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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b1478 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1278 b1479 b3752 b0871 b2779 b2925 b2097 b2407 b3844 b3236 b2690 b2463 b3962 b1982 b3616 b3589 b2210 b4267 b0675 b1415 b3551 b0411 b0822 b2799 b4388 b4219 b1832 b1778 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0508 b4266 b1517 b0606   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.280611 (mmol/gDw/h)
  Minimum Production Rate : 0.912577 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.778849
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.768499
  EX_pi_e : 2.095833
  EX_so4_e : 0.070664
  EX_k_e : 0.054773
  EX_fe2_e : 0.004507
  EX_mg2_e : 0.002434
  EX_ca2_e : 0.001461
  EX_cl_e : 0.001461
  EX_cu2_e : 0.000199
  EX_mn2_e : 0.000194
  EX_zn2_e : 0.000096
  EX_ni2_e : 0.000091

Product: (mmol/gDw/h)
  EX_h2o_e : 46.565768
  EX_co2_e : 26.674180
  EX_h_e : 8.671937
  EX_pyr_e : 3.683667
  Auxiliary production reaction : 0.912577
  EX_acald_e : 0.686756
  EX_fum_e : 0.292090
  DM_oxam_c : 0.000189
  EX_dxylnt_e : 0.000188
  DM_mththf_c : 0.000126
  DM_5drib_c : 0.000063
  DM_4crsol_c : 0.000063

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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