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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b1238 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b2868 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b1380 b1473 b0594   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369891 (mmol/gDw/h)
  Minimum Production Rate : 0.553412 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.438626
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.870323
  EX_pi_e : 2.017033
  EX_so4_e : 0.646557
  EX_k_e : 0.072200
  EX_fe2_e : 0.005941
  EX_mg2_e : 0.003209
  EX_ca2_e : 0.001925
  EX_cl_e : 0.001925
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 47.676139
  EX_co2_e : 26.170825
  EX_h_e : 8.238601
  EX_ac_e : 2.512191
  Auxiliary production reaction : 0.553412
  EX_pyr_e : 0.112158
  EX_hxan_e : 0.000414
  DM_5drib_c : 0.000248
  EX_dxylnt_e : 0.000247
  DM_4crsol_c : 0.000082

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.

Last updated: 21-Sep-2023
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