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 : cdg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2744 b0871 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4117 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b4381 b2406 b4115 b3915 b1297 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b2660 b0221 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.424882 (mmol/gDw/h)
  Minimum Production Rate : 0.187936 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.660695
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.627588
  EX_pi_e : 0.683012
  EX_so4_e : 0.106995
  EX_k_e : 0.082934
  EX_fe3_e : 0.006826
  EX_mg2_e : 0.003686
  EX_ca2_e : 0.002212
  EX_cl_e : 0.002212
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 54.397860
  EX_co2_e : 37.498423
  EX_h_e : 5.864460
  Auxiliary production reaction : 0.187919
  EX_fad_e : 0.136584
  EX_ade_e : 0.011593
  DM_5drib_c : 0.000285
  DM_4crsol_c : 0.000095

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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