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 : xan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 94: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b4382 b0238 b0125 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b2797 b3117 b1814 b4471 b1623 b4015 b2799 b3945 b1602 b0153 b3654 b3714 b3664 b0511 b4064 b4464 b0584 b2366 b2492 b0904 b2954 b3029 b1380 b2660 b0515 b1517 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503367 (mmol/gDw/h)
  Minimum Production Rate : 0.080386 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.752184
  EX_o2_e : 287.514887
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.757862
  EX_pi_e : 0.485551
  EX_so4_e : 0.126758
  EX_k_e : 0.098254
  EX_mg2_e : 0.004367
  EX_ca2_e : 0.002620
  EX_cl_e : 0.002620
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991915
  EX_h2o_e : 552.361900
  EX_co2_e : 38.349945
  EX_ac_e : 0.293053
  EX_xan_e : 0.080386
  DM_mththf_c : 0.000226
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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