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1. Cellular processes

1.1. Cell envelope and cell division

1.1.1. Cell wall synthesis

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

1.1.2. Cell shape

1.1.3. Cell wall degradation/ turnover

1.1.3.1. Autolysis

1.1.3.2. Autolysis/ based on similarity

1.1.3.3. Utilization of cell wall components

1.1.3.4. Endopeptidases

1.1.3.5. N-acetyl-╬▓-D-glucosaminidases

1.1.3.6. Cell wall degradation/ turnover/ Additional genes

1.1.4. Capsule biosynthesis and degradation

1.1.5. Cell wall/ other

1.1.6. Cell wall/ other/ based on similarity

1.1.7. Membrane dynamics

1.1.8. Cell division

1.1.8.1. The Min system

1.1.8.2. Other genes

1.1.9. Cell division/ based on similarity

1.2. Transporters

1.2.1. ABC transporters

1.2.1.1. Importers

1.2.1.1.1. Uptake of carbon sources

1.2.1.1.2. Uptake of amino acids

1.2.1.1.3. Uptake of peptides

1.2.1.1.4. Uptake of compatible solutes for osmoprotection

1.2.1.1.5. Uptake of iron/ siderophores

1.2.1.1.6. Uptake of ions

1.2.1.1.8. ABC transporters of unknown function

1.2.1.2. Exporters

1.2.1.2.1. Efflux of antibiotics

1.2.1.2.2. Export of antibiotic substances

1.2.1.2.3. Export of peptides

1.2.1.2.4. Export of cell wall components

1.2.1.2.5. Export of ions

1.2.1.2.6. Exporters of unknown function

1.2.1.3. Regulatory ABC transporters

1.2.2. Phosphotransferase system

1.2.2.1. General PTS proteins

1.2.2.2. Sugar specific PTS proteins

1.2.3. ECF transporter

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. Transporters/ other

1.2.4.1. Amino acid transporters

1.2.4.1.1. Solute:sodium symporter family

1.2.4.1.2. Other amino acid transporters

1.2.4.2. Peptide transporter

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

1.2.4.11. Other exporters

1.2.4.12. Other transporters

1.2.4.13. Metal ion exporters

1.2.4.14. Multidrug exporters

1.2.4.15. Multidrug exporters/ based on homology

1.3. Homeostasis

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)

1.3.2.1. Copper

1.3.2.2. Manganese

1.3.2.3. Zinc

1.3.2.4. Trace metals/ Other

1.3.3. Acquisition of iron

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

1.3.5. PH homeostasis

2. Metabolism

2.1. Electron transport and ATP synthesis

2.1.1. Regulators of electron transport

2.1.2. Respiration

2.1.2.1. Terminal oxidases

2.1.2.2. Anaerobic respiration

2.1.2.3. Anaerobic respiration/based on similarity

2.1.2.4. Respiration/ other

2.1.3. Electron transport/ other

2.1.4. Electron transport/ other/ based on similarity

2.1.5. ATP synthesis

2.1.5.1. ATPase

2.1.5.2. Substrate-level phosphorylation

2.2. Carbon metabolism

2.2.1. Carbon core metabolism

2.2.1.1. Glycolysis

2.2.1.2. Gluconeogenesis

2.2.1.3. Pentose phosphate pathway

2.2.1.4. TCA cycle

2.2.1.5. Overflow metabolism

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

2.3.2. 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

2.3.3.2. Utilization of urea

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. Lipid metabolism

2.4.1. Utilization of lipids

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. Biosynthesis of lipids

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. Nucleotide metabolism

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 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

2.6.3. Phosphate metabolism

2.6.4. Sulfur metabolism

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. Iron metabolism

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

2.6.5.6. Iron export

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)

