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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2925 b2097 b2926 b3617 b0030 b2407 b3236 b1982 b3946 b2210 b0825 b2406 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 : 0.484634 (mmol/gDw/h)
  Minimum Production Rate : 0.987827 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.617572
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.387297
  EX_pi_e : 2.443136
  EX_so4_e : 0.122041
  EX_k_e : 0.094597
  EX_fe2_e : 0.007784
  EX_mg2_e : 0.004204
  EX_ca2_e : 0.002523
  EX_cl_e : 0.002523
  EX_cu2_e : 0.000344
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.630995
  EX_co2_e : 24.575257
  EX_h_e : 8.762254
  EX_ac_e : 1.143780
  Auxiliary production reaction : 0.987827
  EX_ade_e : 0.435526
  DM_mththf_c : 0.435201
  DM_5drib_c : 0.000325
  DM_4crsol_c : 0.000108

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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