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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2836 b1478 b2066 b1241 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b2498 b4015 b0261 b0411 b2799 b3945 b1602 b3915 b0529 b2492 b0904 b2954 b1380 b2660 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441046 (mmol/gDw/h)
  Minimum Production Rate : 0.684377 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.227783
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.373875
  EX_pi_e : 1.109812
  EX_so4_e : 0.111064
  EX_k_e : 0.086089
  EX_fe3_e : 0.007084
  EX_mg2_e : 0.003826
  EX_ca2_e : 0.002296
  EX_cl_e : 0.002296
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.224880
  EX_co2_e : 36.055078
  EX_h_e : 4.926977
  Auxiliary production reaction : 0.684377
  EX_ura_e : 0.305309
  EX_ac_e : 0.256771
  DM_5drib_c : 0.000296
  DM_4crsol_c : 0.000098

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