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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b2744 b3752 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b1982 b2210 b0261 b0411 b2799 b3945 b1602 b0153 b4381 b2868 b4064 b4464 b2975 b3603 b0529 b2492 b0904 b0591 b1380 b2660 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.337012 (mmol/gDw/h)
  Minimum Production Rate : 0.855064 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.721622
  EX_o2_e : 284.487631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.105938
  EX_pi_e : 1.180148
  EX_so4_e : 0.084866
  EX_k_e : 0.065782
  EX_mg2_e : 0.002924
  EX_ca2_e : 0.001754
  EX_cl_e : 0.001754
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000233
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994587
  EX_h2o_e : 551.487971
  EX_co2_e : 33.084636
  EX_acald_e : 0.937952
  Auxiliary production reaction : 0.855064
  EX_gsn_e : 0.008818
  EX_ade_e : 0.000377
  DM_5drib_c : 0.000226
  DM_4crsol_c : 0.000075

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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