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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2297 b2458 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0261 b0411 b2799 b3945 b1602 b4381 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b1380 b2660 b0514 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.367184 (mmol/gDw/h)
  Minimum Production Rate : 1.154993 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.505847
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.432588
  EX_pi_e : 0.354188
  EX_so4_e : 0.092464
  EX_k_e : 0.071672
  EX_fe2_e : 0.005897
  EX_mg2_e : 0.003185
  EX_ca2_e : 0.001911
  EX_cl_e : 0.001911
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 50.595541
  EX_co2_e : 32.810170
  EX_h_e : 7.701269
  Auxiliary production reaction : 1.154993
  EX_glyclt_e : 0.646634
  EX_ac_e : 0.213769
  EX_ade_e : 0.000411
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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.

Last updated: 21-Sep-2023
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