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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1478 b3399 b0238 b0125 b1241 b4069 b2744 b3708 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b2799 b3945 b1602 b0153 b2913 b0584 b2366 b2492 b0904 b1380 b1511 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475098 (mmol/gDw/h)
  Minimum Production Rate : 0.320314 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.437729
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.434913
  EX_pi_e : 0.879362
  EX_so4_e : 0.119639
  EX_k_e : 0.092736
  EX_fe2_e : 0.007631
  EX_mg2_e : 0.004121
  EX_ca2_e : 0.002473
  EX_cl_e : 0.002473
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.361703
  EX_co2_e : 36.510188
  EX_h_e : 4.945881
  Auxiliary production reaction : 0.421080
  EX_ser__L_e : 0.302299
  EX_ac_e : 0.276595
  EX_ade_e : 0.000320
  DM_mththf_c : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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