Category
1.1. Cell envelope and cell division
1.1.1.1. Biosynthesis of peptidoglycan
1.1.1.2. Autolytic activity required for peptidoglycan synthesis (cell elongation)
1.1.1.3. Biosynthesis of lipoteichoic acid
1.1.1.4. Biosynthesis of teichoic acid
1.1.1.5. Biosynthesis of teichuronic acid
1.1.1.6. Export of anionic polymers and attachment to peptidoglycan
1.1.1.7. Penicillin-binding proteins
1.1.1.8. Biosynthesis of the carrier lipid undecaprenylphosphate
1.1.3. Cell wall degradation/ turnover
1.1.3.2. Autolysis/ based on similarity
1.1.3.3. Utilization of cell wall components
1.1.3.5. N-acetyl-β-D-glucosaminidases
1.1.3.6. Cell wall degradation/ turnover/ Additional genes
1.1.4. Capsule biosynthesis and degradation
1.1.6. Cell wall/ other/ based on similarity
1.1.9. Cell division/ based on similarity
1.2.1.1.1. Uptake of carbon sources
1.2.1.1.2. Uptake of amino acids
1.2.1.1.4. Uptake of compatible solutes for osmoprotection
1.2.1.1.5. Uptake of iron/ siderophores
1.2.1.1.7. Uptake of cofactors
1.2.1.2.1. Efflux of antibiotics
1.2.1.2.2. Export of antibiotic substances
1.2.1.2.4. Export of cell wall components
1.2.1.2.6. Exporters of unknown function
1.2.1.3. Regulatory ABC transporters
1.2.1.4. Unknown ABC transporters
1.2.2. Phosphotransferase system
1.2.2.2. Sugar specific PTS proteins
1.2.3.1. The general components of the ECF transporters
1.2.3.2. The substrate-specific S components of the ECF transporters
1.2.3.3. Class I ECF transporter
1.2.4.1. Amino acid transporters
1.2.4.1.1. Solute:sodium symporter family
1.2.4.1.3. Alanine or glycine cation symporter family
1.2.4.1.6. Dicarboxylate/amino acid:cation symporter
1.2.4.1.7. Sodium-solute symporter
1.2.4.1.8. Additional amino acid transporters
1.2.4.3. Carbohydrate transporter
1.2.4.4. Transporter for organic acids
1.2.4.5. Metal ion transporter
1.2.4.6. Nucleotide/ nucleoside transporter
1.2.4.7. Transporter for cofactors
1.2.4.8. Uptake of other small ions
1.2.4.9. Uptake of compatible solutes
1.2.4.10. Siderophore exporters
1.2.4.15. Multidrug exporters/ based on homology
1.3.1. Metal ion homeostasis (K, Na, Ca, Mg)
1.3.1.1. Magnesium uptake/ efflux
1.3.1.2. Sodium uptake/ export
1.3.1.3. Potassium uptake/ export
1.3.1.4. Metal ion homeostasis/ Other
1.3.2. Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)
1.3.3.1. ABC transporters for the uptake of iron/ siderophores
1.3.3.2. Elemental iron transport system
1.3.3.3. Acquisition of iron / Other
1.3.4. Acquisition of iron/ based on similarity
2.1. Electron transport and ATP synthesis
2.1.1. Regulators of electron transport
2.1.2.2. Anaerobic respiration
2.1.2.3. Anaerobic respiration/based on similarity
2.1.3. Electron transport/ other
2.1.4. Electron transport/ other/ based on similarity
2.1.5.2. Substrate-level phosphorylation
2.2.1.3. Pentose phosphate pathway
2.2.2. Utilization of specific carbon sources
2.2.2.1. Utilization of organic acids
2.2.2.2. Utilization of acetoin
2.2.2.3. Utilization of glycerol/ glycerol-3-phosphate
2.2.2.4. Utilization of ribose
2.2.2.5. Utilization of xylan/ xylose
2.2.2.6. Utilization of arabinan/ arabinose/ arabitol
2.2.2.7. Utilization of fructose
2.2.2.8. Utilization of galactose
2.2.2.9. Utilization of mannose
2.2.2.10. Utilization of mannitol
2.2.2.11. Utilization of glucitol
2.2.2.12. Utilization of rhamnose
2.2.2.13. Utilization of gluconate
2.2.2.14. Utilization of glucarate/galactarate
2.2.2.15. Utilization of hexuronate
