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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b1478 b1241 b0351 b0910 b0871 b2925 b2097 b3236 b1779 b2690 b3962 b1302 b2662 b3616 b3589 b4267 b1033 b0675 b0822 b2799 b0726 b4381 b0114 b2492 b0904 b0515 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.424832 (mmol/gDw/h)
  Minimum Production Rate : 0.342550 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.262632
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.588151
  EX_pi_e : 0.409796
  EX_so4_e : 0.106981
  EX_k_e : 0.082924
  EX_fe2_e : 0.006823
  EX_mg2_e : 0.003685
  EX_ca2_e : 0.002211
  EX_cl_e : 0.002211
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 43.729527
  EX_co2_e : 28.512680
  EX_h_e : 8.244282
  EX_pyr_e : 3.998204
  Auxiliary production reaction : 0.342550
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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