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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b2744 b1479 b2297 b2458 b2925 b2097 b3617 b0160 b3236 b1779 b2690 b2463 b1982 b2210 b0675 b2361 b3945 b4381 b2406 b0112 b2868 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461531 (mmol/gDw/h)
  Minimum Production Rate : 1.429538 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.446407
  EX_nh4_e : 10.112840
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.304272
  EX_so4_e : 0.116223
  EX_k_e : 0.090088
  EX_fe2_e : 0.007413
  EX_mg2_e : 0.004004
  EX_ca2_e : 0.002402
  EX_cl_e : 0.002402
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.603157
  EX_co2_e : 24.858022
  EX_h_e : 8.208234
  Auxiliary production reaction : 1.429538
  EX_acald_e : 0.576155
  EX_ac_e : 0.268697
  EX_ade_e : 0.158286
  DM_mththf_c : 0.157976
  EX_xan_e : 0.012076
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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