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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1241 b0351 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b4015 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b0590 b1727 b4064 b4464 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376884 (mmol/gDw/h)
  Minimum Production Rate : 0.014219 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.143618
  EX_o2_e : 279.967720
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.120889
  EX_pi_e : 0.377763
  EX_so4_e : 0.094907
  EX_k_e : 0.073565
  EX_mg2_e : 0.003269
  EX_ca2_e : 0.001962
  EX_cl_e : 0.001962
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993947
  EX_h2o_e : 542.974313
  EX_co2_e : 29.519417
  EX_pyr_e : 4.336795
  EX_etoh_e : 0.932482
  Auxiliary production reaction : 0.014219
  EX_ade_e : 0.010115
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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