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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b0477 b4139 b0261 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.387791 (mmol/gDw/h)
  Minimum Production Rate : 0.107593 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.031343
  EX_o2_e : 282.241598
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.512624
  EX_pi_e : 0.481658
  EX_so4_e : 0.097654
  EX_k_e : 0.075694
  EX_mg2_e : 0.003364
  EX_ca2_e : 0.002018
  EX_cl_e : 0.002018
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993772
  EX_h2o_e : 544.064139
  EX_co2_e : 32.962118
  EX_ac_e : 5.074737
  Auxiliary production reaction : 0.107593
  EX_hxan_e : 0.000434
  DM_5drib_c : 0.000260
  DM_4crsol_c : 0.000086

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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