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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b1779 b2463 b0937 b1982 b2797 b3117 b1814 b4471 b2210 b1033 b3551 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b0114 b2366 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b1517 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412575 (mmol/gDw/h)
  Minimum Production Rate : 0.262517 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.400017
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.244719
  EX_pi_e : 0.660490
  EX_so4_e : 0.103895
  EX_k_e : 0.080532
  EX_fe2_e : 0.006626
  EX_mg2_e : 0.003579
  EX_ca2_e : 0.002147
  EX_cl_e : 0.002147
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.241150
  EX_co2_e : 34.266205
  EX_h_e : 8.059616
  EX_fum_e : 1.488528
  Auxiliary production reaction : 0.262517
  EX_ac_e : 0.240196
  EX_ade_e : 0.000278
  DM_mththf_c : 0.000185
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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