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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b3553 b3399 b4382 b0586 b1241 b0351 b4069 b2502 b2744 b3708 b1479 b3115 b1849 b2296 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0675 b2361 b1014 b4014 b0261 b2976 b0822 b2799 b0507 b3709 b4381 b2406 b3161 b0112 b0452 b4265 b2975 b0114 b3603 b0306 b1539 b3605 b2492 b0904 b1533 b1380 b1912 b1473 b4266 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301760 (mmol/gDw/h)
  Minimum Production Rate : 0.300557 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.252069
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.657191
  EX_pi_e : 1.192751
  EX_so4_e : 0.662621
  EX_k_e : 0.058901
  EX_fe2_e : 0.004847
  EX_mg2_e : 0.002618
  EX_ca2_e : 0.001571
  EX_cl_e : 0.001571
  EX_cu2_e : 0.000214
  EX_mn2_e : 0.000209
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 49.467800
  EX_co2_e : 34.598836
  EX_h_e : 5.882216
  EX_ac_e : 2.176702
  Auxiliary production reaction : 0.300557
  EX_met__L_e : 0.286075
  DM_oxam_c : 0.008234
  DM_5drib_c : 0.000202
  EX_dxylnt_e : 0.000202
  DM_4crsol_c : 0.000067

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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