Sandbox

All genes are grouped in one or more categories. These categories help to identify genes/proteins with common function, regulation or properties.

To see additional subcategories, please go to the pages for the six top-level categories.

1. Cellular processes

• 1.1. Cell envelope and cell division
  • 1.1.1. Cell wall synthesis
  • 1.1.2. Cell shape
  • 1.1.3. Cell wall degradation/ turnover
  • 1.1.4. Capsule biosynthesis and degradation
  • 1.1.5. Cell wall/ other
  • 1.1.6. Membrane dynamics
  • 1.1.7. Cell division
• 1.2. Transporters
  • 1.2.1. ABC transporters
  • 1.2.2. Phosphotransferase systems
  • 1.2.3. Transporters/ other
• 1.3. Homeostasis
  • 1.3.1. Metal ion homeostasis (K, Na, Ca, Mg)
  • 1.3.2. Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)
  • 1.3.3. Acquisition of iron
  • 1.3.4. pH homeostasis

2. Metabolism

• 2.1. Electron transport and ATP synthesis
  • 2.1.1. Regulators of electron transport
  • 2.1.2. Respiration
  • 2.1.3. Electron transport/ other
  • 2.1.4. ATP synthesis
• 2.2. Carbon metabolism
  • 2.2.1. Carbon core metabolism
  • 2.2.2. Utilization of specific carbon sources
• 2.3. Amino acid/ nitrogen metabolism
  • 2.3.1. Biosynthesis/ acquisition of amino acids
  • 2.3.2. Utilization of amino acids
  • 2.3.3. Utilization of nitrogen sources other than amino acids
  • 2.3.4. Putative amino acid transporter
• 2.4. Lipid metabolism
  • 2.4.1. Utilization of lipids
  • 2.4.2. Biosynthesis of lipids
  • 2.4.3. Lipid metabolism/ other
• 2.5. Nucleotide metabolism
  • 2.5.1. Utilization of nucleotides
  • 2.5.2. Biosynthesis/ acquisition of nucleotides
  • 2.5.3. Metabolism of signalling nucleotides
  • 2.5.4. Nucleotide metabolism/ other
• 2.6. Additional metabolic pathways
  • 2.6.1. Biosynthesis of cell wall components
  • 2.6.2. Biosynthesis of cofactors
  • 2.6.3. Phosphate metabolism
  • 2.6.4. Sulfur metabolism
  • 2.6.5. Iron metabolism
  • 2.6.6. Miscellaneous metabolic pathways

3. Information processing

• 3.1. Genetics
  • 3.1.1. DNA replication
  • 3.1.2. DNA condensation/ segregation
  • 3.1.3. DNA restriction/ modification
  • 3.1.4. DNA repair/ recombination
  • 3.1.5. Genetic competence
  • 3.1.6. Genetics/ other
• 3.2. RNA synthesis and degradation
  • 3.2.1. Transcription
  • 3.2.2. RNA chaperones
  • 3.2.3. DEAD-box RNA helicases
  • 3.2.4. RNases
• 3.3. Protein synthesis, modification and degradation
  • 3.3.1. Translation
  • 3.3.2. Chaperones/ protein folding
  • 3.3.3. Protein modification
  • 3.3.4. Protein secretion
  • 3.3.5. Proteolysis
• 3.4. Regulation of gene expression
  • 3.4.1. Sigma factors and their control

** 3.4.2. Two-component regulatory systems and their control ** 3.4.3. DNA binding transcription factors and their control

• • 3.4.4. Trigger enzymes

** 3.4.5. PRD-type regulators

• • 3.4.6. RNA binding regulators

Transcription factors and their control

4. Lifestyles

• 4.1. Exponential and early post-exponential lifestyles
  • 4.1.1. Motility and chemotaxis
  • 4.1.2. Biofilm formation
  • 4.1.3. Genetic competence

** 4.1.4. Transition state regulators ** 4.1.5. Quorum sensing

• 4.2. Sporulation and Germination
  • 4.2.1. Sporulation proteins
  • 4.2.2. Phosphorelay
  • 4.2.3. Sporulation/ other
  • 4.2.4. Germination
• 4.3. Coping with stress
  • 4.3.1. General stress proteins (controlled by SigB)
  • 4.3.2. Cell envelope stress proteins (controlled by SigM, W, X, Y)
  • 4.3.3. Acid stress proteins (controlled by YvrI-YvrHa)
  • 4.3.4. Heat shock proteins
  • 4.3.5. Cold stress proteins
  • 4.3.6. Coping with hyper-osmotic stress
  • 4.3.7. Coping with hypo-osmotic stress
  • 4.3.8. Resistance against oxidative and electrophile stress
  • 4.3.9. Resistance against other toxic compounds (nitric oxide, phenolic acids, flavonoids, oxalate)
  • 4.3.10.Resistance against toxic metals
  • 4.3.11.Resistance against toxins/ antibiotics
  • 4.3.12.Biosynthesis of antibacterial compounds
  • 4.3.13.Toxins, antitoxins and immunity against toxins
• 4.4. Lifestyles/ miscellaneous

5. Prophages and mobile genetic elements

• 5.1. Prophages
  • 5.1.1. PBSX prophage
  • 5.1.2. SPß prophage
  • 5.1.3. Skin element
  • 5.1.4. Phage-related functions
• 5.2. Mobile genetic elements

6. Groups of genes

• 6.1. Essential genes
• 6.2. Membrane proteins
• 6.3. GTP-binding proteins
• 6.4. Phosphoproteins
• 6.5. Universally conserved proteins
• 6.6. Poorly characterized/ putative enzymes
• 6.7. Proteins of unknown function
• 6.8. Short peptides
• 6.9. ncRNA
• 6.10. Pseudogenes

* 6.11. Regulators of core metabolism