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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b3831 b4069 b2744 b0910 b3115 b1849 b2296 b3617 b0160 b0030 b0517 b0651 b2162 b1779 b1982 b1623 b3665 b0675 b2361 b0261 b4381 b0112 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b2954 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478659 (mmol/gDw/h)
  Minimum Production Rate : 1.587284 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.310768
  EX_o2_e : 275.790264
  EX_nh4_e : 10.428791
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.461718
  EX_so4_e : 0.120536
  EX_k_e : 0.093431
  EX_mg2_e : 0.004152
  EX_ca2_e : 0.002491
  EX_cl_e : 0.002491
  EX_cu2_e : 0.000339
  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 : 999.992312
  EX_h2o_e : 548.144441
  EX_co2_e : 26.515289
  EX_ac_e : 1.611083
  Auxiliary production reaction : 1.587284
  EX_alltn_e : 0.086639
  EX_thymd_e : 0.074114
  EX_ade_e : 0.000536
  DM_5drib_c : 0.000321
  EX_glyclt_e : 0.000320
  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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