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 (20 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b0512 b2297 b2458 b2925 b2097 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447839 (mmol/gDw/h)
  Minimum Production Rate : 1.024250 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.855208
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.494995
  EX_pi_e : 1.456239
  EX_so4_e : 0.112775
  EX_k_e : 0.087415
  EX_fe2_e : 0.007193
  EX_mg2_e : 0.003885
  EX_cl_e : 0.002331
  EX_ca2_e : 0.002331
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.917058
  EX_co2_e : 28.438059
  EX_h_e : 7.986994
  EX_ac_e : 1.189449
  Auxiliary production reaction : 1.024250
  EX_ins_e : 0.156781
  EX_alltn_e : 0.001748
  DM_mththf_c : 0.001448
  DM_5drib_c : 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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