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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3752 b3926 b2297 b2458 b3617 b2407 b1004 b3713 b1109 b0046 b1982 b2210 b1033 b0261 b1602 b2406 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388833 (mmol/gDw/h)
  Minimum Production Rate : 1.490376 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.786770
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.670491
  EX_pi_e : 0.375071
  EX_so4_e : 0.097916
  EX_k_e : 0.075897
  EX_mg2_e : 0.003373
  EX_fe2_e : 0.003209
  EX_fe3_e : 0.003036
  EX_ca2_e : 0.002024
  EX_cl_e : 0.002024
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 51.335760
  EX_co2_e : 33.959703
  EX_h_e : 6.782914
  Auxiliary production reaction : 1.490376
  EX_etoh_e : 0.342310
  EX_ac_e : 0.226373
  DM_5drib_c : 0.000261
  DM_4crsol_c : 0.000087

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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