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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2779 b2407 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3945 b2913 b2406 b0511 b0114 b1539 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.528852 (mmol/gDw/h)
  Minimum Production Rate : 0.304964 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.404256
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.016519
  EX_pi_e : 0.815098
  EX_so4_e : 0.133175
  EX_k_e : 0.103228
  EX_fe2_e : 0.008494
  EX_mg2_e : 0.004588
  EX_ca2_e : 0.002753
  EX_cl_e : 0.002753
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000365
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 42.558364
  EX_co2_e : 27.677957
  EX_h_e : 7.646053
  EX_ac_e : 1.856901
  DM_mththf_c : 0.639136
  EX_glyc__R_e : 0.319922
  Auxiliary production reaction : 0.304964
  DM_5drib_c : 0.000355
  DM_4crsol_c : 0.000118

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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