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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b3617 b3236 b2883 b1982 b2210 b1623 b4381 b4064 b4464 b0114 b0529 b2492 b0904 b0516 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.578688 (mmol/gDw/h)
  Minimum Production Rate : 1.107558 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.781823
  EX_nh4_e : 10.689049
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.665764
  EX_so4_e : 0.145725
  EX_k_e : 0.112956
  EX_fe2_e : 0.009294
  EX_mg2_e : 0.005020
  EX_ca2_e : 0.003012
  EX_cl_e : 0.003012
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.721712
  EX_co2_e : 21.241211
  EX_h_e : 11.712007
  EX_ac_e : 1.955523
  Auxiliary production reaction : 1.107558
  EX_alltn_e : 0.002259
  DM_mththf_c : 0.001871
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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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