RegulonDB RegulonDB 11.2: Gene Form
   

bamD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rluD bamD raiA unknown raiZ yfiH CRP RybB TSS_2938 (cluster) TSS_2938 (cluster) TSS_2937 TSS_2937 TSS_2936 (cluster) TSS_2936 (cluster) TSS_2935 TSS_2935 TSS_2934 (cluster) TSS_2934 (cluster) TSS_2933 TSS_2933 TSS_2932 TSS_2932 TSS_2931 (cluster) TSS_2931 (cluster) raiAp raiAp TSS_2930 TSS_2930 TSS_2929 TSS_2929 TSS_2928 TSS_2928 TSS_2927 TSS_2927 TSS_2926 TSS_2926 TSS_2925 TSS_2925 TSS_2924 TSS_2924 TSS_2923 TSS_2923 TSS_2922 TSS_2922 TSS_2921 (cluster) TSS_2921 (cluster) TSS_2920 (cluster) TSS_2920 (cluster) TSS_2919 TSS_2919 TSS_2918 TSS_2918 TSS_2917 TSS_2917 TSS_2916 (cluster) TSS_2916 (cluster) TSS_2915 TSS_2915 bamDp1 bamDp1 bamDp2 bamDp2 TSS_2914 TSS_2914 TSS_2913 TSS_2913 TSS_2912 TSS_2912 TSS_2911 TSS_2911 TSS_2910 TSS_2910 TSS_2909 TSS_2909

Gene      
Name: bamD    Texpresso search in the literature
Synonym(s): ECK2593, G7352, b2595, ecfD, yfiO
Genome position(nucleotides): 2736146 --> 2736883
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.22
External database links:  
ASAP:
 ABE-0008536
ECHOBASE:
 EB3974
ECOLIHUB:
 bamD
OU-MICROARRAY:
 b2595
STRING:
 511145.b2595
COLOMBOS: bamD


Product      
Name: outer membrane protein assembly factor BamD
Synonym(s): BamD, EcfD, YfiO
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 27.829
Isoelectric point: 6.547
Motif(s):
 
Type Positions Sequence Comment
1 -> 19 MTRMKYLVAAATLSLFLAG
20 -> 245 CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT UniProt: Outer membrane protein assembly factor BamD.
28 -> 236 PDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAK
59 -> 59 D UniProt: In Ref. 4; CAA94434..

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
GO:0016020 - membrane
GO:1990063 - Bam protein complex
molecular_function GO:0005515 - protein binding
biological_process GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly
GO:0051205 - protein insertion into membrane
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IMP] Inferred from mutant phenotype
[IDA-PURIFIED-PROTEIN-NH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Albrecht R., et al., 2010
[2] Hagan CL., et al., 2010
[3] Han L., et al., 2016
[4] Malinverni JC., et al., 2006
[5] Rao S., et al., 2020
[6] Svanberg Frisinger F., et al., 2021
[7] Tachikawa T., et al., 2011
External database links:  
ALPHAFOLD:
 P0AC02
DIP:
 DIP-51120N
ECOCYC:
 G7352-MONOMER
ECOLIWIKI:
 b2595
INTERPRO:
 IPR011990
INTERPRO:
 IPR017689
INTERPRO:
 IPR039565
MINT:
 P0AC02
PDB:
 6LYR
PDB:
 6LYS
PDB:
 6LYU
PDB:
 6SN9
PDB:
 6V05
PDB:
 6LYQ
PDB:
 5LJO
PDB:
 5EKQ
PDB:
 5D0Q
PDB:
 5D0O
PDB:
 5AYW
PDB:
 3TGO
PDB:
 2YHC
PDB:
 3Q5M
PFAM:
 PF13525
PRIDE:
 P0AC02
PROSITE:
 PS51257
REFSEQ:
 NP_417086
SMR:
 P0AC02
UNIPROT:
 P0AC02


Operon      
Name: bamD         
Operon arrangement:
Transcription unit        Promoter
bamD
bamD


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_2909 2735050 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2910 2735058 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2911 2735067 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2912 2735835 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2913 2735898 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2914 2735960 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2915 2736025 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2916 (cluster) 2736071 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2917 2736085 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2918 2736248 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2919 2736286 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2920 (cluster) 2736329 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2921 (cluster) 2736345 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2922 2736549 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2923 2736555 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2924 2736559 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2925 2736561 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2926 2736565 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2927 2736586 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2928 2736612 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2929 2736658 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_2930 2737089 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2931 (cluster) 2737123 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2932 2737131 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2933 2737251 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2934 (cluster) 2737256 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2935 2737260 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2936 (cluster) 2737373 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2937 2737381 forward nd [RS-EPT-CBR] [8]
  promoter TSS_2938 (cluster) 2737413 forward nd [RS-EPT-CBR] [8]


Evidence    

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


Reference(s)    

 [1] Albrecht R., Zeth K., 2010, Crystallization and preliminary X-ray data collection of the Escherichia coli lipoproteins BamC, BamD and BamE., Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 12):1586-90

 [2] Hagan CL., Kim S., Kahne D., 2010, Reconstitution of outer membrane protein assembly from purified components., Science 328(5980):890-2

 [3] Han L., Zheng J., Wang Y., Yang X., Liu Y., Sun C., Cao B., Zhou H., Ni D., Lou J., Zhao Y., Huang Y., 2016, Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins., Nat Struct Mol Biol 23(3):192-6

 [4] Malinverni JC., Werner J., Kim S., Sklar JG., Kahne D., Misra R., Silhavy TJ., 2006, YfiO stabilizes the YaeT complex and is essential for outer membrane protein assembly in Escherichia coli., Mol Microbiol 61(1):151-64

 [5] Rao S., Bates GT., Matthews CR., Newport TD., Vickery ON., Stansfeld PJ., 2020, Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations., Structure 28(4):475-487.e3

 [6] 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)

 [7] Tachikawa T., Kato J., 2011, Suppression of the Temperature-Sensitive Mutation of the bamD Gene Required for the Assembly of Outer Membrane Proteins by Multicopy of the yiaD Gene in Escherichia coli., Biosci Biotechnol Biochem 75(1):162-4

 [8] 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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