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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.720361 (mmol/gDw/h)
  Minimum Production Rate : 0.148992 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.169506
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.695261
  EX_pi_e : 0.843857
  EX_so4_e : 0.490123
  EX_k_e : 0.140609
  EX_fe2_e : 0.011570
  EX_mg2_e : 0.006249
  EX_ca2_e : 0.003749
  EX_cl_e : 0.003749
  EX_cu2_e : 0.000511
  EX_mn2_e : 0.000498
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.092730
  EX_co2_e : 25.941157
  EX_h_e : 7.645051
  EX_ac_e : 0.728106
  EX_cgly_e : 0.308722
  Auxiliary production reaction : 0.148992
  EX_thym_e : 0.148992
  DM_5drib_c : 0.000483
  DM_4crsol_c : 0.000161

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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