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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b4069 b4384 b3752 b3926 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b1602 b4381 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b2660 b1518 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484466 (mmol/gDw/h)
  Minimum Production Rate : 0.159939 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.778886
  EX_o2_e : 287.234393
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.031886
  EX_pi_e : 0.947135
  EX_so4_e : 0.121998
  EX_k_e : 0.094564
  EX_mg2_e : 0.004203
  EX_ca2_e : 0.002522
  EX_cl_e : 0.002522
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992219
  EX_h2o_e : 552.978983
  EX_co2_e : 37.950322
  EX_ac_e : 0.282049
  Auxiliary production reaction : 0.159939
  DM_mththf_c : 0.000217
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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