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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 65
  Gene deletion: b3553 b3399 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b1479 b0871 b2779 b0160 b3236 b1779 b2690 b0121 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0595 b4374 b0675 b2361 b2291 b1748 b1415 b1014 b4014 b0261 b2976 b2799 b3945 b0507 b1907 b0112 b0452 b1444 b0837 b0124 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b1473 b3715 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387239 (mmol/gDw/h)
  Minimum Production Rate : 0.086637 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.731446
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.125714
  EX_pi_e : 0.633426
  EX_so4_e : 0.520860
  EX_k_e : 0.075586
  EX_fe2_e : 0.006221
  EX_mg2_e : 0.003359
  EX_ca2_e : 0.002016
  EX_cl_e : 0.002016
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 50.706567
  EX_co2_e : 37.987107
  EX_h_e : 3.569044
  EX_acald_e : 1.176384
  EX_met__L_e : 0.336714
  Auxiliary production reaction : 0.086631
  DM_oxam_c : 0.000433
  DM_5drib_c : 0.000260
  EX_dxylnt_e : 0.000259
  DM_4crsol_c : 0.000086

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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