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Table 3 Classification of ArcA regulated genes according to Clusters of Orthologous Groups (COGs)

From: Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium

Functional Gene Groupsa # of Genesb
  ArcA-activated ArcA-repressed
Cell division and chromosome partitioning 0 0
Cell envelope and biogenesis, outer membrane 4 4
Cell motility and secretion 1 12
Posttranslational modification, protein turnover, chaperones 1 3
Inorganic ion transport and metabolism 1 12
Signal transduction mechanisms 5 3
Cellular processes c 12 34
Defense Mechanisms c 1 1
Translation, ribosomal structure, and biogenesis 0 7
Transcription 8 18
DNA replication, recombination, and repair 2 4
Information storage and processing c 10 29
Intracell trafficking c 0 1
Energy production and conversion 9 18
Amino acid transport and metabolism 25 30
Nucleotide transport and metabolism 7 2
Carbohydrate transport and metabolism 20 16
Coenzyme metabolism 0 2
Lipid metabolism 1 7
Secondary metabolites biosynthesis, transport, and catabolism 12 4
Metabolism c 74 79
General function prediction only 8 21
Function unknown 8 24
Poorly characterized 23 67
Unknown c 39 112
Total 147 245
  1. aThe differentially expressed genes were classified according to clusters of orthologous groups (COGs) as defined at http://www.ncbi.nlm.nih.gov/COG.
  2. bNumber of genes activated or repressed (by having a ratio ≥ ± 2.5-fold) by ArcA.
  3. cBolded functional gene catagories contain a summary of the unbolded COG functional gene groups that are located in each of the previous lines.