTWSVVGSEIIHDREEQ
309 -> 697 RRWLFYWNHSGVMDQVWRFNVDYTKVSDPSYFNDFDNKYGSSTDGYATQKFSVGYAVQNFNATVSTKQFQVFSEQNTSSYSAEPQLDVNYYQNDVGPFDTRIYGQAVHFVNTRDDMPEATRVHLEPTINLPLSNNWGSINTEAKLLATHYQQTNLDWYNSRNTTKLDESVNRVMPQFKVDGKMVFERDMEMLAPGYTQTLEPRAQYLYVPYRDQSDIYNYDSSLLQSDYSGLFRDRTYGGLDRIASANQVTTGVTSRIYDDAAVERFNISVGQIYYFTESRTGDDNITWENDDKTGSLVWAGDTYWRISERWGLRGGIQYDTRLDNVATSNSSIEYRRDEDRLVQLNYRYASPEYIQATLPKYYSTAEQYKNGISQVGAVASWPIADRW
529 -> 538 DSSLLQSDYS UniProt: Impairs assembly of the LptD/LptE complex. Does not form native disulfide bonds. Severely compromises outer membrane integrity..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.3 - lipopolysaccharide
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0019867 - outer membrane
GO:0016020 - membrane
GO:1990351 - transporter complex
molecular_function GO:0005515 - protein binding
biological_process GO:0015921 - lipopolysaccharide export
GO:0015920 - lipopolysaccharide transport
GO:0010033 - response to organic substance
GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly
GO:0061024 - membrane organization
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Braun M., et al., 2002
[2] Hamdallah I., et al., 2018
[3] Lee J., et al., 2016
[4] Svanberg Frisinger F., et al., 2021
External database links:  
ALPHAFOLD:
 P31554
DIP:
 DIP-10029N
ECOCYC:
 EG11569-MONOMER
ECOLIWIKI:
 b0054
INTERPRO:
 IPR005653
INTERPRO:
 IPR007543
INTERPRO:
 IPR020889
PDB:
 4RHB
PFAM:
 PF03968
PFAM:
 PF04453
PRIDE:
 P31554
PRODB:
 PRO_000023116
REFSEQ:
 NP_414596
SMR:
 P31554
UNIPROT:
 P31554


Operon      
Name: lptD-surA-pdxA-rsmA-apaGH         
Operon arrangement:
Transcription unit        Promoter
apaGH
rsmA-apaGH
imp
imp
imp-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH


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_90 53904 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_91 54275 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_92 54363 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_93 54605 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_94 54746 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_95 54754 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_96 (cluster) 54762 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_97 54765 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_98 54884 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_99 55120 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_100 55146 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_101 55785 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_102 (cluster) 55791 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_103 (cluster) 55800 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_104 55908 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_105 55916 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_106 55920 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_107 56036 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_108 (cluster) 56466 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_109 56724 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_112 57253 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_113 57261 forward nd [RS-EPT-CBR] [5]
  promoter djlAp3 57268 forward nd [COMP-AINF] [6]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Braun M., Silhavy TJ., 2002, Imp/OstA is required for cell envelope biogenesis in Escherichia coli., Mol Microbiol 45(5):1289-302

 [2] Hamdallah I., Torok N., Bischof KM., Majdalani N., Chadalavada S., Mdluli N., Creamer KE., Clark M., Holdener C., Basting PJ., Gottesman S., Slonczewski JL., 2018, Experimental Evolution of Escherichia coli K-12 at High pH and with RpoS Induction., Appl Environ Microbiol 84(15)

 [3] Lee J., Xue M., Wzorek JS., Wu T., Grabowicz M., Gronenberg LS., Sutterlin HA., Davis RM., Ruiz N., Silhavy TJ., Kahne DE., 2016, Characterization of a stalled complex on the β-barrel assembly machine., Proc Natl Acad Sci U S A 113(31):8717-22

 [4] Svanberg Frisinger F., Jana B., Donadio S., Guardabassi L., 2021, In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli., Antibiotics (Basel) 10(6)

 [5] 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.

 [6] 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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