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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b0871 b2297 b2458 b2925 b2097 b0160 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b3945 b0507 b0112 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b3035 b2578 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572987 (mmol/gDw/h)
  Minimum Production Rate : 0.242670 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.206803
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.887545
  EX_pi_e : 1.280716
  EX_so4_e : 0.144290
  EX_k_e : 0.111843
  EX_fe2_e : 0.009203
  EX_mg2_e : 0.004971
  EX_ca2_e : 0.002982
  EX_cl_e : 0.002982
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.586482
  EX_co2_e : 26.043334
  EX_h_e : 8.370510
  EX_pyr_e : 1.557456
  EX_ac_e : 0.333585
  Auxiliary production reaction : 0.242670
  DM_oxam_c : 0.000641
  DM_5drib_c : 0.000384
  DM_4crsol_c : 0.000128

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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