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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b3617 b3124 b2883 b0517 b1982 b1623 b0411 b4381 b0114 b0529 b2492 b0904 b0514 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449160 (mmol/gDw/h)
  Minimum Production Rate : 0.859654 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.111638
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.289510
  EX_pi_e : 1.292917
  EX_so4_e : 0.113108
  EX_k_e : 0.087673
  EX_fe2_e : 0.007214
  EX_mg2_e : 0.003896
  EX_ca2_e : 0.002338
  EX_cl_e : 0.002338
  EX_cu2_e : 0.000318
  EX_mn2_e : 0.000310
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.237785
  EX_co2_e : 29.920507
  EX_h_e : 9.084527
  EX_ac_e : 1.517819
  Auxiliary production reaction : 0.859654
  DM_mththf_c : 0.001652
  EX_glyc__R_e : 0.001027
  DM_5drib_c : 0.000101
  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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