Category
SW 1 Cellular processes
SW 1.1 Cell envelope and cell division
SW 1.1.1 Cell wall synthesis
SW 1.1.1.1 Biosynthesis of peptidoglycan
alr | amj | asd | dapA | dapB | dapF | dapG |
dat | ddl | gcaD | glmM | glmR | glmS | ldcB |
ldt | mraY | murAA | murAB | murB | murC | murD |
murE | murF | murG | murJ | patA | pgcA | racE |
spoVB | spoVE | walJ | yabM | yciB | ykuQ | ykuR |
ylmD | yrpC |
SW 1.1.1.2 Autolytic activity required for peptidoglycan synthesis (cell elongation)
SW 1.1.1.3 Biosynthesis of lipoteichoic acid
SW 1.1.1.4 Biosynthesis of teichoic acid
SW 1.1.1.5 Biosynthesis of teichuronic acid
SW 1.1.1.6 Export of anionic polymers and attachment to peptidoglycan
SW 1.1.1.7 Penicillin-binding proteins
SW 1.1.1.8 Biosynthesis of the carrier lipid undecaprenylphosphate
SW 1.1.2 Cell shape
SW 1.1.3 Cell wall degradation/ turnover
amiE | blyA | cwlA | cwlH | cwlK | cwlO | cwlP |
cwlQ | cwlS | cwlT | gamA | gamP | gamR | glpQ |
iseA | lytA | lytB | lytC | lytD | lytE | lytF |
lytG | lytH | lytS | lytT | murP | murQ | murR |
nagA | nagB | nagZ | pbpE | xepA | xlyA | xlyB |
ykvT | yocH | yqgT | yqiI | ytkC |
SW 1.1.3.1 Autolysis
SW 1.1.3.2 Autolysis/ based on similarity
SW 1.1.3.3 Utilization of cell wall components
SW 1.1.3.4 Endopeptidases
SW 1.1.3.5 N-acetyl-β-D-glucosaminidases
SW 1.1.3.6 Cell wall degradation/ turnover/ Additional genes
SW 1.1.4 Capsule biosynthesis and degradation
SW 1.1.5 Cell wall/ other
clpC | cpgA | cwlC | cwlD | cwlJ | lytH | pdaA |
pdaC | reoM | reoY | spoIID | spoIIM | spoIIP | walH |
walI | walK | walR | wapA | wprA | ydjM | ykfB |
ykfC | yqgT | yrrL |
SW 1.1.6 Cell wall/ other/ based on similarity
SW 1.1.7 Membrane dynamics
SW 1.1.8 Cell division
ddcA | disA | divIB | divIC | divIVA | dynA | ezrA |
ftsA | ftsH | ftsL | ftsW | ftsZ | gpsB | mciZ |
minC | minD | minJ | noc | pbpB | plsX | racA |
rasP | refZ | sepF | sftA | spoVG | tseB | ugtP |
walJ | whiA | yisK | yneA | yodL | ypbE | yrrS |
zapA |
SW 1.1.8.1 The Min system
SW 1.1.8.2 Other genes
ddcA | disA | divIB | divIC | divIVA | dynA | ezrA |
ftsA | ftsH | ftsL | ftsW | ftsZ | gpsB | mciZ |
noc | pbpB | plsX | racA | rasP | refZ | sepF |
sftA | spoVG | tseB | ugtP | walJ | whiA | yisK |
yneA | yodL | ypbE | yrrS | zapA |
SW 1.1.9 Cell division/ based on similarity
SW 1.2 Transporters
SW 1.2.1 ABC transporters
SW 1.2.1.1 Importers
SW 1.2.1.1.1 Uptake of carbon sources
araN | araP | araQ | frlM | frlN | frlO | ganP |
ganS | mdxE | mdxF | mdxG | melC | melD | melE |
msmX | nupN | nupO | nupP | nupQ | rbsA | rbsB |
rbsC | rbsD | rhiF | rhiG | rhiL | ytcP | ytcQ |
yteP | yurJ |
SW 1.2.1.1.2 Uptake of amino acids
SW 1.2.1.1.3 Uptake of peptides
SW 1.2.1.1.4 Uptake of compatible solutes for osmoprotection
SW 1.2.1.1.5 Uptake of iron/ siderophores
SW 1.2.1.1.6 Uptake of ions
SW 1.2.1.1.7 Uptake of cofactors
SW 1.2.1.2 Exporters
SW 1.2.1.2.1 Efflux of antibiotics
SW 1.2.1.2.2 Export of antibiotic substances
SW 1.2.1.2.3 Export of peptides
SW 1.2.1.2.4 Export of cell wall components
SW 1.2.1.2.5 Export of ions
SW 1.2.1.2.6 Exporters of unknown function
ycbN | yclH | yclI | ydbJ | ydbK | yfiB | yfiC |
ygaD | yhaP | yhaQ | yhcE | yhcG | yhcH | yhcI |
yknU | yknV | ythP | ythQ | yvfR | yvfS | yvrN |
yvrO | ywjA | yybJ | yybK | yybL |
SW 1.2.1.3 Regulatory ABC transporters
SW 1.2.1.4 Unknown ABC transporters
SW 1.2.2 Phosphotransferase system
bglP | fruA | gamP | gmuA | gmuB | gmuC | levD |
levE | levF | levG | licA | licB | licC | malP |
manP | mtlA | mtlF | murP | nagP | ptsA | ptsG |
ptsH | ptsI | sacP | sacX | treP | ywbA | yyzE |
SW 1.2.2.1 General PTS proteins
SW 1.2.2.2 Sugar specific PTS proteins
bglP | fruA | gamP | gmuA | gmuB | gmuC | levD |
levE | levF | levG | licA | licB | licC | malP |
manP | mtlA | mtlF | murP | nagP | ptsA | ptsG |
sacP | sacX | treP | ywbA | yyzE |
SW 1.2.3 ECF transporter
SW 1.2.3.1 The general components of the ECF transporters
