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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b1238 b0583 b2883 b2388 b1982 b0394 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b4381 b2406 b0653 b4077 b2663 b0114 b1539 b2492 b0904 b3653 b2578 b1533 b3927 b3825 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.712210 (mmol/gDw/h)
  Minimum Production Rate : 0.301690 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.343334
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.200260
  EX_pi_e : 1.290383
  EX_so4_e : 0.179349
  EX_k_e : 0.139018
  EX_fe2_e : 0.011439
  EX_mg2_e : 0.006178
  EX_ca2_e : 0.003707
  EX_cl_e : 0.003707
  EX_cu2_e : 0.000505
  EX_mn2_e : 0.000492
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.140301
  EX_co2_e : 25.109138
  EX_h_e : 7.863780
  EX_ac_e : 0.414639
  Auxiliary production reaction : 0.301690
  DM_5drib_c : 0.000478
  DM_4crsol_c : 0.000159

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
Contact