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 (63 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b2913 b3915 b0452 b0529 b2492 b0904 b2954 b1298 b1380 b1985 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.352985 (mmol/gDw/h)
  Minimum Production Rate : 0.792082 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.375552
  EX_o2_e : 288.799454
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.982117
  EX_pi_e : 1.132574
  EX_so4_e : 0.088889
  EX_k_e : 0.068900
  EX_mg2_e : 0.003062
  EX_ca2_e : 0.001837
  EX_cl_e : 0.001837
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994331
  EX_h2o_e : 553.627813
  EX_co2_e : 37.969076
  Auxiliary production reaction : 0.792082
  EX_ac_e : 0.205503
  EX_hxan_e : 0.000395
  DM_5drib_c : 0.000237
  DM_4crsol_c : 0.000079

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.

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Last updated: 09-Jul-2025
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