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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b3399 b4069 b2744 b3926 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b0937 b1982 b0675 b2361 b0411 b3945 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.448800 (mmol/gDw/h)
  Minimum Production Rate : 0.146731 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.103762
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.775567
  EX_pi_e : 0.579646
  EX_so4_e : 0.113017
  EX_k_e : 0.087603
  EX_fe2_e : 0.007208
  EX_mg2_e : 0.003893
  EX_ca2_e : 0.002336
  EX_cl_e : 0.002336
  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 : 51.825503
  EX_co2_e : 37.517837
  EX_h_e : 5.787924
  EX_3hpp_e : 0.474320
  EX_ac_e : 0.261285
  EX_hxan_e : 0.158777
  Auxiliary production reaction : 0.146731
  DM_mththf_c : 0.000201
  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