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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4069 b2744 b3708 b3008 b3115 b1849 b2296 b1238 b0583 b2883 b2388 b2688 b2797 b3117 b1814 b4471 b2440 b3565 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b0494 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.712143 (mmol/gDw/h)
  Minimum Production Rate : 0.103720 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.615633
  EX_o2_e : 274.078952
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.611666
  EX_pi_e : 0.998096
  EX_so4_e : 0.477600
  EX_k_e : 0.139005
  EX_mg2_e : 0.006178
  EX_ca2_e : 0.003707
  EX_cl_e : 0.003707
  EX_cu2_e : 0.000505
  EX_mn2_e : 0.000492
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988562
  EX_h2o_e : 547.351399
  EX_co2_e : 26.191629
  EX_ac_e : 0.712868
  EX_met__L_e : 0.194549
  Auxiliary production reaction : 0.103720
  DM_mththf_c : 0.000319
  DM_5drib_c : 0.000160
  DM_4crsol_c : 0.000159

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