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 : ap4a_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3399 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b1238 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b3945 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.762745 (mmol/gDw/h)
  Minimum Production Rate : 0.087508 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.943436
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.113509
  EX_pi_e : 1.085779
  EX_so4_e : 0.192074
  EX_k_e : 0.148882
  EX_fe2_e : 0.012250
  EX_mg2_e : 0.006617
  EX_ca2_e : 0.003970
  EX_cl_e : 0.003970
  EX_cu2_e : 0.000541
  EX_mn2_e : 0.000527
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000246
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.800249
  EX_co2_e : 25.971146
  EX_h_e : 7.857864
  EX_pyr_e : 0.322707
  Auxiliary production reaction : 0.087508
  DM_oxam_c : 0.000854
  DM_5drib_c : 0.000512
  DM_4crsol_c : 0.000170

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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