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 : gdpfuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b4382 b4069 b4384 b2744 b3752 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b0477 b4139 b1033 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b1727 b0114 b0509 b3125 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480350 (mmol/gDw/h)
  Minimum Production Rate : 0.059232 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.119140
  EX_o2_e : 287.895380
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.486048
  EX_pi_e : 0.581813
  EX_so4_e : 0.120962
  EX_k_e : 0.093761
  EX_mg2_e : 0.004167
  EX_ca2_e : 0.002500
  EX_cl_e : 0.002500
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992285
  EX_h2o_e : 552.288009
  EX_co2_e : 38.773067
  EX_ac_e : 0.279653
  Auxiliary production reaction : 0.059232
  EX_hxan_e : 0.000538
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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