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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0583 b0120 b1982 b2797 b3117 b1814 b4471 b2440 b0261 b0507 b3709 b2239 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.747011 (mmol/gDw/h)
  Minimum Production Rate : 0.102855 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.347645
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.788542
  EX_pi_e : 1.029197
  EX_so4_e : 0.290968
  EX_k_e : 0.145811
  EX_fe2_e : 0.011998
  EX_mg2_e : 0.006480
  EX_ca2_e : 0.003888
  EX_cl_e : 0.003888
  EX_cu2_e : 0.000530
  EX_mn2_e : 0.000516
  EX_zn2_e : 0.000255
  EX_ni2_e : 0.000241
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.548938
  EX_co2_e : 26.043611
  EX_h_e : 7.174015
  Auxiliary production reaction : 0.102855
  DM_oxam_c : 0.000836
  DM_5drib_c : 0.000501
  DM_4crsol_c : 0.000167
  EX_g3pe_e : 0.000060

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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