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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b3617 b2407 b0517 b1982 b0507 b4381 b2406 b2943 b0837 b0124 b0114 b0529 b2492 b0904 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412716 (mmol/gDw/h)
  Minimum Production Rate : 0.789903 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.850795
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.413257
  EX_pi_e : 1.188011
  EX_so4_e : 0.103930
  EX_k_e : 0.080559
  EX_fe2_e : 0.006629
  EX_mg2_e : 0.003580
  EX_ca2_e : 0.002148
  EX_cl_e : 0.002148
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 52.745755
  EX_co2_e : 32.356953
  EX_h_e : 9.143100
  EX_ac_e : 1.394665
  Auxiliary production reaction : 0.789903
  EX_alltn_e : 0.001611
  DM_mththf_c : 0.001334
  DM_5drib_c : 0.000277
  EX_glyclt_e : 0.000276
  DM_4crsol_c : 0.000092

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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