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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b3236 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b2406 b0114 b2366 b2492 b0904 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.426334 (mmol/gDw/h)
  Minimum Production Rate : 0.342707 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.329084
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.319054
  EX_pi_e : 1.439364
  EX_so4_e : 0.107359
  EX_k_e : 0.083217
  EX_fe2_e : 0.006847
  EX_mg2_e : 0.003698
  EX_ca2_e : 0.002219
  EX_cl_e : 0.002219
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000295
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.977572
  EX_co2_e : 36.919364
  EX_h_e : 4.946596
  EX_acald_e : 1.076203
  Auxiliary production reaction : 0.342707
  EX_alltn_e : 0.000287
  DM_mththf_c : 0.000191
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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