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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b4384 b2744 b2297 b2458 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b3915 b0452 b0529 b2492 b0904 b2954 b3927 b1380 b2660 b1985 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.362714 (mmol/gDw/h)
  Minimum Production Rate : 0.813913 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.215138
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.988872
  EX_pi_e : 0.349876
  EX_so4_e : 0.091339
  EX_k_e : 0.070799
  EX_fe3_e : 0.005826
  EX_mg2_e : 0.003147
  EX_cl_e : 0.001888
  EX_ca2_e : 0.001888
  EX_cu2_e : 0.000257
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 54.266506
  EX_co2_e : 37.361874
  EX_h_e : 7.621346
  Auxiliary production reaction : 0.813913
  EX_ac_e : 0.211167
  EX_ade_e : 0.000406
  DM_5drib_c : 0.000243
  DM_4crsol_c : 0.000081

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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