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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b2836 b3399 b0474 b2518 b2502 b2744 b3708 b3008 b0871 b1004 b3713 b1109 b0046 b1982 b2797 b3117 b1814 b4471 b2210 b0675 b2361 b0261 b1602 b4381 b2406 b0114 b0755 b3612 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b1380 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480807 (mmol/gDw/h)
  Minimum Production Rate : 0.146672 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.211136
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.632694
  EX_pi_e : 0.610462
  EX_so4_e : 0.121077
  EX_k_e : 0.093850
  EX_fe2_e : 0.007722
  EX_mg2_e : 0.004171
  EX_ca2_e : 0.002503
  EX_cl_e : 0.002503
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.667445
  EX_co2_e : 39.090623
  EX_h_e : 4.711193
  Auxiliary production reaction : 0.146672
  DM_5drib_c : 0.000323
  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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