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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b3115 b1849 b2296 b3617 b2407 b3236 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b3551 b0261 b4219 b1832 b1778 b2406 b0114 b2366 b2492 b0904 b1533 b2835 b1710 b2480 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430179 (mmol/gDw/h)
  Minimum Production Rate : 0.956742 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.204088
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.603793
  EX_pi_e : 1.371695
  EX_so4_e : 0.108328
  EX_k_e : 0.083968
  EX_mg2_e : 0.003732
  EX_fe2_e : 0.003550
  EX_fe3_e : 0.003359
  EX_ca2_e : 0.002239
  EX_cl_e : 0.002239
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.309793
  EX_co2_e : 28.629646
  EX_h_e : 8.421339
  EX_ac_e : 1.652354
  Auxiliary production reaction : 0.956742
  EX_mal__L_e : 0.449166
  EX_xan_e : 0.000290
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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