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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b1982 b2797 b3117 b1814 b4471 b3449 b4374 b0675 b2361 b2291 b0261 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.574044 (mmol/gDw/h)
  Minimum Production Rate : 0.065859 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.517379
  EX_o2_e : 283.760207
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.661273
  EX_pi_e : 0.685443
  EX_so4_e : 0.210414
  EX_k_e : 0.112049
  EX_mg2_e : 0.004980
  EX_ca2_e : 0.002988
  EX_cl_e : 0.002988
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990780
  EX_h2o_e : 551.393587
  EX_co2_e : 35.052556
  Auxiliary production reaction : 0.065859
  DM_oxam_c : 0.000642
  DM_5drib_c : 0.000385
  DM_4crsol_c : 0.000128

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