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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4069 b4384 b3115 b1849 b2296 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0937 b0477 b4139 b1033 b3665 b2799 b3945 b1602 b4381 b2406 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b3662 b1518 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.432302 (mmol/gDw/h)
  Minimum Production Rate : 0.503151 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.087789
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.178277
  EX_pi_e : 0.920152
  EX_so4_e : 0.108862
  EX_k_e : 0.084382
  EX_mg2_e : 0.003750
  EX_fe2_e : 0.003568
  EX_fe3_e : 0.003375
  EX_cl_e : 0.002250
  EX_ca2_e : 0.002250
  EX_cu2_e : 0.000307
  EX_mn2_e : 0.000299
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.941139
  EX_co2_e : 36.914168
  EX_h_e : 5.233520
  Auxiliary production reaction : 0.503151
  EX_etoh_e : 0.406145
  EX_ac_e : 0.251680
  DM_mththf_c : 0.000194
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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