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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2407 b3124 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4374 b2361 b2291 b0261 b0411 b0112 b2789 b3127 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.450121 (mmol/gDw/h)
  Minimum Production Rate : 0.673466 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.019581
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.576027
  EX_pi_e : 2.454586
  EX_so4_e : 0.113349
  EX_k_e : 0.087860
  EX_fe2_e : 0.007229
  EX_mg2_e : 0.003905
  EX_ca2_e : 0.002343
  EX_cl_e : 0.002343
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.662638
  EX_co2_e : 23.958945
  EX_h_e : 8.541199
  EX_ac_e : 1.710141
  Auxiliary production reaction : 0.673466
  DM_oxam_c : 0.000504
  DM_5drib_c : 0.000302
  EX_glyclt_e : 0.000301
  DM_4crsol_c : 0.000100

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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