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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2836 b3399 b0474 b2518 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b0517 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b0114 b2366 b0529 b2492 b0904 b2947 b1533 b3927 b1380 b2413   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.568856 (mmol/gDw/h)
  Minimum Production Rate : 0.193414 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.271302
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.917248
  EX_pi_e : 0.742135
  EX_so4_e : 0.143249
  EX_k_e : 0.111037
  EX_fe2_e : 0.009136
  EX_mg2_e : 0.004935
  EX_ca2_e : 0.002961
  EX_cl_e : 0.002961
  EX_cu2_e : 0.000403
  EX_mn2_e : 0.000393
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.226776
  EX_co2_e : 26.744048
  EX_h_e : 8.715873
  EX_pyr_e : 2.715345
  Auxiliary production reaction : 0.193414
  DM_5drib_c : 0.001966
  DM_4crsol_c : 0.001711

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