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 : dhmptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b3617 b0030 b2407 b3124 b1982 b1033 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483923 (mmol/gDw/h)
  Minimum Production Rate : 1.573117 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.879433
  EX_nh4_e : 13.092454
  EX_glc__D_e : 10.000000
  EX_pi_e : 5.186147
  EX_so4_e : 0.121861
  EX_k_e : 0.094458
  EX_fe2_e : 0.007772
  EX_mg2_e : 0.004198
  EX_ca2_e : 0.002519
  EX_cl_e : 0.002519
  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 : 55.208718
  EX_co2_e : 21.978044
  EX_h_e : 9.167235
  EX_acald_e : 1.999140
  Auxiliary production reaction : 1.573117
  DM_oxam_c : 0.000542
  DM_5drib_c : 0.000325
  EX_glyclt_e : 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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