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 (44 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b3617 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b0591 b1533 b3821 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.348503 (mmol/gDw/h)
  Minimum Production Rate : 1.042854 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.402233
  EX_nh4_e : 11.064177
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.336168
  EX_so4_e : 0.087760
  EX_k_e : 0.068025
  EX_fe2_e : 0.005597
  EX_mg2_e : 0.003023
  EX_ca2_e : 0.001814
  EX_cl_e : 0.001814
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000241
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 47.034899
  EX_co2_e : 19.059730
  EX_h_e : 14.434385
  EX_ac_e : 2.888582
  Auxiliary production reaction : 1.042854
  DM_oxam_c : 0.000390
  DM_5drib_c : 0.000234
  DM_4crsol_c : 0.000078

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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