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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b2297 b2458 b2779 b2925 b2097 b1612 b1611 b2883 b4122 b2690 b2797 b3117 b1814 b4471 b0411 b3945 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b0515 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383243 (mmol/gDw/h)
  Minimum Production Rate : 0.457530 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.363577
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.180132
  EX_pi_e : 1.284738
  EX_so4_e : 0.096508
  EX_k_e : 0.074806
  EX_fe2_e : 0.006155
  EX_mg2_e : 0.003325
  EX_ca2_e : 0.001995
  EX_cl_e : 0.001995
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 40.759782
  EX_co2_e : 28.811914
  EX_h_e : 7.835544
  EX_glyc__R_e : 3.666997
  Auxiliary production reaction : 0.457530
  EX_fum_e : 0.420214
  EX_ac_e : 0.223119
  EX_alltn_e : 0.010286
  DM_mththf_c : 0.000172
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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