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 (33 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b4269 b0493 b3846 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2210 b1033 b0411 b2799 b3945 b1602 b4381 b3915 b0114 b0529 b2492 b0904 b1380 b2660 b1511 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.351658 (mmol/gDw/h)
  Minimum Production Rate : 0.328207 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.823453
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.783444
  EX_pi_e : 0.339211
  EX_so4_e : 0.088555
  EX_k_e : 0.068641
  EX_fe3_e : 0.005648
  EX_mg2_e : 0.003051
  EX_ca2_e : 0.001830
  EX_cl_e : 0.001830
  EX_cu2_e : 0.000249
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 44.308384
  EX_co2_e : 27.828306
  EX_h_e : 9.134546
  EX_pyr_e : 4.897007
  Auxiliary production reaction : 0.328207
  EX_hxa_e : 0.015149
  EX_hxan_e : 0.000237
  DM_mththf_c : 0.000158
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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.

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Last updated: 21-Sep-2023
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