SW 1.2.3.2 The substrate-specific S components of the ECF transporters
SW 1.2.3.3 Class I ECF transporter
SW 1.2.4 Transporters/ other
SW 1.2.4.1 Amino acid transporters
aapA | aimA | alsT | azlC | azlD | bcaP | braB |
brnQ | dctP | gabP | gerAB | gerBB | gerKB | glnT |
gltP | gltT | hutM | opuE | putP | rocC | rocE |
steT | tcyP | ybgF | ybxG | ycgH | ydgF | yecA |
yfkT | yflA | yhjB | yndE | yodF | yrbD | ytnA |
yvbW | yveA | yvsH | ywcA |
SW 1.2.4.1.1 Solute:sodium symporter family
SW 1.2.4.1.3 Alanine or glycine cation symporter family
SW 1.2.4.1.4 APC superfamily
SW 1.2.4.1.5 BCAA transporters
SW 1.2.4.1.6 Dicarboxylate/amino acid:cation symporter
SW 1.2.4.1.7 Sodium-solute symporter
SW 1.2.4.1.8 Additional amino acid transporters
SW 1.2.4.10 Siderophore exporters
SW 1.2.4.11 Other exporters
SW 1.2.4.12 Other transporters
csbC | cstA | dltB | lmrB | mtrA | spoVV | tetB |
ybaS | ybcL | ycbK | yccK | yceJ | ycgH | ycsG |
ydbO | yddS | ydeG | ydeR | ydgH | ydgK | ydhB |
yecA | yfhI | yfiS | yfiU | yfkF | yfkL | yflA |
yfmI | yfmO | yfnC | yhjB | yitG | yjbB | yjnA |
ypdP | yrkJ | ytnM | yunE | yvgK |
SW 1.2.4.13 Metal ion exporters
SW 1.2.4.14 Multidrug exporters
SW 1.2.4.15 Multidrug exporters/ based on homology
SW 1.2.4.2 Peptide transporter
SW 1.2.4.3 Carbohydrate transporter
SW 1.2.4.4 Transporter for organic acids
SW 1.2.4.5 Metal ion transporter
arsB | aseA | cadA | chaA | copA | copZ | corA |
czcD | efeO | efeU | khtT | khtU | kimA | ktrA |
ktrB | ktrC | ktrD | mgtE | mntH | mrpA | mrpB |
mrpC | mrpD | mrpE | mrpF | mrpG | nhaK | pfeT |
ycnJ |
SW 1.2.4.6 Nucleotide/ nucleoside transporter
SW 1.2.4.7 Transporter for cofactors
SW 1.2.4.8 Uptake of other small ions
SW 1.2.4.9 Uptake of compatible solutes
SW 1.3 Homeostasis
SW 1.3.1 Metal ion homeostasis (K, Na, Ca, Mg)
chaA | citM | corA | cpaA | khtS | khtT | khtU |
kimA | ktrA | ktrB | ktrC | ktrD | mgtE | mpfA |
mrpA | mrpB | mrpC | mrpD | mrpE | mrpF | mrpG |
natA | natB | natR | nhaC | nhaK | yetJ | yfjQ |
yhdT | yloB | yqhB | yrkA | yugO | yugS |
SW 1.3.1.1 Magnesium uptake/ efflux
SW 1.3.1.2 Sodium uptake/ export
SW 1.3.1.3 Potassium uptake/ export
SW 1.3.1.4 Metal ion homeostasis/ Other
SW 1.3.2 Trace metal homeostasis (Cu, Zn, Ni, Mn, Mo)
copA | copZ | csoR | czcD | czcO | czrA | mneP |
mneS | mntA | mntB | mntC | mntD | mntH | mntR |
yceF | ycnJ | ycnK | yhjQ | ykoY | yvgL | yvgM |
zagA | zinT | znuA | znuB | znuC | zur |
SW 1.3.2.1 Copper
SW 1.3.2.2 Manganese
SW 1.3.2.3 Zinc
SW 1.3.2.4 Trace metals/ Other
SW 1.3.3 Acquisition of iron
besA | btr | cypX | dhbA | dhbB | dhbC | dhbE |
dhbF | dps | efeB | efeO | efeU | fbpA | fbpB |
fbpC | fecC | fecD | fecE | fecF | feuA | feuB |
feuC | fhuB | fhuC | fhuD | fhuG | fpbN | fpbO |
fpbP | fpbQ | fur | hmoA | hmoB | mrgA | pchR |
ybbA | yfhA | yfiY | yfiZ | yhfQ | ylaN | ymfD |
ytpQ | yusV | yvmC | yxeB |
SW 1.3.3.1 ABC transporters for the uptake of iron/ siderophores
SW 1.3.3.2 Elemental iron transport system
SW 1.3.3.3 Acquisition of iron / Other
SW 1.3.4 Acquisition of iron/ based on similarity
SW 1.3.5 PH homeostasis
SW 2 Metabolism
SW 2.1 Electron transport and ATP synthesis
SW 2.1.1 Regulators of electron transport
SW 2.1.2 Respiration
cccA | cccB | ccdA | ctaC | ctaD | ctaE | ctaF |
ctaG | cydA | cydB | cydC | cydD | narG | narH |
narI | narJ | narK | nasD | nasE | nasF | ndh |
ndhF | qcrA | qcrB | qcrC | qoxA | qoxB | qoxC |
qoxD | resA | resB | resC | sco | yojN | ythA |
ythB | ywcJ |
SW 2.1.2.1 Terminal oxidases
SW 2.1.2.2 Anaerobic respiration
SW 2.1.2.3 Anaerobic respiration/based on similarity
SW 2.1.2.4 Respiration/ other
SW 2.1.3 Electron transport/ other
SW 2.1.4 Electron transport/ other/ based on similarity
SW 2.1.5 ATP synthesis
SW 2.1.5.1 ATPase
SW 2.1.5.2 Substrate-level phosphorylation
SW 2.2 Carbon metabolism
SW 2.2.1 Carbon core metabolism
ackA | alsD | alsR | alsS | bdhA | ccpC | ccpN |
cggR | citB | citG | citZ | eno | fbaA | fbp |
