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 (42 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b4381 b2406 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.345026 (mmol/gDw/h)
  Minimum Production Rate : 0.533619 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.851789
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.508662
  EX_pi_e : 1.400053
  EX_so4_e : 0.086885
  EX_k_e : 0.067347
  EX_fe2_e : 0.005541
  EX_mg2_e : 0.002993
  EX_ca2_e : 0.001796
  EX_cl_e : 0.001796
  EX_cu2_e : 0.000245
  EX_mn2_e : 0.000238
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_h2o_e : 53.375107
  EX_co2_e : 32.963766
  EX_h_e : 6.162107
  EX_ac_e : 0.810320
  Auxiliary production reaction : 0.533619
  EX_ade_e : 0.009414
  DM_5drib_c : 0.000232
  DM_4crsol_c : 0.000077

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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