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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b3926 b0871 b3617 b2407 b1004 b3713 b1109 b0046 b1982 b2210 b0261 b0411 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409370 (mmol/gDw/h)
  Minimum Production Rate : 0.970101 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.074927
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.052790
  EX_pi_e : 1.364981
  EX_so4_e : 0.103088
  EX_k_e : 0.079906
  EX_mg2_e : 0.003551
  EX_fe2_e : 0.003379
  EX_fe3_e : 0.003196
  EX_cl_e : 0.002131
  EX_ca2_e : 0.002131
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.562406
  EX_co2_e : 33.769090
  EX_h_e : 6.426180
  Auxiliary production reaction : 0.970101
  EX_thymd_e : 0.360664
  DM_5drib_c : 0.000275
  DM_4crsol_c : 0.000091

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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