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 : prfp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b2366 b2492 b0904 b1533 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.546711 (mmol/gDw/h)
  Minimum Production Rate : 0.817984 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 988.800782
  EX_o2_e : 272.010756
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.994354
  EX_pi_e : 2.163329
  EX_so4_e : 0.137673
  EX_k_e : 0.106714
  EX_mg2_e : 0.004743
  EX_ca2_e : 0.002846
  EX_cl_e : 0.002846
  EX_cu2_e : 0.000388
  EX_mn2_e : 0.000378
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991219
  EX_h2o_e : 546.201337
  EX_co2_e : 21.134806
  EX_ac_e : 2.077117
  Auxiliary production reaction : 0.817984
  DM_5drib_c : 0.000367
  DM_4crsol_c : 0.000122

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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