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

Gene deletion strategy (42 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b3161 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b1533 b1473 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347523 (mmol/gDw/h)
  Minimum Production Rate : 1.039921 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.513600
  EX_nh4_e : 11.033060
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.335223
  EX_so4_e : 0.087513
  EX_k_e : 0.067834
  EX_fe2_e : 0.005582
  EX_mg2_e : 0.003015
  EX_ca2_e : 0.001809
  EX_cl_e : 0.001809
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 47.071363
  EX_co2_e : 19.174873
  EX_h_e : 14.393789
  EX_ac_e : 2.880458
  Auxiliary production reaction : 1.039921
  DM_oxam_c : 0.000389
  DM_5drib_c : 0.000233
  DM_4crsol_c : 0.000077

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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