gapA | gapB | glcT | glpX | gndA | icd | lctP |
ldh | mdh | mgsA | odhA | odhB | pckA | pdhA |
pdhB | pdhC | pdhD | pfkA | pgi | pgk | pgm |
pta | ptsG | pycA | pyk | rex | rpe | sdhA |
sdhB | sdhC | sucC | sucD | tkt | tpi | ykgB |
yqfL | ywjH | ywlF | zwf |
SW 2.2.1.1 Glycolysis
SW 2.2.1.2 Gluconeogenesis
SW 2.2.1.3 Pentose phosphate pathway
SW 2.2.1.4 TCA cycle
SW 2.2.1.5 Overflow metabolism
SW 2.2.2 Utilization of specific carbon sources
SW 2.2.2.1 Utilization of organic acids
acsA | acuA | acuC | cimH | citH | citM | citS |
citT | cstA | dctB | dctP | dctR | dctS | lutA |
lutB | lutC | lutP | lutR | maeA | maeN | malK |
malR | malS | mleA | mleN | pftA | pftB | ybaR |
yflS | yoaB | yraO | ytsJ |
SW 2.2.2.10 Utilization of mannitol
SW 2.2.2.11 Utilization of glucitol
SW 2.2.2.12 Utilization of rhamnose
SW 2.2.2.13 Utilization of gluconate
SW 2.2.2.14 Utilization of glucarate/galactarate
SW 2.2.2.15 Utilization of hexuronate
SW 2.2.2.16 Utilization of inositol
SW 2.2.2.17 Utilization of amino sugars
SW 2.2.2.18 Utilization of beta-glucosides
SW 2.2.2.19 Utilization of sucrose
SW 2.2.2.2 Utilization of acetoin
SW 2.2.2.20 Utilization of trehalose
SW 2.2.2.21 Utilization of melibiose
SW 2.2.2.22 Utilization of maltose
SW 2.2.2.23 Utilization of starch/ maltodextrin
SW 2.2.2.24 Utilization of galactan
SW 2.2.2.25 Utilization of glucomannan
SW 2.2.2.26 Utilization of pectin
SW 2.2.2.27 Utilization of other polymeric carbohydrates
SW 2.2.2.28 Utilization of other pentoses and hexoses
SW 2.2.2.3 Utilization of glycerol/ glycerol-3-phosphate
SW 2.2.2.4 Utilization of ribose
SW 2.2.2.5 Utilization of xylan/ xylose
SW 2.2.2.6 Utilization of arabinan/ arabinose/ arabitol
SW 2.2.2.7 Utilization of fructose
SW 2.2.2.8 Utilization of galactose
SW 2.2.2.9 Utilization of mannose
SW 2.3 Amino acid/ nitrogen metabolism
SW 2.3.1 Biosynthesis/ acquisition of amino acids
SW 2.3.1.1 Biosynthesis/ acquisition of glutamate/ glutamine/ ammonium assimilation
SW 2.3.1.10 Biosynthesis/ acquisition of methionine/ S-adenosylmethionine
SW 2.3.1.11 Biosynthesis/ acquisition of methionine/ S-adenosylmethionine/ based on similarity
SW 2.3.1.12 Biosynthesis/ acquisition of branched-chain amino acids
SW 2.3.1.13 Biosynthesis/ acquisition of aromatic amino acids
SW 2.3.1.14 Biosynthesis/ acquisition of histidine
SW 2.3.1.15 Biosynthesis/acquisition of L- and D-alanine
SW 2.3.1.2 Biosynthesis/ acquisition of proline
SW 2.3.1.4 Biosynthesis/ acquisition of arginine
SW 2.3.1.5 Biosynthesis/ acquisition of aspartate/ asparagine
SW 2.3.1.6 Biosynthesis/ acquisition of lysine/ threonine
SW 2.3.1.7 Biosynthesis/ acquisition of lysine/ threonine/ based on similarity
SW 2.3.1.8 Biosynthesis/ acquisition of serine/ glycine/ alanine
SW 2.3.1.9 Biosynthesis/ acquisition of cysteine
SW 2.3.2 Utilization of amino acids
SW 2.3.2.1 Utilization of glutamine/ glutamate
SW 2.3.2.10 Utilization of gamma-amino butyric acid
SW 2.3.2.2 Utilization of proline
SW 2.3.2.4 Utilization of arginine/ ornithine
SW 2.3.2.5 Utilization of histidine
SW 2.3.2.6 Utilization of asparagine/ aspartate
SW 2.3.2.7 Utilization of alanine/ serine
SW 2.3.2.8 Utilization of threonine/ glycine
SW 2.3.2.9 Utilization of branched-chain amino acids
azlB | azlC | azlD | bcaP | bcd | bkdAA | bkdAB |
bkdB | bkdR | buk | citB | lpdV | mmgA | mmgB |
mmgC | mmgD | mmgE | mmgF | ptb | yngE | yngF |
yngG | yngH | yngHB | yngI | yngJ |
SW 2.3.3 Utilization of nitrogen sources other than amino acids
SW 2.3.3.1 Utilization of nitrate/ nitrite
SW 2.3.3.2 Utilization of urea
SW 2.3.3.3 Utilization of amino sugars
SW 2.3.3.4 Utilization of peptides
SW 2.3.3.5 Utilization of proteins
SW 2.3.4 Putative amino acid transporter
SW 2.4 Lipid metabolism
SW 2.4.1 Utilization of lipids
acdA | acsA | acuA | acuC | cotR | etfA | etfB |
fadA | fadB | fadE | fadF | fadG | fadH | fadM |
fadN | fadR | glpD | glpP | glpQ | glpT | lcfA |
