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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b2937 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b0529 b2492 b0904 b2954 b1380 b1695 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443375 (mmol/gDw/h)
  Minimum Production Rate : 0.350970 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.849189
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.252774
  EX_pi_e : 0.778652
  EX_so4_e : 0.111651
  EX_k_e : 0.086544
  EX_fe3_e : 0.007121
  EX_mg2_e : 0.003846
  EX_ca2_e : 0.002308
  EX_cl_e : 0.002308
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.400464
  EX_co2_e : 37.714084
  EX_h_e : 5.803517
  Auxiliary production reaction : 0.350970
  EX_ac_e : 0.258126
  EX_ade_e : 0.012097
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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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