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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1478 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b0160 b2690 b0675 b2361 b2291 b0822 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403657 (mmol/gDw/h)
  Minimum Production Rate : 0.091033 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.244755
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.632835
  EX_pi_e : 0.389370
  EX_so4_e : 0.101649
  EX_k_e : 0.078791
  EX_fe2_e : 0.006483
  EX_mg2_e : 0.003502
  EX_ca2_e : 0.002101
  EX_cl_e : 0.002101
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.451176
  EX_co2_e : 37.243602
  EX_h_e : 4.846024
  EX_ac_e : 0.590184
  DM_oxam_c : 0.273370
  Auxiliary production reaction : 0.091033
  EX_glyc__R_e : 0.000135
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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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