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Table 1 Candidate promoters with different strengths selected based on omics datasets

From: Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

Gene ID Gene name Operon Gene function Array RNA-Seq Proteomics EGFP/opmCherry (log phase) EGFP/opmCherry (sta phase)
Candidate promoters with strong strength
 ZMO0177 gap   Glyceraldehyde-3-phosphate dehydrogenase, type I 15.06 11.2 9.23 0.38 ± 0.0202 0.47 ± 0.0191
 ZMO1360 pdc   Thiamine pyrophosphate protein TPP binding domain-containing protein 14.52 11.78 8.59 0.24 ± 0.0220 0.22 ± 0.0086
 ZMO0516 Tuf ND Elongation factor Tu 15.33 11.58 8.08 0.24 ± 0.0162 0.30 ± 0.0148
 ZMO1608 eno   Phosphopyruvate hydratase 15.22 13.2 8.97 0.23 ± 0.0145 0.34 ± 0.0093
 ZMO0997 eda Yes 2-Dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase 14.97 14.6 8.46 0.18 ± 0.0178 0.15 ± 0.0167
 ZMO0367 zwf   Glucose-6-phosphate 1-dehydrogenase 14.92 11.19 7.38 0.16 ± 0.0057 0.14 ± 0.0124
 ZMO1719 frk   ROK family protein 15.06 12.2 6.85 0.12 ± 0.0038 0.17 ± 0.0098
 ZMO1609    Hypothetical protein 15.26 12.77 5.78 0.12 ± 0.0061 0.14 ± 0.0038
 ZMO0689 gfo   Oxidoreductase domain-containing protein 14.49 11.68 6.38 0.10 ± 0.0075 0.13 ± 0.0130
 ZMO1721 gloA3 ND Glyoxalase/bleomycin resistance protein/dioxygenase 14.35 12.66 5.97 0.09 ± 0.0044 0.11 ± 0.0022
 ZMO0514 rpsG Yes 30S ribosomal protein S7 15.31 10.79 5.54 0.07 ± 0.0062 0.07 ± 0.0015
 ZMO0515   Yes Elongation factor G 15.07 11.14 5.83 0.07 ± 0.0062 0.07 ± 0.0015
 ZMO1596 adhB   Iron-containing alcohol dehydrogenase 15.32 10.98 7.07 0.07 ± 0.0084 0.07 ± 0.0030
 ZMO1141 ilvC Yes Ketol-acid reductoisomerase 15.41 12.39 6.76 0.05 ± 0.0012 0.04 ± 0.0006
 ZMO0241 atpD Yes F0F1 ATP synthase subunit beta 15.09 11.73 7.77 0.05 ± 0.0030 0.04 ± 0.0029
 ZMO0244    Histone family protein DNA-binding protein 14.79 12.98 6.1 0.04 ± 0.0013 0.04 ± 0.0007
 Po1721        0.04 ± 0.0020 0.03 ± 0.0007
 ZMO0493 glnA Yes Glutamine synthetase, type I 14.53 10.02 6.17 0.03 ± 0.0023 0.03 ± 0.0005
 ZMO1779   Yes Antibiotic biosynthesis monooxygenase 15.08 11.24 7.52 0.02 ± 0.0005 0.02 ± 0.0008
Candidate promoters with medium strength
 ZMO1351 clcD1 Yes Carboxymethylenebutenolidase 12.93 6.81 3.14 0.14 ± 0.0064 0.16 ± 0.0036
 ZMO0056 glmS   Glucosamine–fructose-6-phosphate aminotransferase 12.93 6.91 2.45 0.12 ± 0.0021 0.11 ± 0.0024
 ZMO0559    Hypothetical protein 12.68 6.75 3.1 0.11 ± 0.0064 0.08 ± 0.0039
 ZMO1385    Toxic anion resistance family protein 12.83 6.93 2.55 0.06 ± 0.0012 0.05 ± 0.0018
 ZMO0127   Yes S1/P1 nuclease 12.84 7.11 3.13 0.05 ± 0.0015 0.05 ± 0.0014
 ZMO1100   Yes Nucleotidyl transferase 12.58 7.18 2.82 0.05 ± 0.0012 0.05 ± 0.0023
 ZMO1392    Hypothetical protein 12.46 7.43 2.45 0.04 ± 0.0012 0.04 ± 0.0012
 ZMO0326    7-cyano-7-deazaguanine reductase 12.65 7.41 2.7 0.03 ± 0.0018 0.04 ± 0.0012
 ZMO0570 prmA   Ribosomal L11 methyltransferase 12.38 7.32 2.45 0.03 ± 0.0030 0.04 ± 0.0013
Candidate promoters with weak strength
 ZMO1231 recJ   Single-stranded-DNA-specific exonuclease RecJ 11.03 5.7 0.07 0.08 ± 0.0023 0.07 ± 0.0029
 ZMO1980 gidB Yes Methyltransferase GidB 10.59 5.27 0.07 0.05 ± 0.0025 0.05 ± 0.0029
 ZMO1484    UvrD/REP helicase 10.93 5.4 0.07 0.05 ± 0.0013 0.05 ± 0.0026
 ZMO0145   Yes Peptidase M28 11.37 4.98 0.07 0.04 ± 0.0018 0.04 ± 0.0006
 ZMO0101    NAD-dependent epimerase/dehydratase 10.61 5.05 0.07 0.04 ± 0.0013 0.04 ± 0.0014
 ZMO1194 dprA Yes DNA protecting protein DprA 10.7 4.77 0.07 0.04 ± 0.0011 0.03 ± 0.0006
 ZMO1644    DEAD/DEAH box helicase domain-containing protein 10.61 4.98 0.07 0.03 ± 0.0013 0.03 ± 0.0007
 ZMO1582    Uracil-DNA glycosylase superfamily protein 10.33 4.63 0.07 0.03 ± 0.0004 0.03 ± 0.0003
 ZMO0005 cysD Yes Sulfate adenylyltransferase subunit 2 11.5 5.28 0.07 0.03 ± 0.0012 0.03 ± 0.0009
 ZMO0300 xseA   Exodeoxyribonuclease VII large subunit 11.6 4.71 0.07 0.03 ± 0.0010 0.03 ± 0.0013
  1. The operon information is predicted by DOOR2 prediction server. The values of array, RNA-Seq and proteomics of each gene are the average log2-transformed values under different growth conditions
  2. ND non-determined, Log phase exponential phase, Sta phase stationary phase