Table 2 Repressed genes with ≤ 0.5 fold change in expression level FDR (p-value ≤ 0.05)

Cluster VII Iron uptake and metabolism

pvdS

RNA polymerase sigma-70 factor, ECF subfamily

0.01

0.09

fpvA

outer membrane ferripyoverdine receptor

0.47

PSPPH_4765

RNA polymerase sigma-70 family protein

0.26

0.55

PSPPH_1911

pyoverdine chromophore precursor synthetase

0.04

0.14

PSPPH_1912

diaminobutyrate--2-oxoglutarate transaminase

0.26

0.53

PSPPH_1923

pyoverdine sidechain peptide synthetase I, epsilon-Lys module

0.03

0.25

PSPPH_1924

pyoverdine sidechain peptide synthetase II, D-Asp-L-Thr component

0.03

0.09

PSPPH_1925

pyoverdine sidechain peptide synthetase III, L-Thr-L-Ser component

0.02

0.10

PSPPH_1926

pyoverdine sidechain peptide synthetase IV, D-Asp-L-Ser component

0.08

0.27

PSPPH_1929

pyoverdine ABC transporter, ATP-binding/permease protein

0.26

0.40

PSPPH_1930

conserved hypothetical protein

0.11

PSPPH_1933

Tat (twin-arginine translocation) pathway signal sequence domain protein

0.05

0.28

PSPPH_1934

outer membrane efflux lipoprotein, NodT family

0.14

PSPPH_2751

achromobactin biosynthetic protein AcsD

0.26

pchA

isochorismate synthase

0.18

0.25

PSPPH_2895

ABC transporter, ATP-binding/permease protein

0.07

PSPPH_2896

ABC transporter, ATP-binding/permease protein

0.14

0.18

PSPPH_2897

yersiniabactin non-ribosomal peptide synthetase

0.15

0.13

exbD1

TonB system transport protein ExbD1

0.16

0.30

PSPPH_3266

TonB-dependent siderophore receptor, putative

0.48

PSPPH_2117

FecR protein superfamily

0.15

0.41

0.61

PSPPH_5185

iron compound ABC transporter, iron compound-binding protein

0.13

0.19

PSPPH_2957

Mn2+/Fe2+ transporter, NRAMP family

0.20

0.08

0.07

PSPPH_3288

Predicted periplasmic lipoprotein involved in iron transport

0.17

Cluster VIII Unknown function

PSPPH_4882

conserved hypothetical protein

0.11

0.06

0.05

PSPPH_2116

conserved hypothetical protein

0.12

0.32

0.65

PSPPH_1082

conserved hypothetical protein

0.14

0.28

0.63

PSPPH_5155

conserved hypothetical protein

0.37

0.20

0.31

PSPPH_1173

conserved hypothetical protein

0.46

0.66

PSPPH_1243

conserved hypothetical protein

0.18

PSPPH_2103

conserved hypothetical protein

0.20

PSPPH_5180

conserved hypothetical protein

0.50

Cluster IX None particular cluster

PSPPH_2486

acetyltransferase, GNAT family

0.37

0.45

0.58

PSPPH_2918

membrane protein, putative

0.37

0.13

0.12

PSPPH_2919

carbonic anhydrase, putative

0.27

0.18

0.19

osmC

hydroperoxide resistance protein OsmC

0.22

0.45

0.63

PSPPH_4984

prophage PSPPH06, site-specific recombinase, phage integrase family

0.11

0.25

0.62

PSPPH_2219

transcriptional regulator, AsnC family

0.09

0.15

0.59

PSPPH_3916

membrane protein, putative

0.07

0.01

0.02

PSPPH_2216

zinc carboxypeptidase domain protein

0.04

0.20

0.54

PSPPH_2747

transcriptional regulator, Cro/CI family

0.49

0.59

PSPPH_B0005

transcriptional regulator, Cro/CI family

0.46

0.45

PSPPH_3928

ABC transporter, binding protein

0.34

0.63

PSPPH_0189

ATP-dependent DNA helicase RecG

0.34

0.42

PSPPH_4962

prophage PSPPH06, C4-type zinc finger protein, DksA/TraR family

0.24

0.16

PSPPH_0194

ActC family protein

0.24

0.56

PSPPH_2746

dipeptide ABC transporter, ATP binding protein

0.14

0.33

PSPPH_0970

O-methyltransferase I

0.12

0.24

PSPPH_0592

high-affinity branched-chain amino acid ABC transporter, permease protein BraE

0.08

0.30

eda2

2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase

0.43

PSPPH_4761

glutathione S-transferase family protein

0.43

PSPPH_1737

transcriptional regulator, LysR family

0.42

PSPPH_4723

molybdate transport regulator ModE, putative

0.41

PSPPH_3100

isocitrate dehydrogenase, NADP-dependent

0.40

PSPPH_3284

beta-lactamase

0.34

PSPPH_1244

transcriptional regulator, AsnC family

0.30

PSPPH_3265

acetyltransferase, GNAT family

0.27

pilo

type IV pilus biogenesis protein PilO

0.16

PSPPH_5152

pyridoxal kinase

0.43