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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b3399 b1241 b3831 b4069 b2744 b2297 b2458 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b1982 b4139 b2498 b1033 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b0590 b0509 b3125 b0529 b2492 b0904 b2954 b1380 b2660 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.457540 (mmol/gDw/h)
  Minimum Production Rate : 0.081376 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.859755
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.619569
  EX_pi_e : 0.604098
  EX_so4_e : 0.115218
  EX_k_e : 0.089309
  EX_mg2_e : 0.003969
  EX_fe2_e : 0.003776
  EX_fe3_e : 0.003572
  EX_ca2_e : 0.002381
  EX_cl_e : 0.002381
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.322194
  EX_co2_e : 36.761870
  EX_h_e : 5.908054
  EX_ura_e : 0.553248
  EX_ac_e : 0.266373
  Auxiliary production reaction : 0.081376
  EX_hxan_e : 0.000512
  DM_5drib_c : 0.000307
  DM_4crsol_c : 0.000102

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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