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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3553 b4382 b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b0121 b1982 b2797 b3117 b1814 b4471 b1033 b0595 b4014 b0261 b2976 b0507 b3709 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.661172 (mmol/gDw/h)
  Minimum Production Rate : 0.085951 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.710678
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.490079
  EX_pi_e : 1.283863
  EX_so4_e : 0.252447
  EX_k_e : 0.129056
  EX_fe2_e : 0.010619
  EX_mg2_e : 0.005736
  EX_ca2_e : 0.003441
  EX_cl_e : 0.003441
  EX_cu2_e : 0.000469
  EX_mn2_e : 0.000457
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000214
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.034618
  EX_co2_e : 24.527202
  EX_h_e : 8.164162
  EX_ac_e : 0.470876
  EX_fad_e : 0.194120
  Auxiliary production reaction : 0.085951
  DM_oxam_c : 0.000740
  DM_5drib_c : 0.000444
  DM_4crsol_c : 0.000147

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
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