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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0937 b1982 b4139 b1033 b1623 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b4381 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.446317 (mmol/gDw/h)
  Minimum Production Rate : 0.226461 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.860270
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.015948
  EX_pi_e : 0.883441
  EX_so4_e : 0.112391
  EX_k_e : 0.087118
  EX_mg2_e : 0.003872
  EX_fe2_e : 0.003683
  EX_fe3_e : 0.003485
  EX_ca2_e : 0.002323
  EX_cl_e : 0.002323
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.236209
  EX_co2_e : 37.215555
  EX_h_e : 5.137838
  EX_ac_e : 0.290573
  Auxiliary production reaction : 0.226461
  EX_urea_e : 0.030733
  EX_hxan_e : 0.000499
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000100

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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