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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b3617 b1982 b0675 b2361 b0261 b4381 b2406 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.460290 (mmol/gDw/h)
  Minimum Production Rate : 1.740179 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.954929
  EX_nh4_e : 13.684546
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.443998
  EX_so4_e : 0.115910
  EX_k_e : 0.089845
  EX_fe2_e : 0.007393
  EX_mg2_e : 0.003993
  EX_ca2_e : 0.002396
  EX_cl_e : 0.002396
  EX_cu2_e : 0.000326
  EX_mn2_e : 0.000318
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.149905
  EX_co2_e : 20.568014
  EX_h_e : 15.381063
  EX_ac_e : 2.425722
  Auxiliary production reaction : 1.740179
  DM_oxam_c : 0.012559
  DM_5drib_c : 0.000309
  DM_4crsol_c : 0.000103

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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