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1. Cellular processes

1.1. Cell envelope and cell division

1.1.1. Cell wall synthesis Biosynthesis of peptidoglycan Autolytic activity required for peptidoglycan synthesis (cell elongation) Biosynthesis of lipoteichoic acid Biosynthesis of teichoic acid Biosynthesis of teichuronic acid Export of anionic polymers and attachment to peptidoglycan Penicillin-binding proteins Biosynthesis of the carrier lipid undecaprenylphosphate

1.1.2. Cell shape

1.1.3. Cell wall degradation/ turnover Autolysis Autolysis/ based on similarity Utilization of cell wall components Endopeptidases N-acetyl-╬▓-D-glucosaminidases 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 The Min system Other genes

1.1.9. Cell division/ based on similarity

1.2. Transporters

1.2.1. ABC transporters Importers Uptake of carbon sources Uptake of amino acids Uptake of peptides Uptake of compatible solutes for osmoprotection Uptake of iron/ siderophores Uptake of ions ABC transporters of unknown function Exporters Efflux of antibiotics Export of antibiotic substances Export of peptides Export of cell wall components Export of ions Exporters of unknown function Regulatory ABC transporters

1.2.2. Phosphotransferase system General PTS proteins Sugar specific PTS proteins

1.2.3. ECF transporter The general components of the ECF transporters The substrate-specific S components of the ECF transporters Class I ECF transporter

1.2.4. Transporters/ other Amino acid transporters Solute:sodium symporter family Other amino acid transporters Peptide transporter Carbohydrate transporter Transporter for organic acids Metal ion transporter Nucleotide/ nucleoside transporter Transporter for cofactors Uptake of other small ions Uptake of compatible solutes Siderophore exporters Other exporters Other transporters Metal ion exporters Multidrug exporters Multidrug exporters/ based on homology

1.3. Homeostasis

1.3.1. Metal ion homeostasis (K, Na, Ca, Mg) Magnesium uptake/ efflux Sodium uptake/ export Potassium uptake/ export Metal ion homeostasis/ Other

1.3.2. Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo) Copper Manganese Zinc Trace metals/ Other

1.3.3. Acquisition of iron ABC transporters for the uptake of iron/ siderophores Elemental iron transport system 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 Terminal oxidases Anaerobic respiration Anaerobic respiration/based on similarity Respiration/ other

2.1.3. Electron transport/ other

2.1.4. Electron transport/ other/ based on similarity

2.1.5. ATP synthesis ATPase Substrate-level phosphorylation

2.2. Carbon metabolism

2.2.1. Carbon core metabolism Glycolysis Gluconeogenesis Pentose phosphate pathway TCA cycle Overflow metabolism

2.2.2. Utilization of specific carbon sources Utilization of organic acids Utilization of acetoin Utilization of glycerol/ glycerol-3-phosphate Utilization of ribose Utilization of xylan/ xylose Utilization of arabinan/ arabinose/ arabitol Utilization of fructose Utilization of galactose Utilization of mannose Utilization of mannitol Utilization of glucitol Utilization of rhamnose Utilization of gluconate Utilization of glucarate/galactarate Utilization of hexuronate Utilization of inositol Utilization of amino sugars Utilization of beta-glucosides Utilization of sucrose Utilization of trehalose Utilization of melibiose Utilization of maltose Utilization of starch/ maltodextrin Utilization of galactan Utilization of glucomannan Utilization of pectin Utilization of other polymeric carbohydrates Utilization of other pentoses and hexoses

2.3. Amino acid/ nitrogen metabolism

2.3.1. Biosynthesis/ acquisition of amino acids Biosynthesis/ acquisition of glutamate/ glutamine/ ammonium assimilation Biosynthesis/ acquisition of proline Biosynthesis/ acquisition of proline/ based on similarity Biosynthesis/ acquisition of arginine Biosynthesis/ acquisition of aspartate/ asparagine Biosynthesis/ acquisition of lysine/ threonine Biosynthesis/ acquisition of lysine/ threonine/ based on similarity Biosynthesis/ acquisition of serine/ glycine/ alanine Biosynthesis/ acquisition of cysteine Biosynthesis/ acquisition of methionine/ S-adenosylmethionine Biosynthesis/ acquisition of methionine/ S-adenosylmethionine/ based on similarity Biosynthesis/ acquisition of branched-chain amino acids Biosynthesis/ acquisition of aromatic amino acids Biosynthesis/ acquisition of histidine

2.3.2. Utilization of amino acids Utilization of glutamine/ glutamate Utilization of proline Utilization of proline/ based on similarity Utilization of arginine/ ornithine Utilization of histidine Utilization of asparagine/ aspartate Utilization of alanine/ serine Utilization of threonine/ glycine Utilization of branched-chain amino acids Utilization of gamma-amino butyric acid

2.3.3. Utilization of nitrogen sources other than amino acids Utilization of nitrate/ nitrite Utilization of urea Utilization of amino sugars Utilization of peptides Utilization of proteins

2.3.4. Putative amino acid transporter

2.4. Lipid metabolism

2.4.1. Utilization of lipids Utilization of phospholipids Utilization of phospholipids/ based on similarity Utilization of fatty acids Utilization of lipids/ other

