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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2502 b2744 b2297 b2458 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b1982 b4139 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b3915 b2975 b3603 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b1695 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425416 (mmol/gDw/h)
  Minimum Production Rate : 0.239345 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.062638
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.272250
  EX_pi_e : 0.410359
  EX_so4_e : 0.107128
  EX_k_e : 0.083038
  EX_fe3_e : 0.006833
  EX_mg2_e : 0.003690
  EX_ca2_e : 0.002214
  EX_cl_e : 0.002214
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.036017
  EX_co2_e : 37.253063
  EX_h_e : 6.319878
  EX_ac_e : 0.247671
  Auxiliary production reaction : 0.239345
  EX_ade_e : 0.000476
  DM_5drib_c : 0.000285
  DM_4crsol_c : 0.000095

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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