2.2.2.16. Utilization of inositol
2.2.2.17. Utilization of amino sugars
2.2.2.18. Utilization of beta-glucosides
2.2.2.19. Utilization of sucrose
2.2.2.20. Utilization of trehalose
2.2.2.21. Utilization of melibiose
2.2.2.22. Utilization of maltose
2.2.2.23. Utilization of starch/ maltodextrin
2.2.2.24. Utilization of galactan
2.2.2.25. Utilization of glucomannan
2.2.2.26. Utilization of pectin
2.2.2.27. Utilization of other polymeric carbohydrates
2.2.2.28. Utilization of other pentoses and hexoses
2.3. Amino acid/ nitrogen metabolism
2.3.1. Biosynthesis/ acquisition of amino acids
2.3.1.1. Biosynthesis/ acquisition of glutamate/ glutamine/ ammonium assimilation
2.3.1.2. Biosynthesis/ acquisition of proline
2.3.1.3. Biosynthesis/ acquisition of proline/ based on similarity
2.3.1.4. Biosynthesis/ acquisition of arginine
2.3.1.5. Biosynthesis/ acquisition of aspartate/ asparagine
2.3.1.6. Biosynthesis/ acquisition of lysine/ threonine
2.3.1.7. Biosynthesis/ acquisition of lysine/ threonine/ based on similarity
2.3.1.8. Biosynthesis/ acquisition of serine/ glycine/ alanine
2.3.1.9. Biosynthesis/ acquisition of cysteine
2.3.1.10. Biosynthesis/ acquisition of methionine/ S-adenosylmethionine
2.3.1.11. Biosynthesis/ acquisition of methionine/ S-adenosylmethionine/ based on similarity
2.3.1.12. Biosynthesis/ acquisition of branched-chain amino acids
2.3.1.13. Biosynthesis/ acquisition of aromatic amino acids
2.3.1.14. Biosynthesis/ acquisition of histidine
2.3.1.15. Biosynthesis/acquisition of L- and D-alanine
2.3.2. Utilization of amino acids
2.3.2.1. Utilization of glutamine/ glutamate
2.3.2.2. Utilization of proline
2.3.2.3. Utilization of proline/ based on similarity
2.3.2.4. Utilization of arginine/ ornithine
2.3.2.5. Utilization of histidine
2.3.2.6. Utilization of asparagine/ aspartate
2.3.2.7. Utilization of alanine/ serine
2.3.2.8. Utilization of threonine/ glycine
2.3.2.9. Utilization of branched-chain amino acids
2.3.2.10. Utilization of gamma-amino butyric acid
2.3.3. Utilization of nitrogen sources other than amino acids
2.3.3.1. Utilization of nitrate/ nitrite
2.3.3.3. Utilization of amino sugars
2.3.3.4. Utilization of peptides
2.3.3.5. Utilization of proteins
2.3.4. Putative amino acid transporter
2.4.1.1. Utilization of phospholipids
2.4.1.2. Utilization of phospholipids/ based on similarity
2.4.1.3. Utilization of fatty acids
2.4.1.4. Utilization of lipids/ other
2.4.2.1. Biosynthesis of fatty acids
2.4.2.2. Biosynthesis of phospholipids
2.4.2.3. Biosynthesis of isoprenoids
2.4.3. Lipid metabolism/ other
2.5.1. Utilization of nucleotides
2.5.2. Biosynthesis/ acquisition of nucleotides
2.5.2.1. Biosynthesis/ acquisition of purine nucleotides
2.5.2.2. Biosynthesis/ acquisition of purine nucleotides/ based on similarity
2.5.2.3. Purine salvage and interconversion
2.5.2.4. Biosynthesis/ acquisition of pyrimidine nucleotides
2.5.2.5. Biosynthesis/ acquisition of nucleotides/ other
2.5.2.6. Biosynthesis/ acquisition of nucleotides/ other/ based on similarity
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
2.6.1.1. Biosynthesis of peptidoglycan
2.6.1.2. Biosynthesis of lipoteichoic acid
2.6.1.3. Biosynthesis of teichoic acid
2.6.1.4. Biosynthesis of teichuronic acid
2.6.1.5. Biosynthesis of the carrier lipid undecaprenylphosphate
2.6.2. Biosynthesis of cofactors
2.6.2.1. Biosynthesis/ acquisition of biotin
2.6.2.2. Biosynthesis/ acquisition of riboflavin/ FAD
