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 (74 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b3399 b3942 b1732 b0474 b2518 b4384 b2744 b3708 b3008 b3752 b3926 b0871 b3115 b1849 b2296 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b3665 b1602 b4381 b2406 b0452 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3927 b1380 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420694 (mmol/gDw/h)
  Minimum Production Rate : 0.291090 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.208916
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.834548
  EX_pi_e : 0.405804
  EX_so4_e : 0.105939
  EX_k_e : 0.082117
  EX_fe2_e : 0.006757
  EX_mg2_e : 0.003650
  EX_ca2_e : 0.002190
  EX_cl_e : 0.002190
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.032101
  EX_co2_e : 28.454990
  EX_h_e : 8.333252
  EX_pyr_e : 3.885570
  Auxiliary production reaction : 0.291090
  DM_mththf_c : 0.000188
  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