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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b1602 b4381 b2406 b0114 b0529 b2492 b0904 b1380 b0515 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434782 (mmol/gDw/h)
  Minimum Production Rate : 0.706977 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.198482
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.231662
  EX_pi_e : 1.833347
  EX_so4_e : 0.109487
  EX_k_e : 0.084866
  EX_fe2_e : 0.006983
  EX_mg2_e : 0.003772
  EX_ca2_e : 0.002263
  EX_cl_e : 0.002263
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.576756
  EX_co2_e : 32.902621
  EX_h_e : 6.824318
  EX_acald_e : 1.089544
  Auxiliary production reaction : 0.706977
  EX_alltn_e : 0.000293
  EX_glyclt_e : 0.000291
  DM_mththf_c : 0.000195
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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.

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Last updated: 21-Sep-2023
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