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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4381 b2406 b2868 b0114 b1539 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610558 (mmol/gDw/h)
  Minimum Production Rate : 0.609280 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.316919
  EX_o2_e : 272.289896
  EX_nh4_e : 10.251292
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.198227
  EX_so4_e : 0.153751
  EX_k_e : 0.119177
  EX_mg2_e : 0.005297
  EX_ca2_e : 0.003178
  EX_cl_e : 0.003178
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990194
  EX_h2o_e : 546.418274
  EX_co2_e : 21.766424
  EX_ac_e : 2.624465
  Auxiliary production reaction : 0.609280
  EX_hxan_e : 0.000411
  EX_mththf_e : 0.000274
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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