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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b2744 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b0153 b0452 b0591 b2197 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.640005 (mmol/gDw/h)
  Minimum Production Rate : 0.337912 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.108713
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.819716
  EX_pi_e : 0.617353
  EX_so4_e : 0.161166
  EX_k_e : 0.124924
  EX_fe2_e : 0.010279
  EX_mg2_e : 0.005552
  EX_ca2_e : 0.003331
  EX_cl_e : 0.003331
  EX_cu2_e : 0.000454
  EX_mn2_e : 0.000442
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 43.000758
  EX_co2_e : 23.163312
  EX_h_e : 8.461034
  EX_succ_e : 0.667392
  EX_ura_e : 0.453858
  Auxiliary production reaction : 0.337912
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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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