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 : 25drapp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2502 b4384 b2744 b0871 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b3908 b1656 b0937 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b4381 b0755 b3612 b0529 b2492 b0904 b1300 b2954 b1380 b2660 b1985 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397385 (mmol/gDw/h)
  Minimum Production Rate : 0.602543 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.921753
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.306218
  EX_pi_e : 0.985863
  EX_so4_e : 0.100069
  EX_k_e : 0.077567
  EX_mg2_e : 0.003447
  EX_fe2_e : 0.003280
  EX_fe3_e : 0.003103
  EX_ca2_e : 0.002068
  EX_cl_e : 0.002068
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 54.784896
  EX_co2_e : 38.263175
  EX_h_e : 6.668929
  Auxiliary production reaction : 0.602543
  EX_hxan_e : 0.000445
  DM_5drib_c : 0.000267
  DM_4crsol_c : 0.000089

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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