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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b2297 b2458 b2779 b3617 b0160 b3236 b1982 b2210 b4374 b0675 b2361 b2291 b0114 b0529 b2492 b0904 b0515 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532490 (mmol/gDw/h)
  Minimum Production Rate : 1.019139 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.233575
  EX_o2_e : 276.260466
  EX_nh4_e : 10.854858
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.571061
  EX_so4_e : 0.134092
  EX_k_e : 0.103938
  EX_mg2_e : 0.004619
  EX_ca2_e : 0.002772
  EX_cl_e : 0.002772
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991448
  EX_h2o_e : 552.675225
  EX_co2_e : 24.335413
  EX_ac_e : 1.799409
  Auxiliary production reaction : 1.019139
  EX_alltn_e : 0.002079
  EX_mththf_e : 0.001722
  DM_5drib_c : 0.000357
  DM_4crsol_c : 0.000119

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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