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Table 5 Putative genes related to functional enzymes for potential PGPR effects predicted from the genome sequence of Pseudomonas lutea OK2T

From: High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium

Function ID Name
Phosphate solubilization
 KO:K01113 alkaline phosphatase D [EC:3.1.3.1] (phoD)
 KO:K03778* D-lactate dehydrogenase [EC:1.1.1.28] (ldhA) *
 KO:K00031 isocitrate dehydrogenase [EC:1.1.1.42] (icd)
 KO:K01647 citrate synthase [EC:2.3.3.1] (gltA)
 KO:K00117 quinoprotein glucose dehydrogenase [EC:1.1.5.2] (gcd)
Antibiotic resistance
 KO:K17836* beta-lactamase class A (penicillinase) [EC:3.5.2.6] (penP) *
 KO:K08218 MFS transporter, PAT family, beta-lactamase induction signal transducer AmpG (ampG)
 KO:K03806 beta-lactamase expression regulator, N-acetyl-anhydromuramyl-L-alanine amidase AmpD protein (ampD)
 KO:K03807 Membrane protein required for beta-lactamase induction, AmpE protein (ampE)
 KO:K05365 penicillin-binding protein 1B [EC:2.4.1.129 3.4.-.-] (mrcB)
 KO:K05366 penicillin-binding protein 1A [EC:2.4.1.-3.4.-.-] (mrcA)
 KO:K05367 penicillin-binding protein 1C [EC:2.4.1.-] (pbpC)
 KO:K05515 penicillin-binding protein 2 (mrdA)
 KO:K07552 MFS transporter, DHA1 family, bicyclomycin/chloramphenicol resistance protein (bcr)
 KO:K08223 MFS transporter, FSR family, fosmidomycin resistance protein (fsr)
 KO:K05595* multiple antibiotic resistance protein (marC) *
 KO:K18138 multidrug efflux pump (acrB, mexB, adeJ, smeE, mtrD, cmeB)
 KO:K07799 putative multidrug efflux transporter MdtA (mdtA)
 KO:K07788 RND superfamily, multidrug transport protein MdtB (mdtB)
 KO:K07789 RND superfamily, multidrug transport protein MdtC (mdtC)
Toxins
 KO:K11068 membrane damaging toxins Type II toxin, pore-forming toxin hemolysin III (hlyIII)
Metal ion resistance
 KO:K07213 copper chaperone
 KO:K07245 putative copper resistance protein D (pcoD)
 KO:K07665 two-component system, OmpR family, copper resistance phosphate regulon response regulator CusR (cusR)
 KO:K06189 magnesium and cobalt transporter (corC)
 KO:K08970* nickel/cobalt exporter (rcnA) *
 KO:K06213 magnesium transporter (mgtE)
 KO:K16074 zinc transporter (zntB)
 KO:K09815 zinc transport system substrate-binding protein (znuA)
 KO:K09816 zinc transport system permease protein (znuB)
 KO:K09823 Fur family transcriptional regulator, zinc uptake regulator (zur)
 KO:K03893 arsenical pump membrane protein (arsB)
 KO:K11811* arsenical resistance protein ArsH (arsH) *
Siderophore
 KO:K02362 enterobactin synthetase component D [EC:2.7.8.-] (entD)
 KO:K16090 catecholate siderophore receptor (fiu)
Attachment and colonization in the plant rhizosphere
 KO:K04095* cell filamentation protein (fic) *
 KO:K06596* chemosensory pili system protein ChpA (sensor histidine kinase/response regulator) (chpA) *
 KO:K02655, K02656, K02662, K02663, K02664, K02665, K02666, K02671, K02672, K02673, K02674, K02676, K02650*, K02652, K02653 type IV pilus assembly protein
PilE (pilE), PilF (pilF), PilM (pilM), PilN (pilN), PilO (pilO), PilP (pilP), PilQ (pilQ), PilV (pilV), PilW (pilW), PilX (pilX), PilY1 (pilY1), PilZ (pilZ), PilA (pilA)*, PilB (pilB), PilC (pilC)
 KO:K08086, K02280 pilus assembly protein
FimV (fimV), CpaC (cpaC)
 KO:K02657, K02658 twitching motility two-component system response regulator PilG (pilG), PilH (pilH)
 KO:K02659, K02660, K02669, K02670* twitching motility protein
PilI (pilI), PilJ (pilJ), PilT (pilT), PilU (pilU) *
Secretion system
 KO:K03196*, K03198*, K03199*, K03200*, K03203*, K03204*, K03205* type IV secretion system protein
VirB11 (virB11) *, VirB3 (virB3) *, VirB4 (virB4) *, VirB5 (virB5) *, VirB8 (virB8) *, VirB9 (virB9) *, VirD4 (virD4) *
 KO:K11891*, K11892*, K11893*, K11894*, K11895*, K11896*, K11900*, K11901* type VI secretion system protein
ImpL (impL) *, ImpK (impK) *, ImpJ (impJ) *, ImpI (impI) *, ImpH (impH) *, ImpG (impG) *, ImpC (impC) *, ImpB (impB) *
 KO:K11903*, K11904* type VI secretion system secreted protein
Hcp (hcp) *, VgrG (vgrG) *
 KO:K11905* type VI secretion system protein*
 KO:K11906*, K11907*, K11910* type VI secretion system protein
VasD (vasD) *, VasG (vasG) *, VasJ (vasJ) *
Plant hormone auxin biosynthesis
 KO:K01696 tryptophan synthase [EC:4.2.1.20] (trpB)
 KO:K00766 anthranilate phosphoribosyltransferase [EC:2.4.2.18] (trpD)
 KO:K01817 phosphoribosylanthranilate isomerase [EC:5.3.1.24] (trpF)
  1. aBased on the function profiles obtained from the KO database [25, 26], under the IMG-ER pipeline [23]
  2. *Predicted only in the genome sequence of P. lutea OK2T (IMG Genome ID 2593339262) upon comparison with the complete genome sequence of P. rhizosphaerae IH5T (=DSM 16299T, IMG Genome ID 2593339263) [34]