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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b2297 b2458 b2779 b2926 b0030 b2407 b0583 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b2406 b0112 b0114 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.634063 (mmol/gDw/h)
  Minimum Production Rate : 0.125940 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.851566
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.125480
  EX_pi_e : 0.611621
  EX_so4_e : 0.159670
  EX_k_e : 0.123765
  EX_fe2_e : 0.010184
  EX_mg2_e : 0.005500
  EX_ca2_e : 0.003300
  EX_cl_e : 0.003300
  EX_cu2_e : 0.000450
  EX_mn2_e : 0.000438
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.283919
  EX_co2_e : 29.279248
  EX_h_e : 6.826285
  EX_ac_e : 0.369143
  DM_oxam_c : 0.252589
  DM_5drib_c : 0.252305
  DM_4crsol_c : 0.252021
  EX_glyc__R_e : 0.125940
  EX_etha_e : 0.025062

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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