lcfB | lip | lipB | lipC | nap | pnbA | scoA |
scoB | ybfK | yhdW | yqiK |
SW 2.4.1.1 Utilization of phospholipids
SW 2.4.1.2 Utilization of phospholipids/ based on similarity
SW 2.4.1.3 Utilization of fatty acids
SW 2.4.1.4 Utilization of lipids/ other
SW 2.4.2 Biosynthesis of lipids
accA | accB | accC | accD | acpA | acpS | birA |
cdsA | clsA | degV | dxs | fabD | fabF | fabG |
fabHA | fabHB | fabI | fabL | fakA | fapR | fni |
gpsA | ispC | ispD | ispE | ispF | ispG | ispH |
mprF | nudF | pgpB | pgsA | plsC | plsX | plsY |
psd | pssA | uppS | ycsD | yhdN | yhfR | yisP |
yitS | yqhY | yqiD | ywiE | ywjE | ywpB |
SW 2.4.2.1 Biosynthesis of fatty acids
SW 2.4.2.2 Biosynthesis of phospholipids
SW 2.4.2.3 Biosynthesis of isoprenoids
SW 2.4.3 Lipid metabolism/ other
SW 2.5 Nucleotide metabolism
SW 2.5.1 Utilization of nucleotides
SW 2.5.2 Biosynthesis/ acquisition of nucleotides
SW 2.5.2.1 Biosynthesis/ acquisition of purine nucleotides
adk | gmk | guaA | guaB | nupG | nupN | nupO |
nupP | nupQ | pbuG | pbuX | prs | purA | purB |
purC | purD | purE | purF | purH | purK | purL |
purM | purN | purQ | purR | purS | purT | ykkE |
SW 2.5.2.2 Biosynthesis/ acquisition of purine nucleotides/ based on similarity
SW 2.5.2.3 Purine salvage and interconversion
SW 2.5.2.4 Biosynthesis/ acquisition of pyrimidine nucleotides
SW 2.5.2.5 Biosynthesis/ acquisition of nucleotides/ other
SW 2.5.2.6 Biosynthesis/ acquisition of nucleotides/ other/ based on similarity
SW 2.5.3 Metabolism of signalling nucleotides
SW 2.5.4 Nucleotide metabolism/ other
SW 2.6 Additional metabolic pathways
SW 2.6.1 Biosynthesis of cell wall components
SW 2.6.1.1 Biosynthesis of peptidoglycan
alr | amj | asd | dapA | dapB | dapF | dapG |
dat | ddl | gcaD | glmM | glmR | glmS | ldcB |
ldt | mraY | murAA | murAB | murB | murC | murD |
murE | murF | murG | murJ | patA | pgcA | racE |
spoVB | spoVE | walJ | yabM | yciB | ykuQ | ykuR |
ylmD | yrpC |
SW 2.6.1.2 Biosynthesis of lipoteichoic acid
SW 2.6.1.3 Biosynthesis of teichoic acid
SW 2.6.1.4 Biosynthesis of teichuronic acid
SW 2.6.1.5 Biosynthesis of the carrier lipid undecaprenylphosphate
SW 2.6.2 Biosynthesis of cofactors
SW 2.6.2.1 Biosynthesis/ acquisition of biotin
SW 2.6.2.10 Biosynthesis of molybdopterin
SW 2.6.2.11 Biosynthesis of NAD(P)
SW 2.6.2.12 Biosynthesis of pyridoxal phosphate
SW 2.6.2.13 Biosynthesis/ acquisition of cobalamine (B12))
SW 2.6.2.2 Biosynthesis/ acquisition of riboflavin/ FAD
SW 2.6.2.3 Biosynthesis/ acquisition of thiamine
SW 2.6.2.4 Biosynthesis of coenzyme A
SW 2.6.2.5 Biosynthesis of folate
SW 2.6.2.6 Biosynthesis of heme/ siroheme
SW 2.6.2.7 Biosynthesis and scavenging of lipoic acid
SW 2.6.2.8 Biosynthesis of menaquinone
SW 2.6.2.9 Biosynthesis of menaquinone/ based on similarity
SW 2.6.3 Phosphate metabolism
SW 2.6.4 Sulfur metabolism
ascR | cmoI | cmoJ | cmoO | cymR | cysC | cysH |
cysI | cysJ | cysL | cysP | defB | mtrA | ribR |
sat | snaA | snaB | sndA | sndB | ssuA | ssuB |
ssuC | ssuD | yisZ | yitA | yitB | yxeK | yxeM |
yxeN | yxeO |
SW 2.6.4.1 Conversion of S-methyl cysteine to cysteine
SW 2.6.4.2 sulfur metabolism/ general
SW 2.6.4.3 Conversion of S-(2-succino)cysteine to cysteine
SW 2.6.5 Iron metabolism
SW 2.6.5.1 Acquisition of iron / Other
SW 2.6.5.2 Acquisition of iron/ based on similarity
SW 2.6.5.3 Biosynthesis of iron-sulfur clusters
SW 2.6.5.4 ABC transporters for the uptake of iron/ siderophores
SW 2.6.5.5 Elemental iron transport system
SW 2.6.5.6 Iron export
SW 2.6.6 Miscellaneous metabolic pathways
SW 2.6.6.1 Biosynthesis of antibacterial compounds
SW 2.6.6.2 Biosynthesis of bacillithiol
SW 2.6.6.3 Biosynthesis of dipicolinate
SW 2.6.6.4 Biosynthesis of glycine betaine
SW 2.6.6.5 Biosynthesis of glycogen
SW 2.6.6.6 Metabolism of polyamines
SW 2.6.6.7 Biosynthesis of rhamnose (for the exosporium)
SW 2.6.6.8 Biosynthesis of legionaminic acid (for spore crust))
SW 2.7 Detoxification reactions
