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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 59
  Gene deletion: b2836 b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b4384 b3403 b3708 b0871 b2925 b2097 b2926 b1850 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1033 b1493 b3517 b2799 b3945 b1602 b0507 b2223 b4381 b2406 b3915 b1539 b2492 b0904 b2954 b1533 b3029 b1380 b1301 b2660 b3662 b1518 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421074 (mmol/gDw/h)
  Minimum Production Rate : 0.016726 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 41.647765
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.565694
  EX_pi_e : 0.406170
  EX_so4_e : 0.106036
  EX_k_e : 0.082191
  EX_fe3_e : 0.006765
  EX_mg2_e : 0.003653
  EX_cl_e : 0.002192
  EX_ca2_e : 0.002192
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.716323
  EX_co2_e : 42.564047
  EX_h_e : 3.910608
  Auxiliary production reaction : 0.016717
  EX_ade_e : 0.000283
  EX_mththf_e : 0.000189
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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