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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b0030 b2407 b2797 b3117 b1814 b4471 b0595 b3665 b3709 b2406 b3161 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b3447 b1511 b4141 b1798 b3662 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.535776 (mmol/gDw/h)
  Minimum Production Rate : 0.136554 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.552443
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.742216
  EX_pi_e : 0.926475
  EX_so4_e : 0.271473
  EX_k_e : 0.104580
  EX_mg2_e : 0.004648
  EX_fe2_e : 0.004422
  EX_fe3_e : 0.004183
  EX_cl_e : 0.002789
  EX_ca2_e : 0.002789
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000370
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.847311
  EX_co2_e : 33.833400
  EX_h_e : 5.785247
  EX_ac_e : 0.448475
  Auxiliary production reaction : 0.136554
  EX_mththf_e : 0.000240
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000119

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