Supplementary Table 7:Genes Enriched 4-Fold Or More in Seqa Immunoprecipitations From
Supplementary Table 7:Genes enriched 4-fold or more in SeqA immunoprecipitations from unsynchronised CMT940 cultures.The table shows a list of genes that have a SeqA binding signal (i.e.Cy5/Cy3 ratio) of >4 at time point A.
Transcriptional RegulationaaeR / predicted DNA-binding transcriptional regulator,
agaR / DNA-binding transcriptional dual regulator
atoS / 2-component system, regulation of transcription
betI / DNA-binding transcriptional repressor
envY / DNA-binding transcriptional activator of porin
hyfR / transcriptional regulator
nanR / DNA binding transcriptional dual regulator
rpoD / RNA polymerase sigma factor
rpoN / RNA polymerase sigma factor
sgrR / DNA-binding transcriptional regulator
yghO / predicted DNA-binding transcriptional regulator
hepA / RNA polymerase-associated helicase protein
qseC / sensory histidine kinase in two-component regulatory system with QseB
rcsC / hybrid sensory kinase in two-component
Chromosome replication
dinG / ATP-dependent helicase, possible role in DNA replication
dnaA / chromosomal replication initiator protein DnaA,
dnaC / chromosome replication; initiation and chain elongation
gyrA / DNA gyrase (type II topoisomerase), subunit A
hda / regulator of DnaA that prevents premature reinitiation of DNA replication
obgE / GTPase involved in DNA replication and ribosome assembly
parE / topoisomerase IV subunit B
polA / DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease
ftsW / essential cell division protein
mukF / Involved in chromosome partioning, Ca2+ binding
DNA repair
nfi / endonuclease V (deoxyinosine 3'-endonuclease) DNA repair
recB / exonuclease V (RecBCD complex), beta subunit
Nucleotide metabolism
nrdB / ribonucleoside diphosphate reductase 1, beta
pnuC / nucleobase, nucleoside and nucleotide interconversion
pyrD / 'de novo' pyrimidine base biosynthetic process
pyrI / 'de novo' pyrimidine base biosynthetic process
rnd / ribonuclease D
sthA / pyridine nucleotide transhydrogenase, soluble
uraA / uracil NCS2 transporter
ushA / 5'-nucleotidase / UDP-sugar hydrolase
Peptidoglycan biosynthesis
ddlA / D-alanine-D-alanine ligase A
pbpC / putative peptidoglycan enzyme
slt / lytic murein transglycosylase
Amino acid metabolism
ldcC / lysine decarboxylase 2, constitutive
yhdY / predicted amino-acid transporter subunit
ykgF / predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain
aroG / 3-deoxy-D-arabino-heptulosonate-7-phosphate
aslA / arylsulfatase
Protease activity
degS / serine endoprotease
lon / protease
ypdE / predicted peptidase
Methyl transferase
rlmB / 23S rRNA 2'-O-ribose G2251 methyltransferase monomer
rlmL / 23S rRNA mG2445 methyltransferase
smtA / predicted S-adenosyl-L-methionine-dependent methyltransferase
yhdJ / predicted methyltransferase
RNA related functions
casE / subunit of CRISPR-associated complex for antiviral defense
tgt / tRNA-guanine transglycosylase
glnS / glutamyl-tRNA synthetase
miaB / isopentenyl-adenosine A37 tRNA methylthiolase MiaB
selB / selenocysteinyl-tRNA-specific translation factor
Lipid biosynthesis
pgpA / phosphatidylglycerophosphatase A
lpxD / UDP-3-O-(3-hydroxymyristoyl)-glucosamine
Transport
aaeB / Aromatic Carboxylic Acid Efflux Transport System Protein B
afuC / CP4-6 prophage; predicted ferric transporter
