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 (44 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b0871 b2297 b2458 b2925 b2097 b3617 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b4374 b2361 b2291 b3945 b2868 b0114 b1539 b2492 b0904 b1533 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.457434 (mmol/gDw/h)
  Minimum Production Rate : 1.103119 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.736442
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.044602
  EX_pi_e : 1.544362
  EX_so4_e : 0.115191
  EX_k_e : 0.089288
  EX_fe2_e : 0.007347
  EX_mg2_e : 0.003968
  EX_ca2_e : 0.002381
  EX_cl_e : 0.002381
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.702434
  EX_co2_e : 29.106204
  EX_h_e : 6.615084
  Auxiliary production reaction : 1.103119
  EX_acald_e : 0.787003
  EX_pyr_e : 0.204526
  EX_hxan_e : 0.000308
  DM_mththf_c : 0.000205
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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