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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b3399 b0474 b2518 b4069 b4384 b2744 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b0030 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1982 b4139 b3946 b0825 b1033 b1623 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b1695 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363201 (mmol/gDw/h)
  Minimum Production Rate : 0.053808 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.756115
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.462654
  EX_pi_e : 0.457962
  EX_so4_e : 0.091461
  EX_k_e : 0.070894
  EX_fe3_e : 0.005833
  EX_mg2_e : 0.003151
  EX_ca2_e : 0.001890
  EX_cl_e : 0.001890
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 44.200163
  EX_co2_e : 33.208869
  EX_h_e : 9.177762
  EX_ac_e : 5.402195
  Auxiliary production reaction : 0.053808
  EX_ade_e : 0.000406
  DM_5drib_c : 0.000244
  DM_4crsol_c : 0.000081

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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