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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b3915 b2975 b3603 b0529 b2492 b0904 b1380 b2660 b1695 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384313 (mmol/gDw/h)
  Minimum Production Rate : 0.093494 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.298419
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.378855
  EX_pi_e : 0.557697
  EX_so4_e : 0.096779
  EX_k_e : 0.075015
  EX_fe3_e : 0.006174
  EX_mg2_e : 0.003334
  EX_ca2_e : 0.002000
  EX_cl_e : 0.002000
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 53.080598
  EX_co2_e : 34.547533
  EX_h_e : 7.151103
  EX_ac_e : 0.665880
  EX_hxan_e : 0.432471
  EX_thymd_e : 0.421985
  Auxiliary production reaction : 0.093493
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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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