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 (55 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4382 b3942 b1732 b3846 b2341 b1241 b0351 b4384 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b2799 b3945 b1602 b3915 b1727 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366709 (mmol/gDw/h)
  Minimum Production Rate : 0.096716 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.250311
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.960427
  EX_pi_e : 0.450446
  EX_so4_e : 0.092345
  EX_k_e : 0.071579
  EX_fe3_e : 0.005890
  EX_mg2_e : 0.003181
  EX_ca2_e : 0.001909
  EX_cl_e : 0.001909
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 43.420590
  EX_co2_e : 28.425651
  EX_h_e : 8.689469
  EX_pyr_e : 5.314110
  Auxiliary production reaction : 0.096716
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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