MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b3942 b1732 b1241 b0351 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b2690 b2463 b1302 b2662 b2210 b0675 b0822 b1602 b0452 b1727 b1380 b0606 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453350 (mmol/gDw/h)
  Minimum Production Rate : 3.415339 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.747030
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.896142
  EX_pi_e : 0.437304
  EX_so4_e : 0.114163
  EX_k_e : 0.088491
  EX_mg2_e : 0.003933
  EX_fe2_e : 0.003741
  EX_fe3_e : 0.003540
  EX_ca2_e : 0.002360
  EX_cl_e : 0.002360
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 37.669993
  EX_co2_e : 29.115379
  EX_h_e : 6.199767
  EX_12ppd__R_e : 3.415339
  EX_for_e : 2.030666
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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: 21-Sep-2023
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