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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b2799 b3945 b1602 b0153 b4381 b2406 b1727 b0114 b0584 b0529 b2492 b0904 b3927 b1380 b2660 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400206 (mmol/gDw/h)
  Minimum Production Rate : 0.906472 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.174610
  EX_o2_e : 283.940659
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.137379
  EX_pi_e : 2.198985
  EX_so4_e : 0.100780
  EX_k_e : 0.078118
  EX_mg2_e : 0.003472
  EX_ca2_e : 0.002083
  EX_cl_e : 0.002083
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993572
  EX_h2o_e : 551.710197
  EX_co2_e : 34.241207
  Auxiliary production reaction : 0.906472
  EX_etoh_e : 0.352395
  EX_ac_e : 0.232995
  EX_ade_e : 0.000448
  DM_5drib_c : 0.000269
  DM_4crsol_c : 0.000089

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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