cusA / copper/silver transporting efflux system
dppA / dipeptide transporter
fryA / fused predicted PTS enzymes: Hpr
gltL / glutamate and aspartate transporter subunit
kefA / Transporter
mdtO / predicted multidrug efflux system component
mgtA / magnesium transporter (MgtA)
panF / pantothenate:sodium symporter
phnD / phosphonate/organophosphate ester transporter
potH / putrescine transporter subunit: membrane
potI / putrescine ABC transporter
ptsA / enzyme; Transport of small molecules:
ptsI / PTS enzyme I
trkA / NAD-binding component of TrK potassium transporter
ybhR / predicted transporter subunit: membrane
ybhS / ABC transporter
yghU / glutathione transferase-like protein possibly involved in glutathionylspermidine metabolism
yhhJ / predicted transporter subunit: membrane component of ABC superfamily
yicJ / GPH transporter
yjbH / predicted porin
yjfF / predicted sugar transporter subunit: membrane
yjjK / fused predicted transporter subunits of ABC
ytfR / ABC transporter
Unknown
yjiN / unknown
ykiA / unknown
ygiQ / unknown
yicR / unknown
yfeS / unknown
ybfF / unknown
Misc
etk / autophosphorylating protein tyrosine kinase
eutH / predicted inner membrane protein
nfrA / bacteriophage N4 receptor, outer membrane
psiE / predicted phosphate starvation inducible
yfaL / protein with similarity to antigen 43
yghJ / predicted inner membrane lipoprotein
Metabolism
aceB / malate synthase A
araA / L-arabinose isomerase
betA / choline dehydrogenase, a flavoprotein
cof / pyridoxal phosphatase / HMP-PP hydrolase
cysI / sulfite reductase, beta subunit, NAD(P)-binding,
cysN / sulfate adenylyltransferase, subunit 1
dmsA / dimethyl sulfoxide reductase, anaerobic, subunit
ebgA / cryptic beta-D-galactosidase, alpha subunit
entE / 2,3-dihydroxybenzoate-AMP ligase
eutC / ethanolamine ammonia-lyase, probable catalytic subunit
fadH / 2,4-dienoyl-CoA reductase, NADH and FMN-linked
frlB / fructoselysine 6-phosphate deglycase
galE / UDP-glucose 4-epimerase monomer
glgP / glycogen phosphorylase
glpA / glycerol-3-phosphate-dehydrogenase
gsp / fused glutathionylspermidine amidase
hemN / anaerobic coproporphyrinogen III oxidase
ispG / 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
katG / catalase/hydroperoxidase HPI(I)
kbaY / tagatose 6-phosphate aldolase 1, kbaY subunit
maeB / malate dehydrogenase
malP / maltodextrin phosphorylase
malZ / maltodextrin glucosidase
mioC / flavoprotein involved in biotin synthesis
mngB / alpha-mannosidase
nanA / N-acetylneuraminate lyase
pgi / phosphoglucose isomerase
prpB / 2-methylisocitrate lyase
prpE / putative propionyl-CoA synthetase
scpA / methylmalonyl-CoA mutase
scpB / methylmalonyl-CoA decarboxylase
scpC / propionyl-CoA:succinate CoA transferase
sucA / 2-oxoglutarate decarboxylase
sucB / dihydrolipoyltranssuccinase
sucD / succinyl-CoA synthetase, NAD(P)-binding, alpha
ttdB / L-tartrate dehydratase, ß subunit (TtdB)
ulaG / predicted L-ascorbate 6-phosphate lactonase
uxaA / altronate hydrolase
yahF / predicted acyl-CoA synthetase with NAD(P)-binding domain and succinyl-CoA synthetase domain
ybbO / predicted oxidoreductase with NAD(P)-binding
ybiW / predicted pyruvate formate lyase
ybjN / predicted oxidoreductase
yfiQ / fused predicted acyl-CoA synthetase: NAD(P)-binding subunit, ATP-binding subunit
yjfC / predicted synthetase/amidase