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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b3617 b2407 b1982 b0261 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.521217 (mmol/gDw/h)
  Minimum Production Rate : 0.847175 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.095787
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.324028
  EX_pi_e : 0.502769
  EX_so4_e : 0.131253
  EX_k_e : 0.101738
  EX_fe2_e : 0.008371
  EX_mg2_e : 0.004522
  EX_ca2_e : 0.002713
  EX_cl_e : 0.002713
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000360
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 42.131848
  EX_co2_e : 22.436568
  EX_h_e : 8.179361
  EX_acald_e : 1.306029
  DM_oxam_c : 0.847758
  DM_5drib_c : 0.847525
  DM_4crsol_c : 0.847291
  Auxiliary production reaction : 0.847175
  EX_glyclt_e : 0.000349

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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