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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2779 b3617 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b0755 b3612 b2492 b0904 b1533 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.451309 (mmol/gDw/h)
  Minimum Production Rate : 0.225075 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.952938
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.250740
  EX_pi_e : 1.110562
  EX_so4_e : 1.013951
  EX_mobd_e : 0.225079
  EX_k_e : 0.088092
  EX_fe2_e : 0.007248
  EX_mg2_e : 0.003915
  EX_ca2_e : 0.002349
  EX_cl_e : 0.002349
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.512471
  EX_co2_e : 27.690309
  EX_h_e : 8.338664
  EX_ac_e : 3.515618
  Auxiliary production reaction : 0.225075
  DM_oxam_c : 0.000505
  DM_5drib_c : 0.000303
  DM_4crsol_c : 0.000101

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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