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 (80 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b0477 b4139 b1033 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b1297 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.428495 (mmol/gDw/h)
  Minimum Production Rate : 0.448533 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.855182
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.423764
  EX_pi_e : 0.861862
  EX_so4_e : 0.107904
  EX_k_e : 0.083639
  EX_fe3_e : 0.006882
  EX_mg2_e : 0.003717
  EX_ca2_e : 0.002230
  EX_cl_e : 0.002230
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.674736
  EX_co2_e : 37.424619
  EX_h_e : 5.989583
  Auxiliary production reaction : 0.448533
  EX_ac_e : 0.249464
  EX_hxan_e : 0.000479
  DM_5drib_c : 0.000288
  DM_4crsol_c : 0.000096

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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