2.4.2. Biosynthesis of lipids Biosynthesis of fatty acids Biosynthesis of phospholipids 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 Biosynthesis/ acquisition of purine nucleotides Biosynthesis/ acquisition of purine nucleotides/ based on similarity Purine salvage and interconversion Biosynthesis/ acquisition of pyrimidine nucleotides Biosynthesis/ acquisition of nucleotides/ other 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 Biosynthesis of peptidoglycan Biosynthesis of lipoteichoic acid Biosynthesis of teichoic acid Biosynthesis of teichuronic acid Biosynthesis of the carrier lipid undecaprenylphosphate

2.6.2. Biosynthesis of cofactors Biosynthesis/ acquisition of biotin Biosynthesis/ acquisition of riboflavin/ FAD Biosynthesis/ acquisition of thiamine Biosynthesis of coenzyme A Biosynthesis of folate Biosynthesis of heme/ siroheme Biosynthesis of lipoic acid Biosynthesis of menaquinone Biosynthesis of menaquinone/ based on similarity Biosynthesis of molybdopterin Biosynthesis of NAD(P) Biosynthesis of pyridoxal phosphate

2.6.3. Phosphate metabolism

2.6.4. Sulfur metabolism Conversion of S-methyl cysteine to cysteine sulfur metabolism/ general Conversion of S-(2-succino)cysteine to cysteine

2.6.5. Iron metabolism Acquisition of iron / Other Acquisition of iron/ based on similarity Biosynthesis of iron-sulfur clusters ABC transporters for the uptake of iron/ siderophores Elemental iron transport system Iron export

2.6.6. Miscellaneous metabolic pathways Biosynthesis of antibacterial compounds Biosynthesis of bacillithiol Biosynthesis of dipicolinate Biosynthesis of glycine betaine Biosynthesis of glycogen Metabolism of polyamines 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 Excision of prophages A/P endonucleases Spore-encoded non-homologous end joining system Double strand breaks repair Oxidized guanine (GO) DNA repair system Other proteins

3.1.6. DNA repair/ recombination/ based on similarity

3.1.7. Genetic competence

3.1.8. Genetics/ other/ based on similarity

3.2. RNA synthesis and degradation

3.2.1. Transcription RNA polymerase Sigma factors Transcription elongation/ termination Prophage/ phage transcription

3.2.2. RNA chaperones

3.2.3. DEAD-box RNA helicases

3.2.4. RNases Exoribonucleases Endoribonucleases RNA pyrophosphohydrolase RNases/ Other

3.2.5. RNase/ based on similarity

3.3. Protein synthesis, modification and degradation

3.3.1. Translation Ribosomal RNA rRNA modification and maturation rRNA modification and maturation/ based on similarity Ribosomal proteins Ribosomal protein/ based on similarity Ribosome assembly tRNA tRNA modification and maturation tRNA modification and maturation/ based on similarity Aminoacyl-tRNA synthetases Translation factors Translation/ other Translation/ other/ based on similarity 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 Protein maturation Protein kinases Protein kinase/ based on similarity Protein phosphatases Protein acetylases/ deacetylases Protein acetylase/ deacetylase/ based on similarity Protein deaminase Protein modification/ other

3.3.5. Protein secretion

3.3.6. Protein secretion/ based on similarity

3.3.7. Proteolysis Protein quality control Extracellular feeding proteases Proteolysis during sporulation/ germination Additional proteins involved in proteolysis

3.4. Regulation of gene expression

3.4.1. Sigma factors and their control Sigma factors Control of sigma factors

3.4.2. Transcription factors and their control Two-component system response regulators Control of two-component response regulators Two-component sensor kinase Response regulator aspartate phosphatase Control of response regulators/ other PRD-type regulators Control of PRD-type regulators Transcription factors/ other Transcription factor/ other/ based on similarity Control of transcription factor (other than two-component system)

3.4.3. Trigger enzyme Trigger enzymes of the PTS that control the activity of PRD-containing transcription factors Trigger enzymes that control gene expression by protein-protein interaction with transcription factors Trigger enzymes that act directly as transcription factors by binding DNA Trigger enzyme that acts by binding of a specific RNA element 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 The kinases Proteins controlling the activity of the kinases The phosphotransferases The ultimate target Phosphatases controlling the phosphorelay 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 Signal transduction in motility and chemotaxis Soluble signalling proteins Coupling proteins Soluble chemoreceptors Membrane-bound chemoreceptors Additional chemotaxis signal transduction and regulatory proteins Flagellar proteins Flagellar proteins/ based on similarity Motility and chemotaxis/ other

4.1.2. Biofilm formation Matrix polysaccharide synthesis Amyloid protein synthesis, secretion and assembly Repellent surface layer Regulation Other proteins required for biofilm formation 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 Spore coat proteins Class I Class II Class III Class IV Class V Class VI Not yet assigned Spore coat protein/ based on similarity Small acid-soluble spore proteins Sporulation proteins/ other Newly identified sporulation proteins (based on transcription profiling)

4.2.2. phosphorelay The kinases Proteins controlling the activity of the kinases The phosphotransferases The ultimate target Phosphatases controlling the phosphorelay Other protein controlling the activity of the phosphorelay

4.2.3. Sporulation/ other

4.2.4. Germination Germinant receptors 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 Type 1 TA systems Type 2 TA systems 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