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 : nadphx__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b4384 b3708 b3008 b0871 b2925 b2097 b0030 b2407 b0583 b0517 b1779 b0120 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0261 b1701 b1805 b0507 b2406 b0112 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610918 (mmol/gDw/h)
  Minimum Production Rate : 0.140227 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.453966
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.582188
  EX_pi_e : 1.009977
  EX_so4_e : 0.153841
  EX_k_e : 0.119247
  EX_fe2_e : 0.009812
  EX_mg2_e : 0.005300
  EX_ca2_e : 0.003180
  EX_cl_e : 0.003180
  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_h2o_e : 47.261293
  EX_co2_e : 26.491084
  EX_h_e : 8.145452
  EX_pyr_e : 1.828223
  Auxiliary production reaction : 0.140227
  EX_alltn_e : 0.000684
  DM_5drib_c : 0.000410
  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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