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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b3752 b0871 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b1602 b0153 b1727 b0114 b0584 b0529 b2492 b0904 b1380 b2660 b1771 b1511 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460763 (mmol/gDw/h)
  Minimum Production Rate : 0.018524 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.479503
  EX_o2_e : 285.373968
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.255624
  EX_pi_e : 0.444455
  EX_so4_e : 0.116029
  EX_k_e : 0.089938
  EX_mg2_e : 0.003997
  EX_cl_e : 0.002398
  EX_ca2_e : 0.002398
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992600
  EX_h2o_e : 549.469960
  EX_co2_e : 37.299222
  EX_12ppd__S_e : 0.774179
  EX_ade_e : 0.055884
  DM_mththf_c : 0.055780
  Auxiliary production reaction : 0.018524
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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