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 : udp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b2242 b1478 b0469 b4382 b1241 b4069 b4384 b2744 b3614 b0910 b2297 b2458 b2926 b2781 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3908 b1656 b0207 b1759 b3012 b4374 b0675 b2799 b1602 b4138 b4123 b0621 b3915 b0529 b2492 b0904 b1781 b3001 b3028 b1380 b3918 b0325 b4042 b2660 b1771 b1206 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333046 (mmol/gDw/h)
  Minimum Production Rate : 0.700029 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.826727
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.117494
  EX_pi_e : 1.721316
  EX_so4_e : 0.083868
  EX_k_e : 0.065008
  EX_fe3_e : 0.005349
  EX_mg2_e : 0.002889
  EX_ca2_e : 0.001734
  EX_cl_e : 0.001734
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 49.265887
  EX_co2_e : 33.701416
  EX_h_e : 6.929692
  EX_succ_e : 0.870671
  EX_ac_e : 0.779096
  Auxiliary production reaction : 0.700029
  EX_glyclt_e : 0.523149
  EX_ura_e : 0.060282
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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