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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b1033 b4014 b0261 b2976 b2799 b3945 b1602 b2342 b3845 b2913 b2406 b3915 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b1300 b2954 b1380 b3662 b2285 b1378 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.426426 (mmol/gDw/h)
  Minimum Production Rate : 0.125833 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.688428
  EX_o2_e : 287.179051
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.866083
  EX_pi_e : 0.411333
  EX_so4_e : 0.107383
  EX_k_e : 0.083235
  EX_mg2_e : 0.003699
  EX_ca2_e : 0.002220
  EX_cl_e : 0.002220
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000295
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993151
  EX_h2o_e : 552.497579
  EX_co2_e : 37.838003
  EX_ade_e : 0.252143
  DM_5drib_c : 0.251952
  DM_4crsol_c : 0.251761
  Auxiliary production reaction : 0.125833

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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