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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2407 b1982 b3616 b3589 b1033 b0261 b0411 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509479 (mmol/gDw/h)
  Minimum Production Rate : 0.751972 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.486471
  EX_nh4_e : 11.664430
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.491447
  EX_so4_e : 0.128297
  EX_k_e : 0.099447
  EX_fe2_e : 0.008183
  EX_mg2_e : 0.004420
  EX_ca2_e : 0.002652
  EX_cl_e : 0.002652
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.896435
  EX_co2_e : 19.716634
  EX_h_e : 12.644523
  EX_thymd_e : 1.200834
  EX_ac_e : 1.048584
  Auxiliary production reaction : 0.751972
  DM_oxam_c : 0.000570
  DM_5drib_c : 0.000342
  DM_4crsol_c : 0.000114

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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