MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iMM904 [2].
Target metabolite : ppi_x
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 234
  Remaining genes: YFR055W YCR034W YMR307W YMR306W YDR284C YBR029C YDR487C YBR249C YGL055W YDR454C YJR016C YDR354W YER090W YKL211C YLR134W YHR018C YOR236W YOL058W YKL216W YCR053W YDR127W YDR158W YGL154C YBR115C YJL167W YPR145W YER073W YPL028W YNR016C YJL130C YER052C YLR027C YER069W YMR062C YMR108W YPR128C YCL009C YER055C YGR199W YPR183W YPL036W YKL182W YPL231W YNR043W YLR355C YBR153W YOL066C YLR304C YBL099W YBR039W YKL016C YJR121W YOL140W YDL004W YPL078C YLR295C YLR153C YDR298C YDR377W YDL181W YAL054C Q0085 Q0080 Q0130 YPL271W YMR323W YBL030C YOL064C YDR226W YNL280C YHR042W YJR105W YGL012W YGL001C YLR100W YGR060W YKL001C YLR359W YNL220W YDL052C YEL039C YER043C YGR037C YLR028C YOR128C YPR060C YFL018C YKL060C YGL148W YDR111C YCR005C YJR103W YHR051W YMR256C YDL067C YGL187C YLR038C YGL191W Q0275 YMR217W YNL052W Q0045 YLR395C Q0250 YBL045C YGR204W YDR529C YEL024W YGR256W YPR191W YGR183C YJL166W Q0105 YFR033C YOR065W YGR012W YLR438W YOR130C YDL022W YML106W YPR167C YGR209C YNL241C YBR196C YBR218C YBL033C YHL012W YNL071W YGR193C YPR192W YBR221C YLR081W YDR234W YER178W YJR009C YGR157W YMR205C YDR408C YGR240C YBL011W YIL074C YCR012W YIL094C YCL030C YDL021W YFR025C YKL127W YLR058C YHR137W YKR058W YLR258W YPR035W YLR450W YML126C YER023W YJR139C YPR113W YJR077C YHR025W YIL116W YCL040W YMR300C YJL198W YDL171C YER053C YLR174W YBR248C YOR202W YFL045C YOR074C YJR148W YMR220W YDR050C YDR353W YMR261C YBR011C YDR074W YBR126C YHR216W YNL316C YOR245C YPL117C YGL026C YGL234W YDR007W YCL018W YGL009C YAR015W YOR108W YGR061C YIL020C YKL024C YKL181W YNL169C YER026C YHR007C YGR208W YHR072W YNL268W YAL038W YOL143C YBR256C YEL017C_A YCR024C_A YOR095C YNR050C YML081C_A YIR034C YJR010W YDL055C YER003C YHR001W_A YCR073W_A YDR502C YER091C YML082W YGR125W YMR208W YJR073C YGR175C YHR190W YHR046C YJL153C YFR030W YPL023C YMR145C YML120C YKL218C YKL067W YPR138C YPR074C YJL088W YOR184W YEL021W   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.084488 (mmol/gDw/h)
  Minimum Production Rate : 0.089388 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 2.413048
  EX_o2_e : 2.000000
  EX_nh4_e : 0.501470
  EX_pi_e : 0.204285
  EX_so4_e : 0.006531

Product: (mmol/gDw/h)
  EX_h2o_e : 5.115210
  EX_co2_e : 3.882112
  EX_acald_e : 3.533992
  EX_h_e : 0.443449
  Auxiliary production reaction : 0.089388
  EX_2mppal_e : 0.064929
  EX_fum_e : 0.031194
  EX_succ_e : 0.009344
  EX_pap_e : 0.004403
  EX_lys__L_e : 0.003312
  EX_2hb_e : 0.001439

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 27-Sep-2023
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