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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b2297 b2458 b3617 b0160 b2407 b3236 b0907 b2463 b1982 b2210 b0675 b2361 b3551 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1710 b2480 b1518 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.487281 (mmol/gDw/h)
  Minimum Production Rate : 1.868376 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.530715
  EX_nh4_e : 10.869034
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.470034
  EX_so4_e : 0.122707
  EX_k_e : 0.095114
  EX_mg2_e : 0.004227
  EX_fe2_e : 0.004022
  EX_fe3_e : 0.003805
  EX_cl_e : 0.002536
  EX_ca2_e : 0.002536
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000337
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.649602
  EX_co2_e : 18.193386
  EX_h_e : 12.581501
  Auxiliary production reaction : 1.868376
  EX_ac_e : 1.476346
  EX_mal__L_e : 0.508789
  EX_xan_e : 0.000328
  DM_mththf_c : 0.000218
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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