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 (47 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b3115 b1849 b2296 b2779 b0160 b3844 b3236 b2463 b1982 b3616 b3589 b2210 b0675 b2361 b3551 b2913 b4219 b1832 b1778 b4381 b0114 b0529 b2492 b0904 b1710 b2480 b1517 b0606   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430273 (mmol/gDw/h)
  Minimum Production Rate : 1.649792 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.271352
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.597449
  EX_pi_e : 3.714627
  EX_so4_e : 0.108351
  EX_k_e : 0.083986
  EX_fe2_e : 0.006911
  EX_mg2_e : 0.003733
  EX_cl_e : 0.002240
  EX_ca2_e : 0.002240
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.199549
  EX_co2_e : 23.091319
  EX_h_e : 9.452965
  Auxiliary production reaction : 1.649792
  EX_ac_e : 1.303530
  EX_fum_e : 0.447585
  EX_xan_e : 0.000290
  DM_mththf_c : 0.000193
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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