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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b0937 b1982 b2210 b3551 b0261 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372989 (mmol/gDw/h)
  Minimum Production Rate : 0.020739 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.780408
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.092560
  EX_pi_e : 0.380527
  EX_so4_e : 0.093926
  EX_k_e : 0.072805
  EX_fe2_e : 0.005991
  EX_mg2_e : 0.003236
  EX_ca2_e : 0.001941
  EX_cl_e : 0.001941
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.897983
  EX_co2_e : 33.878274
  EX_h_e : 8.823545
  EX_glyclt_e : 5.311324
  Auxiliary production reaction : 0.020739
  EX_ade_e : 0.000417
  DM_5drib_c : 0.000250
  DM_4crsol_c : 0.000083

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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