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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3916 b1241 b0351 b4069 b4384 b2297 b2458 b1850 b0030 b2407 b1982 b1200 b3616 b3589 b0261 b4381 b2406 b0112 b0114 b1723 b0529 b2492 b0904 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445883 (mmol/gDw/h)
  Minimum Production Rate : 1.709045 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.954032
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.944628
  EX_pi_e : 2.139146
  EX_so4_e : 1.165164
  EX_k_e : 0.087033
  EX_fe2_e : 0.007161
  EX_mg2_e : 0.003868
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.042217
  EX_co2_e : 21.591831
  EX_h_e : 11.190528
  EX_ac_e : 2.361166
  Auxiliary production reaction : 1.709045
  EX_h2s_e : 1.052882
  EX_alltn_e : 0.000499
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000099

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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