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 (56 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b1478 b3399 b4382 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2779 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0822 b4381 b2406 b0112 b2868 b0114 b2366 b2492 b0904 b1533 b4042 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513076 (mmol/gDw/h)
  Minimum Production Rate : 0.451731 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.886460
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.691899
  EX_pi_e : 0.946647
  EX_so4_e : 0.129203
  EX_k_e : 0.100149
  EX_fe2_e : 0.008241
  EX_mg2_e : 0.004451
  EX_ca2_e : 0.002671
  EX_cl_e : 0.002671
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.385731
  EX_co2_e : 26.070213
  EX_h_e : 10.040547
  EX_ac_e : 1.723577
  EX_ade_e : 0.529058
  DM_mththf_c : 0.528714
  Auxiliary production reaction : 0.451731
  EX_xan_e : 0.013425
  DM_5drib_c : 0.000344
  EX_glyc__R_e : 0.000172
  DM_4crsol_c : 0.000114

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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