SW 3 Information processing
SW 3.1 Genetics
SW 3.1.1 DNA replication
dnaA | dnaB | dnaC | dnaD | dnaE | dnaG | dnaI |
dnaN | dnaX | exoR | holA | holB | ligA | ligB |
polA | polC | priA | recD2 | recJ | recQ | rnhB |
rnhC | rtp | sirA | ssbA | ssbB | topB | xtmA |
xtmB | yabA |
SW 3.1.2 DNA replication/ based on similarity
SW 3.1.3 DNA condensation/ segregation
SW 3.1.4 DNA restriction/ modification
SW 3.1.5 DNA repair/ recombination
SW 3.1.5.1 Excision of prophages
SW 3.1.5.2 A/P endonucleases
SW 3.1.5.3 Spore-encoded non-homologous end joining system
SW 3.1.5.4 Double strand breaks repair
SW 3.1.5.5 Oxidized guanine (GO) DNA repair system
SW 3.1.5.6 Other proteins
SW 3.1.5.7 Mismatch repair (MMR)
SW 3.1.6 DNA repair/ recombination/ based on similarity
SW 3.1.7 Genetic competence
SW 3.1.8 Genetics/ other/ based on similarity
SW 3.1.9 Newly identified competence genes
cpgA | cysE | glyA | gpsA | greA | ndh | pdhB |
pdhC | pdxS | pdxT | pfkA | pgi | pgk | prmC |
ptsI | purB | pyrF | rplK | tpi | tsaC | yfhF |
yjlC | ykcB | yqhH | ytrA | ywlF |
SW 3.2 RNA synthesis and degradation
SW 3.2.1 Transcription
greA | mfd | nusA | nusB | nusG | rho | rpoA |
rpoB | rpoC | rpoE | rpoY | rsoA | sigA | sigB |
sigD | sigE | sigF | sigG | sigH | sigI | sigK |
sigKC | sigL | sigM | sigO | sigV | sigW | sigX |
sigY | sigZ | xpf | ylaC | yloH | yonO |
SW 3.2.1.1 RNA polymerase
SW 3.2.1.2 Sigma factors
SW 3.2.1.3 Transcription elongation/ termination
SW 3.2.1.4 Prophage/ phage transcription
SW 3.2.2 RNA chaperones
SW 3.2.3 DEAD-box RNA helicases
SW 3.2.4 RNases
eno | mrnC | nahA | ndoA | nrnA | nrnB | pnpA |
rimM | rnc | rnhB | rnhC | rnjA | rnjB | rnmV |
rnpA | rnpB | rnr | rny | rnz | rph | rppH |
SR7P | yaaT | yacP | yhaM | yhcR | ylbF | ymcA |
yqfG | yurI |
SW 3.2.4.1 Exoribonucleases
SW 3.2.4.2 Endoribonucleases
SW 3.2.4.3 RNA pyrophosphohydrolase
SW 3.2.4.4 RNases/ Other
SW 3.2.4.5 Effectors of RNA degradation
SW 3.2.5 RNase/ based on similarity
SW 3.3 Protein synthesis, modification and degradation
SW 3.3.1 Translation
SW 3.3.1.1 Ribosomal RNA
SW 3.3.1.10 Aminoacyl-tRNA synthetases
alaS | argS | asnS | aspS | cysS | gatA | gatB |
gatC | gltX | glyQ | glyS | hisS | hisZ | ileS |
leuS | lysS | metS | pheS | pheT | proS | serS |
thrS | thrZ | trpS | tyrS | tyrZ | valS | ytpR |
SW 3.3.1.11 Translation factors
SW 3.3.1.12 Translation/ other
SW 3.3.1.13 Translation/ other/ based on similarity
SW 3.3.1.14 Translation factor modification and maturation
SW 3.3.1.2 rRNA modification and maturation
SW 3.3.1.3 rRNA modification and maturation/ based on similarity
SW 3.3.1.4 Ribosomal proteins
SW 3.3.1.5 Ribosomal protein/ based on similarity
SW 3.3.1.6 Ribosome assembly
SW 3.3.1.7 tRNA
SW 3.3.1.8 tRNA modification and maturation
cca | cspR | fmt | folD | folE | folEB | gidA |
miaA | nifZ | queA | queC | queD | queE | queF |
queG | rnpA | rnpB | rnz | rph | tgt | thdF |
thiI | tilS | tmcAL | trmB | trmD | trmFO | trmK |
trmN6 | trmR | trmU | truA | truB | tsaB | tsaC |
tsaD | tsaE | yaaJ | yacF | yfjN | yloN | ymcB |
yqeV | yrrN | yrrO | yrvM | yrvO |
SW 3.3.1.9 tRNA modification and maturation/ based on similarity
SW 3.3.2 Chaperones/ protein folding
SW 3.3.3 Chaperone/ protein folding/ based on similarity
SW 3.3.4 Protein modification
SW 3.3.4.1 Protein maturation
SW 3.3.4.2 Protein kinases
SW 3.3.4.4 Protein phosphatases
SW 3.3.4.5 Protein acetylases/ deacetylases
SW 3.3.4.6 Protein acetylase/ deacetylase/ based on similarity
SW 3.3.4.7 Protein deaminase
SW 3.3.4.8 Protein modification/ other
SW 3.3.5 Protein secretion
SW 3.3.6 Protein secretion/ based on similarity
SW 3.3.7 Proteolysis
aprE | bpr | clpC | clpE | clpP | clpQ | clpX |
clpY | ctpA | ctpB | ctsR | ddcP | epr | ftsH |
gpr | htpX | htrA | htrB | htrC | immA | ipi |
ispA | lonA | lonB | mecA | mlpA | mpr | nprB |
nprE | prp | prsW | rasP | spoIIGA | spoIVFB | tepA |
vpr | wprA | yabG | yirB | yjbH | ylzJ | ypbH |
