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 (54 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b0822 b2406 b2789 b3127 b1727 b0114 b2366 b2492 b0904 b1533 b0789 b1249 b0516 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522531 (mmol/gDw/h)
  Minimum Production Rate : 0.361077 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.605105
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.412247
  EX_pi_e : 0.865114
  EX_so4_e : 0.131584
  EX_k_e : 0.101994
  EX_fe2_e : 0.008392
  EX_mg2_e : 0.004533
  EX_ca2_e : 0.002720
  EX_cl_e : 0.002720
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.370929
  EX_co2_e : 26.275309
  EX_h_e : 9.736435
  EX_ac_e : 1.804829
  EX_alltn_e : 0.601969
  DM_mththf_c : 0.601619
  Auxiliary production reaction : 0.361077
  DM_5drib_c : 0.000351
  EX_glyclt_e : 0.000350
  DM_4crsol_c : 0.000117

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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