2.6.2.3. Biosynthesis/ acquisition of thiamine
2.6.2.4. Biosynthesis of coenzyme A
2.6.2.5. Biosynthesis of folate
2.6.2.6. Biosynthesis of heme/ siroheme
2.6.2.7. Biosynthesis and scavenging of lipoic acid
2.6.2.8. Biosynthesis of menaquinone
2.6.2.9. Biosynthesis of menaquinone/ based on similarity
2.6.2.10. Biosynthesis of molybdopterin
2.6.2.11. Biosynthesis of NAD(P)
2.6.2.12. Biosynthesis of pyridoxal phosphate
2.6.2.13. Biosynthesis/ acquisition of cobalamine (B12))
2.6.4.1. Conversion of S-methyl cysteine to cysteine
2.6.4.2. sulfur metabolism/ general
2.6.4.3. Conversion of S-(2-succino)cysteine to cysteine
2.6.5.1. Acquisition of iron / Other
2.6.5.2. Acquisition of iron/ based on similarity
2.6.5.3. Biosynthesis of iron-sulfur clusters
2.6.5.4. ABC transporters for the uptake of iron/ siderophores
2.6.5.5. Elemental iron transport system
2.6.6. Miscellaneous metabolic pathways
2.6.6.1. Biosynthesis of antibacterial compounds
2.6.6.2. Biosynthesis of bacillithiol
2.6.6.3. Biosynthesis of dipicolinate
2.6.6.4. Biosynthesis of glycine betaine
2.6.6.5. Biosynthesis of glycogen
2.6.6.6. Metabolism of polyamines
2.6.6.7. Biosynthesis of rhamnose (for the exosporium)
2.6.6.8. Biosynthesis of legionaminic acid (for spore crust))
3.1.2. DNA replication/ based on similarity
3.1.3. DNA condensation/ segregation
3.1.4. DNA restriction/ modification
3.1.5. DNA repair/ recombination
3.1.5.1. Excision of prophages
3.1.5.3. Spore-encoded non-homologous end joining system
3.1.5.4. Double strand breaks repair
3.1.5.5. Oxidized guanine (GO) DNA repair system
3.1.5.7. Mismatch repair (MMR)
3.1.6. DNA repair/ recombination/ based on similarity
3.1.8. Genetics/ other/ based on similarity
3.1.9. Newly identified competence genes
3.2. RNA synthesis and degradation
3.2.1.3. Transcription elongation/ termination
3.2.1.4. Prophage/ phage transcription
3.2.4.3. RNA pyrophosphohydrolase
3.2.4.5. Effectors of RNA degradation
3.2.5. RNase/ based on similarity
3.3. Protein synthesis, modification and degradation
3.3.1.2. rRNA modification and maturation
3.3.1.3. rRNA modification and maturation/ based on similarity
3.3.1.5. Ribosomal protein/ based on similarity
3.3.1.8. tRNA modification and maturation
3.3.1.9. tRNA modification and maturation/ based on similarity
3.3.1.10. Aminoacyl-tRNA synthetases
3.3.1.13. Translation/ other/ based on similarity
3.3.1.14. Translation factor modification and maturation
3.3.2. Chaperones/ protein folding
3.3.3. Chaperone/ protein folding/ based on similarity
3.3.4.5. Protein acetylases/ deacetylases
3.3.4.6. Protein acetylase/ deacetylase/ based on similarity
3.3.4.8. Protein modification/ other
3.3.6. Protein secretion/ based on similarity
3.3.7.1. Protein quality control
3.3.7.2. Extracellular feeding proteases
3.3.7.3. Proteolysis during sporulation/ germination
3.3.7.4. Additional proteins involved in proteolysis
3.4. Regulation of gene expression
3.4.1. Sigma factors and their control
3.4.1.2. Control of sigma factors
3.4.2. Transcription factors and their control
3.4.2.1. Two-component system response regulators
3.4.2.2. Control of two-component response regulators
3.4.2.2.1. Two-component sensor kinase
3.4.2.2.2. Response regulator aspartate phosphatase
3.4.2.2.3. Control of response regulators/ other
3.4.2.4. Control of PRD-type regulators
3.4.2.5. Transcription factors/ other
3.4.2.6. Transcription factor/ other/ based on similarity
