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Table 4 Upregulated and downregulated genes in CaAc and NaAc condition (gene expression ≥ 100, fold change ≥ 2, and p value ≤ .05)

From: Enhanced calcium carbonate-biofilm complex formation by alkali-generating Lysinibacillus boronitolerans YS11 and alkaliphilic Bacillus sp. AK13

Locus taq Gene symbol Product Strand CaAc RPKM NaAc RPKM CaAc/NaAc
Genes upregulated by high Ca2+
 Branched chain amino acid synthesis
  LBYS11_13585   Acetolactate synthase small subunit 144.04 14 10.29
  LBYS11_13570 leuB 3-Isopropylmalate dehydrogenase 124.41 12.67 9.82
  LBYS11_13580   Ketol-acid reductoisomerase 263.2 27.42 9.6
  LBYS11_13560 leuD 3-Isopropylmalate dehydratase small subunit 116.42 12.75 9.13
  LBYS11_13565 leuC 3-Isopropylmalate dehydratase large subunit 144.46 17.55 8.23
  LBYS11_13575   2-Isopropylmalate synthase 165.84 20.78 7.98
  LBYS11_13590 ilvB Acetolactate synthase large subunit IlvB1 131.49 18.13 7.25
  LBYS11_13595 ilvD Dihydroxy-acid dehydratase 223.6 41.14 5.44
 Branched chain fatty acid synthesis
  LBYS11_00205   Hypothetical protein (NCBI blast: 3-oxoacyl-(Acyl-carrier-protein (ACP)) synthase III) + 1150.45 113.55 10.13
  LBYS11_00220   Phosphopantetheine-binding protein + 1044.75 125.49 8.33
  LBYS11_00200   Hypothetical protein: holo-[acyl-carrier-protein] synthase + 956.13 115.3 8.29
  LBYS11_00230   Hypothetical protein: holo-[acyl-carrier-protein] synthase + 1028.85 125.53 8.2
 Lysine synthesis
  LBYS11_00215 lysA Diaminopimelate decarboxylase + 1089.26 118.57 9.19
 Might serve as radioprotective agent
  LBYS11_06125   Glutathionylspermidine synthase + 315.38 82.76 3.81
 Protease involved genes
  LBYS11_00265   Uncharacterized zinc protease YmfH + 754.93 96.72 7.81
  LBYS11_00260   Zinc protease + 685.49 90.94 7.54
  LBYS11_06700   n|Uncharacterized protein YuaG + 560.04 124.56 4.5
  LBYS11_16935 hflK FtsH protease activity modulator HflK|Protein HflK 605.83 146.1 4.15
  LBYS11_16930 hflC Protease modulator HflC|Protein HflC 887.2 231.43 3.83
  LBYS11_17070 sppA Signal peptide peptidase SppA|Putative signal peptide peptidase SppA 139.57 36.6 3.81
 Multidrug efflux pump and swarming motility involved genes
  LBYS11_00190   Multidrug export protein AcrF Cobalt-zinc-cadmium resistance protein CzcA + 336.58 42.35 7.95
  LBYS11_00195   Swarming motility protein SwrC + 800.18 106.83 7.49
  LBYS11_00255   Hypothetical protein Multi antimicrobial extrusion protein (Na(+)/drug antiporter) + 376.26 51.85 7.26
  LBYS11_00250   Hypothetical protein Multi antimicrobial extrusion protein (Na(+)/drug antiporter) + 265.05 37.79 7.01
 TCA cycle involved genes
  LBYS11_00240   Acyl-CoA dehydrogenase + 1676.26 217.77 7.7
  LBYS11_07645   NADP-specific glutamate dehydrogenase 453.98 112.24 4.04
 Hydantoinase
  LBYS11_08510   N-methyl hydantoinase + 162.46 21.19 7.67
  LBYS11_08515   Hydantoinase subunit beta + 225.3 32.87 6.85
 Membrane proteins
  LBYS11_13515   Uncharacterized membrane protein YceF + 664.23 68.7 9.67
  LBYS11_06695   Uncharacterized membrane protein YuaF + 432.69 89.78 4.82
  LBYS11_17065   RDD family protein|Uncharacterized membrane protein YteJ 362.02 93.05 3.89
  LBYS11_20665   Hypothetical protein|UPF0699 transmembrane protein YdbS 148.94 39.48 3.77
 Hypothetical proteins
  LBYS11_00210   Hypothetical protein + 1190.22 124.33 9.57
  LBYS11_00225   Hypothetical protein + 1021.86 116.54 8.77
  LBYS11_00235   Hypothetical protein + 1193.34 140.21 8.51
  LBYS11_00245   Hypothetical protein + 1002.8 129.52 7.74
  LBYS11_09000   Hypothetical protein + 232.67 38.56 6.03
  LBYS11_09005   Hypothetical protein + 186.62 33.96 5.5
  LBYS11_09815   Hypothetical protein + 153.15 32.91 4.65
  LBYS11_21200   Hypothetical protein 143.8 32.67 4.4
  LBYS11_19760   Hypothetical protein|Uncharacterized protein YvlA + 133.72 33.88 3.95
  LBYS11_06120   Hypothetical protein|Uncharacterized serine-rich protein C21513 + 413.46 112.58 3.67
Genes downregulated by high Ca2+
 LBYS11_19235   Copper amine oxidase 63.11 224.53 .28
 LBYS11_08750   Copper amine oxidase + 52.07 239.12 .22
 LBYS11_20870   Zinc transporter ZupT 133.27 521.26 .26
 LBYS11_01430   Divalent metal cation transporter 8.88 211.74 .04
 LBYS11_20140   Guanine/hypoxanthine permease 9.31 157.38 .06