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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b0871 b2779 b2926 b3617 b1238 b1982 b0675 b2361 b0261 b2913 b4381 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415603 (mmol/gDw/h)
  Minimum Production Rate : 1.351026 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.674515
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.893049
  EX_pi_e : 0.400893
  EX_so4_e : 0.104657
  EX_k_e : 0.081123
  EX_fe2_e : 0.006675
  EX_mg2_e : 0.003605
  EX_ca2_e : 0.002163
  EX_cl_e : 0.002163
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.476116
  EX_co2_e : 26.043072
  EX_h_e : 9.223763
  EX_acald_e : 2.368618
  Auxiliary production reaction : 1.351026
  DM_oxam_c : 0.000465
  DM_5drib_c : 0.000279
  DM_4crsol_c : 0.000093

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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