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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b1478 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b2744 b1479 b2297 b2458 b2779 b2925 b2097 b2926 b3617 b3236 b2883 b2690 b2463 b2210 b0675 b0822 b4381 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b4042 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446561 (mmol/gDw/h)
  Minimum Production Rate : 1.345712 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.864731
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.432066
  EX_pi_e : 4.467890
  EX_so4_e : 0.112453
  EX_k_e : 0.087165
  EX_fe2_e : 0.007172
  EX_mg2_e : 0.003874
  EX_ca2_e : 0.002324
  EX_cl_e : 0.002324
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.574057
  EX_co2_e : 24.651004
  EX_h_e : 5.280985
  Auxiliary production reaction : 1.345712
  EX_acald_e : 1.275858
  EX_ac_e : 0.259981
  EX_adn_e : 0.183565
  DM_mththf_c : 0.000200
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000100

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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