ypwA | yqgP | yraA | yydH |
SW 3.3.7.1 Protein quality control
SW 3.3.7.2 Extracellular feeding proteases
SW 3.3.7.3 Proteolysis during sporulation/ germination
SW 3.3.7.4 Additional proteins involved in proteolysis
clpC | clpE | clpP | clpQ | clpX | clpY | ctpA |
ctpB | ctsR | ddcP | ftsH | htpX | immA | ipi |
ispA | lonA | lonB | mecA | mlpA | prp | prsW |
rasP | yabG | yirB | yjbH | ypbH | ypwA | yqgP |
yraA | yydH |
SW 3.4 Regulation of gene expression
SW 3.4.1 Sigma factors and their control
SW 3.4.1.1 Sigma factors
SW 3.4.1.2 Control of sigma factors
SW 3.4.2 Transcription factors and their control
SW 3.4.2.1 Two-component system response regulators
bceR | cheY | citT | comA | cssR | dctR | degU |
desR | glnL | liaR | lnrK | lytT | malR | natR |
phoP | psdR | resD | spo0A | walR | ybdJ | ycbL |
yclJ | ydfI | yesN | yhcZ | ykoG | yneI | yrkP |
yvfU | yvrHb | yxdJ | yxjL |
SW 3.4.2.2 Control of two-component response regulators
SW 3.4.2.2.1 Two-component sensor kinase
bceS | cheA | citS | comP | cssS | dctS | degS |
desK | glnK | kinA | kinB | kinC | kinD | kinE |
liaS | lnrJ | lytS | malK | natK | phoR | psdS |
resE | walK | ybdK | ycbM | yclK | ydfH | yesM |
yhcY | ykoH | yrkQ | yvfT | yvrG | ywpD | yxdK |
yxjM |
SW 3.4.2.2.2 Response regulator aspartate phosphatase
SW 3.4.2.2.3 Control of response regulators/ other
SW 3.4.2.3 PRD-type regulators
SW 3.4.2.4 Control of PRD-type regulators
SW 3.4.2.5 Transcription factors/ other
SW 3.4.2.6 Transcription factor/ other/ based on similarity
SW 3.4.2.7 Control of transcription factor (other than two-component system)
SW 3.4.3 Trigger enzyme
SW 3.4.3.1 Trigger enzymes of the PTS that control the activity of PRD-containing transcription factors
SW 3.4.3.2 Trigger enzymes that control gene expression by protein-protein interaction with transcription factors
SW 3.4.3.3 Trigger enzymes that act directly as transcription factors by binding DNA
SW 3.4.3.4 Trigger enzyme that acts by binding of a specific RNA element
SW 3.4.3.5 Trigger enzymes that control transcription in a yet unknown way
SW 3.4.4 RNA binding regulators
SW 3.4.5 Regulators of core metabolism
SW 3.4.6 Transition state regulators
SW 3.4.7 phosphorelay
bslA | ftsE | ftsX | kapB | kapD | kbaA | kinA |
kinB | kinC | kinD | kinE | kipR | lrpA | lrpB |
obg | oppA | oppB | oppC | oppD | oppF | pepF |
phrA | phrE | phrH | pxpB | pxpC | rapA | rapB |
rapE | rapH | rghR | sda | sivA | sivC | spo0A |
spo0B | spo0E | spo0F | yaaT | yisI | yisP | ylbF |
ymcA | ynzD |
SW 3.4.7.1 The kinases
SW 3.4.7.2 Proteins controlling the activity of the kinases
SW 3.4.7.3 The phosphotransferases
SW 3.4.7.4 The ultimate target
SW 3.4.7.5 Phosphatases controlling the phosphorelay
SW 3.4.7.6 Other protein controlling the activity of the phosphorelay
SW 3.4.8 Quorum sensing
SW 3.4.9 Other regulators
SW 3.5 Targets of second messengers
c-di-AMP riboswitch, kimA | c-di-AMP riboswitch, ktrA | cpaA | darA | darB | dnaG | era |
gdpP | gmk | guaB | hprT | infB | khtT | kimA |
ktrA | ktrC | mgtE | motI | nahA | opuCA | pgpH |
rbgA | xpt | ydaK | ykuI | ynbA | zagA |
SW 3.5.1 Targets of c-di-AMP
SW 3.5.2 Targets of c-di-GMP
SW 3.5.3 Targets of (p)ppGpp
SW 3.5.4 Targets of ZTP
SW 4 Lifestyles
SW 4.1 Exponential and early post-exponential lifestyles
SW 4.1.1 Motility and chemotaxis
SW 4.1.1.1 Signal transduction in motility and chemotaxis
cheA | cheB | cheC | cheD | cheR | cheV | cheW |
cheY | csrA | epr | epsE | flgM | fliY | hemAT |
lonA | luxS | mcpA | mcpB | mcpC | motI | pdeH |
rho | sigD | smiA | swrA | swrAA/2 | swrB | swrD |
tlpA | tlpB | tlpC | yfmS | yoaH | yvaQ |
SW 4.1.1.1.1 Soluble signalling proteins
SW 4.1.1.1.2 Coupling proteins
SW 4.1.1.1.3 Soluble chemoreceptors
SW 4.1.1.1.4 Membrane-bound chemoreceptors
SW 4.1.1.1.5 Additional chemotaxis signal transduction and regulatory proteins
SW 4.1.1.2 Flagellar proteins
flgB | flgC | flgD | flgE | flgK | flgL | flhA |
