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 (55 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b3708 b3008 b0871 b2925 b2097 b2926 b0030 b2407 b2690 b2797 b3117 b1814 b4471 b3665 b3945 b4381 b2406 b0452 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.635576 (mmol/gDw/h)
  Minimum Production Rate : 0.031392 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.538418
  EX_o2_e : 276.468854
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.864163
  EX_pi_e : 0.613080
  EX_so4_e : 0.160051
  EX_k_e : 0.124060
  EX_mg2_e : 0.005514
  EX_cl_e : 0.003308
  EX_ca2_e : 0.003308
  EX_cu2_e : 0.000451
  EX_mn2_e : 0.000439
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989792
  EX_h2o_e : 546.306825
  EX_co2_e : 27.539978
  EX_pyr_e : 1.611452
  Auxiliary production reaction : 0.031392
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000142

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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