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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 66
  Gene deletion: b2836 b3399 b3942 b1732 b0474 b2518 b1241 b0351 b2502 b2744 b3708 b3008 b1479 b0871 b2925 b2097 b2926 b3844 b1238 b3236 b2690 b2463 b3962 b0593 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4267 b2265 b0675 b2361 b1415 b3551 b1014 b2799 b3945 b4219 b1832 b1778 b4381 b2406 b2868 b0114 b0886 b0509 b3125 b2366 b2492 b0904 b2578 b1533 b3927 b1380 b1710 b2480 b1511 b4266 b4141 b1798 b1813 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352520 (mmol/gDw/h)
  Minimum Production Rate : 0.081117 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.077119
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.213855
  EX_pi_e : 0.502236
  EX_so4_e : 0.088772
  EX_k_e : 0.068809
  EX_fe2_e : 0.005663
  EX_mg2_e : 0.003058
  EX_ca2_e : 0.001835
  EX_cl_e : 0.001835
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.805652
  EX_co2_e : 27.831799
  EX_h_e : 8.991016
  EX_pyr_e : 5.384462
  Auxiliary production reaction : 0.081097
  EX_mal__L_e : 0.061492
  EX_ade_e : 0.000237
  DM_mththf_c : 0.000158
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000079

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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