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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b4384 b2744 b0871 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b3908 b1656 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b0153 b4381 b0590 b2868 b4064 b4464 b0529 b2492 b0904 b2954 b3927 b1380 b1301 b2660 b3662 b1985 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410376 (mmol/gDw/h)
  Minimum Production Rate : 0.622241 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.232679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.545527
  EX_pi_e : 0.395851
  EX_so4_e : 0.103341
  EX_k_e : 0.080103
  EX_mg2_e : 0.003560
  EX_fe2_e : 0.003387
  EX_fe3_e : 0.003204
  EX_ca2_e : 0.002136
  EX_cl_e : 0.002136
  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 : 54.614867
  EX_co2_e : 37.552571
  EX_h_e : 6.887404
  Auxiliary production reaction : 0.622241
  EX_ade_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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