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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b4467 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3752 b0871 b2926 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0120 b0207 b3012 b1982 b1525 b4139 b1623 b2661 b4014 b0261 b2976 b0411 b2799 b1602 b0507 b4381 b3915 b2975 b3603 b0529 b2492 b0904 b2954 b1781 b3001 b1492 b3029 b1380 b0325 b2660 b1771 b3662 b1985 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404028 (mmol/gDw/h)
  Minimum Production Rate : 0.610624 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.921990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.418845
  EX_pi_e : 0.389728
  EX_so4_e : 0.101743
  EX_k_e : 0.078863
  EX_fe3_e : 0.006491
  EX_mg2_e : 0.003505
  EX_cl_e : 0.002103
  EX_ca2_e : 0.002103
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.166895
  EX_co2_e : 37.390123
  EX_h_e : 6.774238
  Auxiliary production reaction : 0.610623
  EX_acald_e : 0.263803
  EX_ade_e : 0.000452
  DM_5drib_c : 0.000271
  DM_4crsol_c : 0.000090

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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