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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4069 b4384 b3926 b2297 b2458 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3945 b1602 b2913 b4381 b3915 b0114 b0529 b2492 b0904 b1380 b1511 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477691 (mmol/gDw/h)
  Minimum Production Rate : 0.220735 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.212233
  EX_o2_e : 287.134621
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.263989
  EX_pi_e : 0.460784
  EX_so4_e : 0.120292
  EX_k_e : 0.093242
  EX_mg2_e : 0.004144
  EX_ca2_e : 0.002486
  EX_cl_e : 0.002486
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992328
  EX_h2o_e : 552.644954
  EX_co2_e : 37.603300
  EX_ac_e : 0.278105
  EX_adn_e : 0.220735
  EX_3hpp_e : 0.007808
  EX_hxan_e : 0.000321
  DM_mththf_c : 0.000214
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000107

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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