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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b0529 b2492 b0904 b1380 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.350292 (mmol/gDw/h)
  Minimum Production Rate : 1.083528 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.438097
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.997972
  EX_pi_e : 1.421422
  EX_so4_e : 0.088211
  EX_k_e : 0.068375
  EX_fe2_e : 0.005626
  EX_mg2_e : 0.003039
  EX_cl_e : 0.001823
  EX_ca2_e : 0.001823
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 47.841753
  EX_co2_e : 33.078284
  EX_h_e : 7.346986
  EX_ac_e : 1.913516
  Auxiliary production reaction : 1.083528
  EX_ade_e : 0.009558
  DM_5drib_c : 0.000235
  DM_4crsol_c : 0.000078

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.

Last updated: 21-Sep-2023
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