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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b3617 b0030 b2883 b1779 b1982 b1623 b0411 b4381 b0112 b2868 b0114 b0529 b2492 b0904 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497065 (mmol/gDw/h)
  Minimum Production Rate : 0.469969 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.006019
  EX_nh4_e : 10.121645
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.419410
  EX_so4_e : 0.125171
  EX_k_e : 0.097024
  EX_fe2_e : 0.007983
  EX_mg2_e : 0.004312
  EX_cl_e : 0.002587
  EX_ca2_e : 0.002587
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.679301
  EX_co2_e : 25.213599
  EX_h_e : 10.839169
  EX_ac_e : 2.458489
  Auxiliary production reaction : 0.469969
  EX_hxan_e : 0.013006
  EX_ade_e : 0.000335
  DM_mththf_c : 0.000223
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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