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 : mal__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 14: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b3942 b1732 b1241 b4069 b0871 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b1779 b2463 b3946 b2210 b0825 b1033 b3551 b2799 b3945 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b1206 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386138 (mmol/gDw/h)
  Minimum Production Rate : 0.202003 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.808174
  EX_o2_e : 279.747551
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.170260
  EX_pi_e : 0.372471
  EX_so4_e : 0.097237
  EX_k_e : 0.075371
  EX_mg2_e : 0.003350
  EX_ca2_e : 0.002010
  EX_cl_e : 0.002010
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993798
  EX_h2o_e : 543.271281
  EX_co2_e : 27.866715
  EX_pyr_e : 5.008821
  EX_ac_e : 0.224804
  EX_mal__L_e : 0.202003
  DM_5drib_c : 0.000087
  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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