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__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b4069 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2210 b3551 b3945 b1602 b4219 b1832 b1778 b2492 b0904 b1380 b1710 b2480 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494981 (mmol/gDw/h)
  Minimum Production Rate : 0.437047 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.301377
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.345750
  EX_pi_e : 0.477461
  EX_so4_e : 0.124646
  EX_k_e : 0.096617
  EX_fe2_e : 0.007950
  EX_mg2_e : 0.004294
  EX_ca2_e : 0.002576
  EX_cl_e : 0.002576
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.428749
  EX_co2_e : 37.794723
  EX_h_e : 4.836251
  EX_12ppd__S_e : 0.437047
  EX_ac_e : 0.288171
  DM_mththf_c : 0.000222
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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