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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4467 b0474 b2518 b3831 b2744 b2930 b4232 b3697 b3925 b0871 b2781 b0099 b0160 b1004 b3713 b1109 b0046 b2690 b2210 b2361 b2291 b3945 b1602 b2943 b0114 b2492 b0904 b1380 b3437 b4268 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444729 (mmol/gDw/h)
  Minimum Production Rate : 0.358295 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.830357
  EX_o2_e : 278.992366
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.803032
  EX_pi_e : 0.428988
  EX_so4_e : 0.111992
  EX_k_e : 0.086808
  EX_mg2_e : 0.003858
  EX_ca2_e : 0.002315
  EX_cl_e : 0.002315
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992857
  EX_h2o_e : 543.900921
  EX_co2_e : 28.442577
  EX_pyr_e : 3.717861
  Auxiliary production reaction : 0.358295
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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