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

Gene deletion strategy (24 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2926 b3617 b0030 b1238 b1851 b2883 b1982 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461134 (mmol/gDw/h)
  Minimum Production Rate : 0.678845 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.460877
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.196126
  EX_pi_e : 1.123658
  EX_so4_e : 0.116123
  EX_k_e : 0.090010
  EX_fe2_e : 0.007406
  EX_mg2_e : 0.004000
  EX_cl_e : 0.002400
  EX_ca2_e : 0.002400
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.682516
  EX_co2_e : 23.541483
  EX_h_e : 9.400312
  EX_thymd_e : 1.086090
  Auxiliary production reaction : 0.678845
  EX_ac_e : 0.268466
  EX_alltn_e : 0.001800
  DM_5drib_c : 0.001594
  DM_4crsol_c : 0.001387

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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