flhB | flhF | flhO | flhP | fliD | fliE | fliF |
fliG | fliH | fliI | fliJ | fliK | fliL | fliM |
fliP | fliQ | fliR | fliS | fliT | fliW | fliY |
fliZ | hag | motA | motB | motP | motS | yhbE |
yhbF | yvyG |
SW 4.1.1.3 Flagellar proteins/ based on similarity
SW 4.1.1.4 Motility and chemotaxis/ other
SW 4.1.2 Biofilm formation
SW 4.1.2.1 Matrix polysaccharide synthesis
SW 4.1.2.2 Amyloid protein synthesis, secretion and assembly
SW 4.1.2.3 Repellent surface layer
SW 4.1.2.4 Regulation
SW 4.1.2.5 Other proteins required for biofilm formation
ampS | dhbA | dhbB | dhbC | floT | gpsA | luxS |
menH | remA | remB | rny | rqcH | sdhC | sfp/1 |
sfp/2 | speA | speD | swrA | swrAA/2 | yisP | ylbF |
ymcA | yvcA | ywcC | yxaB |
SW 4.1.2.6 Other proteins required for efficient pellicle biofilm formation
SW 4.1.3 Genetic competence
SW 4.1.4 Swarming
SW 4.2 Sporulation
SW 4.2.1 Sporulation proteins
SW 4.2.1.1 Spore coat proteins
SW 4.2.1.1.1 Class I
SW 4.2.1.1.2 Class II
SW 4.2.1.1.3 Class III
SW 4.2.1.1.4 Class IV
SW 4.2.1.1.5 Class V
SW 4.2.1.1.7 Class VI
SW 4.2.1.1.8 Not yet assigned
cgeA | cgeB | cgeC | cgeD | cgeE | cmpA | cotC |
cotF | cotH | cotI | cotJA | cotJB | cotJC | cotR |
cotSA | cotV | cotX | cotY | gerQ | gerR | gerT |
ldt | safA | spsB | yabG | ydhD | ygaK | yhbB |
yheC | yisJ | yjdH | ykvP | yobN | yodI | ypeP |
yqfT | ywqH |
SW 4.2.1.2 Spore coat protein/ based on similarity
SW 4.2.1.3 Small acid-soluble spore proteins
SW 4.2.1.4 Sporulation proteins/ other
SW 4.2.1.5 Newly identified sporulation proteins (based on transcription profiling)
SW 4.2.2 phosphorelay
bslA | ftsE | ftsX | kapB | kapD | kbaA | kinA |
kinB | kinC | kinD | kinE | kipR | lrpA | lrpB |
obg | oppA | oppB | oppC | oppD | oppF | pepF |
phrA | phrE | phrH | pxpB | pxpC | rapA | rapB |
rapE | rapH | rghR | sda | sivA | sivC | spo0A |
spo0B | spo0E | spo0F | yaaT | yisI | yisP | ylbF |
ymcA | ynzD |
SW 4.2.2.1 The kinases
SW 4.2.2.2 Proteins controlling the activity of the kinases
SW 4.2.2.3 The phosphotransferases
SW 4.2.2.4 The ultimate target
SW 4.2.2.5 Phosphatases controlling the phosphorelay
SW 4.2.2.6 Other protein controlling the activity of the phosphorelay
SW 4.2.3 Sporulation/ other
SW 4.2.4 Germination
csgA | cwlJ | gdh | gerAA | gerAB | gerAC | gerBA |
gerBB | gerBC | gerD | gerE | gerKA | gerKB | gerKC |
gerKD | gerM | gerPA | gerPB | gerPC | gerPD | gerPE |
gerPF | gerQ | gerT | gerW | gpr | lgt | lipC |
prkC | sleB | spoVAD | spoVAEA | spoVAEB | swsB | tepA |
yhcN | ykvU | ylaJ | ylzJ | ypeB | ywcE |
SW 4.2.4.1 Germinant receptors
SW 4.2.4.2 Additional germination proteins
csgA | cwlJ | gdh | gerD | gerE | gerM | gerPA |
gerPB | gerPC | gerPD | gerPE | gerPF | gerQ | gerT |
gerW | gpr | lgt | lipC | prkC | sleB | spoVAD |
spoVAEA | spoVAEB | swsB | tepA | yhcN | ykvU | ylaJ |
ylzJ | ypeB | ywcE |
SW 4.2.5 Germination/ based on similarity
SW 4.3 Coping with stress
SW 4.3.1 General stress proteins (controlled by SigB)
SW 4.3.10 Resistance against other toxic compounds (nitric oxide, phenolic acids, flavonoids, oxalate)
SW 4.3.11 Resistance against toxic metals
SW 4.3.12 Resistance against toxic metals/ based on similarity
SW 4.3.13 Resistance against toxins/ antibiotics
SW 4.3.14 Resistance against toxins/ antibiotics/ based on similarity
bcrC | ybfO | ycbJ | yceJ | ydeR | ydfJ | ydgK |
ydhE | yfhI | yfiS | yfiU | yfkF | yfkL | yfmI |
yfmO | yfmP | yfnC | yhjO | yitG | yitZ | yjbB |
yjiC | ykuC | yojI | yojK | yokD | ypnP | yqjV |
ytbD | yttB | yubD | yuxJ | yvaE | yvkA | yvmA |
yvqJ | ywfA | ywnH | ywoG | yxaM | yxlH | yybF |
SW 4.3.15 Biosynthesis of antibacterial compounds
SW 4.3.16 Biosynthesis of antibacterial compounds/ based on similarity
SW 4.3.17 Toxins, antitoxins and immunity against toxins
bsrE | bsrG | bsrH | ndoA | ndoAI | ratA | sdpA |
sdpB | sdpC | sdpI | sdpR | skfA | skfB | skfC |
skfE | skfF | spoIISA | spoIISB | spoIISC | SR5 | sunA |
