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 : pe180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b1855 b2242 b3553 b0474 b2518 b2744 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0306 b3605 b2197 b3028 b3821 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.459875 (mmol/gDw/h)
  Minimum Production Rate : 0.242573 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.580683
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.860803
  EX_pi_e : 0.686171
  EX_so4_e : 0.115806
  EX_k_e : 0.089764
  EX_fe2_e : 0.007386
  EX_mg2_e : 0.003989
  EX_ca2_e : 0.002394
  EX_cl_e : 0.002394
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 42.937658
  EX_co2_e : 27.957309
  EX_h_e : 5.593670
  EX_succ_e : 0.479554
  EX_ura_e : 0.325812
  Auxiliary production reaction : 0.242573
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000103

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