2.7. Detoxification reactions

3. Information processing

3.1. Genetics

3.1.1. DNA replication

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

3.1.5.2. A/P endonucleases

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

3.1.5.6. Other proteins

3.1.5.7. Mismatch repair (MMR)

3.1.6. DNA repair/ recombination/ based on similarity

3.1.7. Genetic competence

3.1.8. Genetics/ other/ based on similarity

3.1.9. Newly identified competence genes

3.2. RNA synthesis and degradation

3.2.1. Transcription

3.2.1.1. RNA polymerase

3.2.1.2. Sigma factors

3.2.1.3. Transcription elongation/ termination

3.2.1.4. Prophage/ phage transcription

3.2.2. RNA chaperones

3.2.3. DEAD-box RNA helicases

3.2.4. RNases

3.2.4.1. Exoribonucleases

3.2.4.2. Endoribonucleases

3.2.4.3. RNA pyrophosphohydrolase

3.2.4.4. RNases/ Other

3.2.5. RNase/ based on similarity

3.3. Protein synthesis, modification and degradation

3.3.1. Translation

3.3.1.1. Ribosomal RNA

3.3.1.2. rRNA modification and maturation

3.3.1.3. rRNA modification and maturation/ based on similarity

3.3.1.4. Ribosomal proteins

3.3.1.5. Ribosomal protein/ based on similarity

3.3.1.6. Ribosome assembly

3.3.1.7. tRNA

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

3.3.1.11. Translation factors

3.3.1.12. Translation/ other

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. Protein modification

3.3.4.1. Protein maturation

3.3.4.2. Protein kinases

3.3.4.3. Protein kinase/ based on similarity

3.3.4.4. Protein phosphatases

3.3.4.5. Protein acetylases/ deacetylases

3.3.4.6. Protein acetylase/ deacetylase/ based on similarity

3.3.4.7. Protein deaminase

3.3.4.8. Protein modification/ other

3.3.5. Protein secretion

3.3.6. Protein secretion/ based on similarity

3.3.7. Proteolysis

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

3.4.1.1. Sigma factors

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

3.4.2.3. PRD-type regulators

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. Trigger enzyme

3.4.3.1. Trigger enzymes of the PTS that control the activity of PRD-containing transcription factors

3.4.3.2. Trigger enzymes that control gene expression by protein-protein interaction with transcription factors

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

3.4.4. RNA binding regulators

3.4.5. Regulators of core metabolism

3.4.6. Transition state regulators

3.4.7. phosphorelay

3.4.7.1. The kinases

3.4.7.2. Proteins controlling the activity of the kinases

3.4.7.3. The phosphotransferases

3.4.7.4. The ultimate target

3.4.7.5. Phosphatases controlling the phosphorelay

3.4.7.6. Other protein controlling the activity of the phosphorelay

3.4.8. Quorum sensing

3.4.9. Other regulators

4. Lifestyles

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

4.1.1.1.2. Coupling 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

4.1.1.2. Flagellar proteins

4.1.1.3. Flagellar proteins/ based on similarity

4.1.1.4. Motility and chemotaxis/ other

4.1.2. Biofilm formation

4.1.2.1. Matrix polysaccharide synthesis

4.1.2.2. Amyloid protein synthesis, secretion and assembly

4.1.2.3. Repellent surface layer

4.1.2.4. Regulation

4.1.2.5. Other proteins required for biofilm formation

4.1.2.6. Other proteins required for efficient pellicle biofilm formation

4.1.3. Genetic competence

4.1.4. Swarming

4.1.5. Sliding

4.2. Sporulation

4.2.1. Sporulation proteins

4.2.1.1. Spore coat proteins

4.2.1.1.1. Class I

4.2.1.1.2. Class II

4.2.1.1.3. Class III

4.2.1.1.4. Class IV

4.2.1.1.5. Class V

4.2.1.1.7. Class VI

4.2.1.1.8. Not yet assigned

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. phosphorelay

4.2.2.1. The kinases

4.2.2.2. Proteins controlling the activity of the kinases

4.2.2.3. The phosphotransferases

4.2.2.4. The ultimate target

4.2.2.5. Phosphatases controlling the phosphorelay

4.2.2.6. Other protein controlling the activity of the phosphorelay

4.2.3. Sporulation/ other

4.2.4. Germination

4.2.4.1. Germinant receptors

4.2.4.2. Additional germination proteins

4.2.5. Germination/ based on similarity

4.3. Coping with stress

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)

4.3.4. 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 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

4.3.17.1. Type 1 TA systems

4.3.17.2. Type 2 TA systems

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. Prophages

5.1.1. PBSX prophage

5.1.2. SP-beta prophage

5.1.3. Skin element

5.1.4. Prophage 1

5.1.5. Prophage 3

5.1.6. Phage-related functions

5.2. Mobile genetic elements

5.2.1. ICEBs1

5.2.2. Additional genes

6. Groups of genes

6.1. Essential genes

6.2. Membrane proteins

6.3. GTP-binding proteins

6.4. Phosphoproteins

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

6.8. Short peptides

6.9. NcRNA

6.9.1. 6S RNA

6.9.2. tmRNA

6.9.3. Small cytoplasmatic RNA

6.9.4. RNA component of RNase P

6.9.5. Regulatory RNAs

6.9.6. Antisense RNAs of toxin/antitoxin systems

6.9.7. Small RNAs with unknown functions

6.10. Pseudogenes

6.11. Efp-dependent proteins

6.12. Secreted proteins