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Table 4 The comparison of the in silico gene essentiality and experimental P. aeruginosa data are shown under various amino acid auxotrophic conditions.

From: A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: i JN746 as a cell factory

Amino acid PP gene gene Reaction iJN746/PA01€ (growth)
Arginine PP_5185(PP_1346) argA†,(argJ) ACGS,(ORNTAC, ACGS) (+/-)*
  PP_5289 argB ACGK (-/-)
  PP_3633 argC AGPR (-/-)
  PP_5186,(PP_1346) argE†,(argJ) ACODA(ORNTAC, ACGS) (+/-)*
  PP_1088 argG ARGSS (-/-)
  PP_0184 argH ARGSL (-/-)
  PP_1346 argJ† ORNTAC, ACGS (+/-)*
Histidine     
  PP_0292 hisA PRMICIi (-/-)
  PP_0289 hisB IGPDH (-/-)
  PP_0967 hisC HSTPTr (-/-)
  PP_0966 hisD HISTD (-/-)
  PP_5015 hisE PRATPP (-/-)
  PP_0293 hisF IG3PS (-/-)
  PP_0965 hisG ATPPRTr (-/-)
  PP_0290 hisH IG3PS (-/-)
  PP_5014 hisI PRAMPC (-/-)
Isoleucine-valine     
  PP_3446, PP5149 ilvA-1, ilvA-2 SER_AL, THRD_L (+/-)*
  PP_4680 ilvB (ilvI)£ ACHBS, ACLS (-/-)
  PP_4678 ilvC KARA1, KARA2 (-/-)
  PP_5128 ilvD DHAD1, DHAD2 (-/-)
  PP_3511 ilvE VALTA, LEUTA, ILETA (-/-)
  PP_4679 ilvN(ilvH)£ ACHBS, ACLS (-/-)
Leucine     
  PP_1025 leuA IPPS (-/-)
  PP_1988 leuB IPMDr (-/-)
  PP_1985 leuC IPPMIa, IPPMIb (-/-)
  PP_1986 leuD IPPMIa, IPPMIb (-/-)
Tryptophan     
  PP_0082 trpA TRPS1r, TRPS3r (-/-)
  PP_0083 trpB TRPS2, TRPS1r (-/-)
  PP_0422 trpC IGPS (-/-)
  PP_0421 trpD ANPRT (-/-)
  PP_0417 trpE ANS (-/-)
  PP_1995 trpF PRAI (-/-)
  PP_0420 trpG ANS (-/-)
  1. The comparison of the in silico gene essentiality and experimental P. aeruginosa data are shown under various amino acid auxotrophic conditions. The in silico mutants were grown on Glucose-iM9 medium. * No auxotrophy was detected in i JN746, genetic redundancy for these genes was reported in Pseudomonas species. In P. aeruginosa mutants for orthologous genes, a significant residual growth on minimal medium was shown [82]. £ Alternative name in P. aeruginosa. € From [82].