3.4.2.7. Control of transcription factor (other than two-component system)
3.4.3.3. Trigger enzymes that act directly as transcription factors by binding DNA
3.4.3.4. Trigger enzyme that acts by binding of a specific RNA element
3.4.3.5. Trigger enzymes that control transcription in a yet unknown way
3.4.5. Regulators of core metabolism
3.4.6. Transition state regulators
3.4.7.2. Proteins controlling the activity of the kinases
3.4.7.3. The phosphotransferases
3.4.7.5. Phosphatases controlling the phosphorelay
3.4.7.6. Other protein controlling the activity of the phosphorelay
3.5. Targets of second messengers
4.1. Exponential and early post-exponential lifestyles
4.1.1. Motility and chemotaxis
4.1.1.1. Signal transduction in motility and chemotaxis
4.1.1.1.1. Soluble signalling proteins
4.1.1.1.3. Soluble chemoreceptors
4.1.1.1.4. Membrane-bound chemoreceptors
4.1.1.1.5. Additional chemotaxis signal transduction and regulatory proteins
4.1.1.3. Flagellar proteins/ based on similarity
4.1.1.4. Motility and chemotaxis/ other
4.1.2.1. Matrix polysaccharide synthesis
4.1.2.2. Amyloid protein synthesis, secretion and assembly
4.1.2.3. Repellent surface layer
4.1.2.5. Other proteins required for biofilm formation
4.1.2.6. Other proteins required for efficient pellicle biofilm formation
4.2.1.2. Spore coat protein/ based on similarity
4.2.1.3. Small acid-soluble spore proteins
4.2.1.4. Sporulation proteins/ other
4.2.1.5. Newly identified sporulation proteins (based on transcription profiling)
4.2.2.2. Proteins controlling the activity of the kinases
4.2.2.3. The phosphotransferases
4.2.2.5. Phosphatases controlling the phosphorelay
4.2.2.6. Other protein controlling the activity of the phosphorelay
4.2.4.2. Additional germination proteins
4.2.5. Germination/ based on similarity
4.3.1. General stress proteins (controlled by SigB)
4.3.2. Cell envelope stress proteins (controlled by SigM, V, W, X, Y)
4.3.3. Acid stress proteins (controlled by YvrI-YvrHa)
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 oxidative and electrophile stress/ based on similarity
4.3.10. Resistance against other toxic compounds (nitric oxide, phenolic acids, flavonoids, oxalate)
4.3.11. Resistance against toxic metals
4.3.12. Resistance against toxic metals/ based on similarity
4.3.13. Resistance against toxins/ antibiotics
4.3.14. Resistance against toxins/ antibiotics/ based on similarity
4.3.15. Biosynthesis of antibacterial compounds
4.3.16. Biosynthesis of antibacterial compounds/ based on similarity
4.3.17. Toxins, antitoxins and immunity against toxins
4.3.17.3. Toxins, antitoxins and immunity/ Additional genes
4.3.18. Toxins, antitoxins and immunity against toxins/ based on similarity
4.4. Lifestyles/ miscellaneous
5. Prophages and mobile genetic elements
5.1.6. Phage-related functions
6.4.1. Phosphorylation on an Arg residue
6.4.2. Phosphorylation on an Asp residue
6.4.3. Phosphorylation on a Cys residue
6.4.4. Phosphorylation on a His residue
6.4.5. Phosphorylation on a Ser residue
6.4.6. Phosphorylation on a Thr residue
6.4.7. Phosphorylation on a Tyr residue
6.4.8. Phosphorylation on either a Ser, Thr or Tyr residue
6.4.9. Phosphoproteins / Other
6.5. Universally conserved proteins
6.6. Poorly characterized/ putative enzymes
6.7. Proteins of unknown function
6.9.3. Small cytoplasmatic RNA
6.9.4. RNA component of RNase P
6.9.6. Antisense RNAs of toxin/antitoxin systems