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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b4382 b4069 b4384 b1278 b3708 b3008 b0871 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b3236 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b0675 b0261 b0822 b0507 b2406 b0112 b2868 b1727 b0114 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.340223 (mmol/gDw/h)
  Minimum Production Rate : 0.326006 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.936286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.654307
  EX_pi_e : 0.328182
  EX_so4_e : 0.085675
  EX_k_e : 0.066409
  EX_fe2_e : 0.005464
  EX_mg2_e : 0.002951
  EX_ca2_e : 0.001771
  EX_cl_e : 0.001771
  EX_cu2_e : 0.000241
  EX_mn2_e : 0.000235
  EX_zn2_e : 0.000116
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 44.079075
  EX_co2_e : 27.862032
  EX_h_e : 9.250935
  EX_pyr_e : 4.946830
  Auxiliary production reaction : 0.326006
  EX_ac_e : 0.198073
  EX_ade_e : 0.000381
  DM_5drib_c : 0.000228
  DM_4crsol_c : 0.000076

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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