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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b0945 b3399 b1241 b0351 b3831 b4069 b2744 b3708 b0910 b3752 b0512 b2297 b2458 b3617 b2883 b2388 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b3565 b0261 b4381 b0837 b0124 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b0723 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448085 (mmol/gDw/h)
  Minimum Production Rate : 0.208054 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.138968
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.551983
  EX_pi_e : 0.848333
  EX_so4_e : 0.112837
  EX_k_e : 0.087463
  EX_fe2_e : 0.007197
  EX_mg2_e : 0.003887
  EX_cl_e : 0.002332
  EX_ca2_e : 0.002332
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.656613
  EX_co2_e : 32.291393
  EX_h_e : 7.794007
  EX_ac_e : 1.320944
  EX_succ_e : 0.425614
  EX_alltn_e : 0.289460
  EX_thymd_e : 0.277434
  Auxiliary production reaction : 0.208054
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

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