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 : 6hmhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b0261 b0411 b3945 b1602 b4381 b3915 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479148 (mmol/gDw/h)
  Minimum Production Rate : 0.061524 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.412560
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.482383
  EX_pi_e : 0.462190
  EX_so4_e : 0.120659
  EX_k_e : 0.093526
  EX_fe3_e : 0.007696
  EX_mg2_e : 0.004157
  EX_ca2_e : 0.002494
  EX_cl_e : 0.002494
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.547672
  EX_co2_e : 39.283294
  EX_h_e : 4.923965
  EX_3hpp_e : 0.206042
  Auxiliary production reaction : 0.061524
  DM_5drib_c : 0.000322
  DM_4crsol_c : 0.000107

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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