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 : 5aprbu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b2502 b4384 b2744 b3752 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b3908 b1656 b0937 b1982 b4139 b1033 b1623 b2361 b2291 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2913 b0114 b0529 b1539 b2492 b0904 b2954 b1380 b3662 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389966 (mmol/gDw/h)
  Minimum Production Rate : 0.544138 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.347291
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.938270
  EX_pi_e : 0.920301
  EX_so4_e : 0.098201
  EX_k_e : 0.076119
  EX_mg2_e : 0.003383
  EX_fe2_e : 0.003218
  EX_fe3_e : 0.003045
  EX_ca2_e : 0.002030
  EX_cl_e : 0.002030
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 53.018578
  EX_co2_e : 37.816779
  EX_h_e : 6.814099
  Auxiliary production reaction : 0.544138
  EX_ac_e : 0.501221
  EX_urea_e : 0.274188
  EX_hxan_e : 0.000436
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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 (2023).
[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.

Last updated: 09-Jul-2025
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