sunI | txpA | yeeF | yezG | yitM | yitQ | yobK |
yobL | yokI | yokJ | yonT | yoyJ | yqcF | yqcG |
ywqJ | ywqK | yxiD | yxxD |
SW 4.3.17.1 Type 1 TA systems
SW 4.3.17.2 Type 2 TA systems
SW 4.3.17.3 Toxins, antitoxins and immunity/ Additional genes
SW 4.3.18 Toxins, antitoxins and immunity against toxins/ based on similarity
SW 4.3.2 Cell envelope stress proteins (controlled by SigM, V, W, X, Y)
SW 4.3.3 Acid stress proteins (controlled by YvrI-YvrHa)
SW 4.3.4 Heat shock proteins
bcrC | clpC | clpE | clpP | cssR | cssS | ctsR |
disA | dnaJ | dnaK | ftsH | groEL | groES | grpE |
hrcA | htpG | htrA | htrB | mcsA | mcsB | mreBH |
radA | rsgI | sigI | yqeT | yqeU | yqeV |
SW 4.3.5 Cold stress proteins
SW 4.3.6 Coping with hyper-osmotic stress
gbsA | gbsB | gbsR | ktrA | ktrB | ktrC | ktrD |
opcR | opuAA | opuAB | opuAC | opuBA | opuBB | opuBC |
opuBD | opuCA | opuCB | opuCC | opuCD | opuD | opuE |
papA | papB | proA | proH | proJ | yocM |
SW 4.3.7 Coping with hypo-osmotic stress
SW 4.3.8 Resistance against oxidative and electrophile stress
SW 4.3.9 Resistance against oxidative and electrophile stress/ based on similarity
SW 4.4 Lifestyles/ miscellaneous
SW 5 Prophages and mobile genetic elements
SW 5.1 Prophages
SW 5.1.1 PBSX prophage
pghB | xepA | xhlA | xhlB | xkdA | xkdB | xkdC |
xkdD | xkdE | xkdF | xkdG | xkdH | xkdI | xkdJ |
xkdK | xkdM | xkdN | xkdO | xkdP | xkdQ | xkdR |
xkdS | xkdT | xkdU | xkdV | xkdW | xkdX | xkzA |
xkzB | xlyA | xlyB | xpf | xre | xtmA | xtmB |
xtrA | yjqA | yjqC | yjzJ | ykzK | ykzL | ykzM |
SW 5.1.2 SP-beta prophage
SW 5.1.3 Skin element
SW 5.1.4 Prophage 1
SW 5.1.5 Prophage 3
ydiM | ydiO | ydiP | ydiR | ydiS | ydjA | ydjB |
ydjC | ydzT/1 | ydzT/2 | ydzT/3 | ydzT/4 | ydzT/5 | ydzU |
ydzV | ydzW/1 | ydzW/2 | ydzW/3 | ydzW/4 | ydzW/5 | ydzW/6 |
ydzW/7 |
SW 5.1.6 Phage-related functions
SW 5.2 Mobile genetic elements
conB | conC | conD | conE | conG | cwlT | immA |
immR | int | nicK | pcrA | phrI | rapI | xis |
ydcO | ydcP | ydcQ | ydcS | ydcT | yddA | yddF |
yddI | yddJ | yddK | yddM | ydzL | yerB |
SW 5.2.1 ICEBs1
SW 5.2.2 Additional genes
SW 6 Groups of genes
SW 6.1 Essential genes
SW 6.10 Pseudogenes
SW 6.11 Efp-dependent proteins
besA | cotA | ctaD | dppD | fmt | ggt | glmR |
gltA | gmuC | kdgT | recJ | sigE | sndA | spoIIP |
topA | valS | xkdJ | ybfO | ycxA | ydgB | yesN |
yhjG | yitG | ykwB | ylxX | yodT | yomQ | yonJ |
yqbA | yqjN | ytcC | ytcP | yvdQ | yyaN |
SW 6.12 Secreted proteins
SW 6.13 Quasi-essential genes
SW 6.2 Membrane proteins
SW 6.3 GTP-binding proteins
SW 6.4 Phosphoproteins
SW 6.4.1 Phosphorylation on an Arg residue
SW 6.4.2 Phosphorylation on an Asp residue
bceR | cheB | cheV | cheY | citT | comA | cssR |
dctR | degU | desR | glnL | liaR | lnrK | lytT |
malR | natR | phoP | psdR | resD | spo0A | spo0F |
walR | ybdJ | ycbL | yclJ | ydfI | yesN | yhcZ |
ykoG | yneI | yrkP | yvfU | yvrHb | yxdJ | yxjL |
SW 6.4.3 Phosphorylation on a Cys residue
SW 6.4.4 Phosphorylation on a His residue
SW 6.4.5 Phosphorylation on a Ser residue
SW 6.4.6 Phosphorylation on a Thr residue
aroA | cpgA | drm | eno | fbaA | fusA | glmR |
gndA | gpsB | hbs | ltaS | ndk | oppA | pgi |
pgk | prkC | prkD | rsbR | rsbRB | rsbRC | rsbRD |
sodA | tyrZ | yabA | ydcC | yezB | BSGatlas-gene-4209 |
SW 6.4.7 Phosphorylation on a Tyr residue
SW 6.4.8 Phosphorylation on either a Ser, Thr or Tyr residue
ahpC | alsD | aspS | atpA | atpD | dnaK | dppA |
gapA | glgP | glnA | glyA | groEL | gtaB | guaB |
icd | metE | pdhD | pdxS | pgcA | pstS | pta |
rocA | sdhA | sucD | sufC | thiG | tig | tkt |
tufA | wapI | yerB | yfiY | yfjR | yfnI | yhfK |
yoxD | ysnF | ytaG | ytxJ | zur |
SW 6.4.9 Phosphoproteins / Other
SW 6.5 Universally conserved proteins
apt | argS | eno | gltX | groES | pgk | pheS |
prs | rplB | rplC | rplE | rplF | rplK | rplN |
rplR | rpsB | rpsC | rpsD | rpsE | rpsG | rpsH |
rpsJ | rpsM | rpsQ | rpsS | secY | truA | tsaD |