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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b3449 b1033 b0595 b3665 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b2366 b2492 b0904 b1533 b1473 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406619 (mmol/gDw/h)
  Minimum Production Rate : 1.216759 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.315519
  EX_nh4_e : 11.694281
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.392227
  EX_so4_e : 0.102395
  EX_k_e : 0.079369
  EX_fe2_e : 0.006531
  EX_mg2_e : 0.003527
  EX_ca2_e : 0.002116
  EX_cl_e : 0.002116
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.742173
  EX_co2_e : 19.531793
  EX_h_e : 15.626043
  EX_ac_e : 2.153245
  EX_glyclt_e : 1.217031
  Auxiliary production reaction : 1.216759
  EX_ade_e : 0.000455
  DM_5drib_c : 0.000273
  DM_4crsol_c : 0.000091

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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