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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3916 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b3617 b0030 b2407 b1851 b1982 b1200 b0261 b4381 b2406 b0112 b0114 b1723 b0529 b2492 b0904 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483539 (mmol/gDw/h)
  Minimum Production Rate : 1.571869 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.812829
  EX_nh4_e : 13.083690
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.466425
  EX_so4_e : 0.169503
  EX_k_e : 0.094383
  EX_fe2_e : 0.007766
  EX_mg2_e : 0.004195
  EX_cl_e : 0.002517
  EX_ca2_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.499182
  EX_co2_e : 22.007775
  EX_h_e : 12.208984
  EX_acald_e : 1.997554
  Auxiliary production reaction : 1.571869
  EX_h2s_e : 0.047738
  EX_alltn_e : 0.000541
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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