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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b3926 b0871 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4139 b1623 b3665 b0261 b1602 b2406 b3915 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1771 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479146 (mmol/gDw/h)
  Minimum Production Rate : 0.092636 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.126542
  EX_o2_e : 288.614068
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.637913
  EX_pi_e : 0.462187
  EX_so4_e : 0.120658
  EX_k_e : 0.093526
  EX_mg2_e : 0.004157
  EX_ca2_e : 0.002494
  EX_cl_e : 0.002494
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000331
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992304
  EX_h2o_e : 553.074971
  EX_co2_e : 39.406909
  Auxiliary production reaction : 0.092636
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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