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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b2836 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2937 b4139 b3665 b0675 b2361 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b1517 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.331963 (mmol/gDw/h)
  Minimum Production Rate : 0.518535 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.210728
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.810200
  EX_pi_e : 0.320214
  EX_so4_e : 0.083595
  EX_k_e : 0.064797
  EX_fe3_e : 0.005332
  EX_mg2_e : 0.002880
  EX_cl_e : 0.001728
  EX_ca2_e : 0.001728
  EX_cu2_e : 0.000235
  EX_mn2_e : 0.000229
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 52.959119
  EX_co2_e : 35.745504
  EX_h_e : 7.289253
  EX_acald_e : 1.339651
  EX_his__L_e : 0.544117
  Auxiliary production reaction : 0.518535
  EX_glyclt_e : 0.008686
  DM_mththf_c : 0.000149
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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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