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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 73
  Gene deletion: b3553 b1478 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b1479 b3752 b0871 b2779 b2926 b3617 b2407 b3236 b0120 b2463 b3962 b1982 b1302 b2662 b0104 b2797 b3117 b1814 b4471 b2210 b1746 b4267 b1033 b1415 b3551 b1014 b4014 b0261 b2976 b2799 b3945 b1907 b2913 b4219 b1832 b1778 b2406 b0112 b2789 b3127 b4265 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b2835 b1380 b1710 b2480 b1473 b0494 b0594 b4266 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375607 (mmol/gDw/h)
  Minimum Production Rate : 0.252939 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.182200
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.888978
  EX_so4_e : 0.420765
  EX_pi_e : 0.362313
  EX_k_e : 0.073316
  EX_mg2_e : 0.003258
  EX_fe2_e : 0.003101
  EX_fe3_e : 0.002933
  EX_ca2_e : 0.001955
  EX_cl_e : 0.001955
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 49.524888
  EX_co2_e : 36.145954
  EX_h_e : 4.419968
  EX_acald_e : 1.225496
  EX_fum_e : 0.392521
  EX_met__L_e : 0.326179
  EX_trp__L_e : 0.252927
  DM_oxam_c : 0.000420
  DM_5drib_c : 0.000252
  EX_dxylnt_e : 0.000251
  DM_4crsol_c : 0.000084

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