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Table 1 Differentially expressed proteins in mutant PA23-443 compared to the PA23 wild type

From: The requirement for the LysR-type regulator PtrA for Pseudomonas chlororaphis PA23 biocontrol revealed through proteomic and phenotypic analysis

COG Category Locus Tag Predicted Function Fold Changea VdiffScore
Amino acid transport and metabolism MOK_00491 4-aminobutyrate aminotransferase and related aminotransferases 1.59 2.24
  MOK_03651 Monoamine oxidase −2.39 −2.7
  MOK_04019 ornithine carbamoyltransferase −1.48 −1.67
Nucleotide transport and metabolism MOK_04929 hypothetical protein −3.13 −2.54
Carbohydrate transport and metabolism MOK_03378 Chitinase −3.30 −3.76
  MOK_05029 Glucose/sorbosone dehydrogenases −1.68 −2.04
  MOK_05478 Chitinase −2.61 −1.66
Lipid transport and metabolism MOK_04573 Acyl dehydratase −2.16 −2.42
Translation, ribosomal structure and biogenesis MOK_00565 Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) 1.61 1.94
  MOK_01324 ribosomal protein L32 2.33 2.77
  MOK_02337 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit 2.09 1.7
  MOK_04471 ribosomal protein S19, bacterial/organelle 1.49 1.7
Transcription MOK_02056 cold shock domain protein CspD −2.31 −1.81
  MOK_02888 Cold shock proteins 2.30 2.44
  MOK_03359 Cold shock proteins 1.26 1.65
Replication, recombination and repair MOK_00606 competence protein ComEA helix-hairpin-helix repeat region −2.78 −3.04
Cell wall, membrane and envelope biogenesis MOK_05137 Outer membrane protein and related peptidoglycan-associated (lipo)proteins −1.65 −1.79
Cell motility MOK_01499 Flagellin and related hook-associated proteins 2.71 3.26
Post-translational modification, protein turnover and chaperones MOK_00750 monothiol glutaredoxin, Grx4 family 1.20 1.81
  MOK_01830 peroxiredoxin, OsmC subfamily −2.61 −2.69
  MOK_05742 Peroxiredoxin −1.84 −1.78
  MOK_05953 Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family 2.00 1.73
Inorganic ion transport and metabolism MOK_05447 Predicted periplasmic lipoprotein involved in iron transport 1.42 1.73
Secondary metabolites biosynthesis, transport and catabolism MOK_01048 Phenazine biosynthesis protein A/B. −4.22 −4.58
  MOK_01049 Phenazine biosynthesis protein A/B. −3.25 −4.26
  MOK_01053 phenazine biosynthesis protein PhzF family −1.19 −2.1
  MOK_01054 Pyridoxamine-phosphate oxidase −1.25 −2.18
  MOK_01055 Aromatic ring hydroxylase −2.45 −2.43
General function prediction only MOK_01152 Predicted periplasmic or secreted lipoprotein −2.29 −2.42
  MOK_02985 intracellular protease, PfpI family 1.67 1.93
  MOK_03813 Predicted O-methyltransferase −2.12 −1.73
  MOK_05714 Serine protease inhibitor ecotin −1.33 −1.65
Function unknown MOK_00258 Protein of unknown function (DUF3313). −1.81 −2.03
  MOK_00808 hypothetical protein −8.28 −7.73
  MOK_01097 hypothetical protein −2.10 −2.22
  MOK_01302 hypothetical protein −1.32 −2.08
  MOK_01398 hypothetical protein −2.04 −2.19
  MOK_01832 Protein of unknown function (DUF1161). −1.14 −1.94
  MOK_02425 Sigma 54 modulation protein/S30EA ribosomal protein. 1.36 2.22
  MOK_02468 poly(hydroxyalkanoate) granule-associated protein −2.70 −3.66
  MOK_02469 poly(hydroxyalkanoate) granule-associated protein −1.75 −2.32
  MOK_03057 Uncharacterized protein conserved in bacteria −1.86 −2.29
  MOK_03064 type VI secretion protein, VC_A0107 family −2.87 −3.14
  MOK_03065 type VI secretion protein, EvpB/VC_A0108 family −2.72 −3.02
  MOK_03231 outer membrane porin, OprD family. 1.49 1.8
  MOK_03379 Uncharacterized protein conserved in bacteria −4.52 −5.06
  MOK_03717 hypothetical protein −5.36 −6.81
  MOK_03859 hypothetical protein −2.60 −2.27
  MOK_04005 Protein of unknown function (DUF3613). −2.39 −2.06
  MOK_04318 Predicted integral membrane protein −1.80 −2.21
  MOK_04378 Putative phospholipid-binding domain./LysM domain. −2.22 −3.47
  MOK_04746 hypothetical protein −2.29 −2.71
  MOK_04755 hypothetical protein −3.36 −3.84
  MOK_05477 Uncharacterized protein conserved in bacteria −2.09 −1.41
  MOK_05648 hypothetical protein −4.51 −4.7
  MOK_05758 hypothetical protein −4.00 −4.19
  MOK_06084 Iron-sulfur cluster assembly accessory protein 1.72 1.73
  MOK_06136 hypothetical protein −5.20 −5.37
Signal transduction mechanisms MOK_04087 Putative Ser protein kinase −1.38 −2.06
  1. Proteins with Vdiff ≥ +1.65 or Vdiff ≤ −1.65, corresponding to proteins expressed in the upper or lower 5% of the population distribution are shown.
  2. alog2(tag115/tag117).
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