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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2779 b3617 b0160 b1779 b1982 b0675 b2361 b0261 b4381 b0112 b2868 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505934 (mmol/gDw/h)
  Minimum Production Rate : 0.809097 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.905657
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.565309
  EX_pi_e : 2.106220
  EX_so4_e : 0.936501
  EX_k_e : 0.098755
  EX_fe2_e : 0.008126
  EX_mg2_e : 0.004389
  EX_ca2_e : 0.002633
  EX_cl_e : 0.002633
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 51.764254
  EX_co2_e : 26.951782
  EX_h_e : 7.131796
  EX_acald_e : 2.060421
  Auxiliary production reaction : 0.809097
  EX_xan_e : 0.013238
  EX_ade_e : 0.000566
  DM_5drib_c : 0.000339
  DM_4crsol_c : 0.000113

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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