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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b1727 b0114 b0529 b1539 b2492 b0904 b3035 b1380 b2660 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410488 (mmol/gDw/h)
  Minimum Production Rate : 0.371904 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.504229
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.294597
  EX_pi_e : 1.139768
  EX_so4_e : 0.103369
  EX_k_e : 0.080124
  EX_fe2_e : 0.006593
  EX_mg2_e : 0.003561
  EX_ca2_e : 0.002137
  EX_cl_e : 0.002137
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.500057
  EX_co2_e : 35.996803
  EX_h_e : 5.872069
  EX_etoh_e : 0.547400
  Auxiliary production reaction : 0.371904
  EX_ac_e : 0.238981
  EX_hxan_e : 0.000459
  DM_5drib_c : 0.000275
  DM_4crsol_c : 0.000092

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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