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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b4467 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b1779 b2463 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4374 b2361 b2291 b3551 b0261 b0411 b1602 b4219 b1832 b1778 b1727 b0114 b1539 b2492 b0904 b1533 b3821 b1380 b1710 b2480 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373888 (mmol/gDw/h)
  Minimum Production Rate : 0.578752 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.998835
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.238569
  EX_pi_e : 0.939406
  EX_so4_e : 0.094152
  EX_k_e : 0.072980
  EX_mg2_e : 0.003243
  EX_fe2_e : 0.003086
  EX_fe3_e : 0.002919
  EX_ca2_e : 0.001946
  EX_cl_e : 0.001946
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 48.687452
  EX_co2_e : 34.478856
  EX_h_e : 6.435386
  EX_etoh_e : 0.643681
  Auxiliary production reaction : 0.578752
  EX_his__L_e : 0.540063
  EX_ac_e : 0.217672
  EX_hxan_e : 0.000418
  DM_5drib_c : 0.000251
  DM_4crsol_c : 0.000083

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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