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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4382 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b1479 b0871 b2297 b2458 b2925 b2097 b2926 b0030 b2407 b3236 b2690 b2463 b3962 b3616 b3589 b2210 b4267 b3551 b3945 b4219 b1832 b1778 b2868 b0114 b0529 b2492 b0904 b0325 b1710 b2480 b0508 b4266 b1518 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.338194 (mmol/gDw/h)
  Minimum Production Rate : 0.333051 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.977926
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.247062
  EX_pi_e : 0.659274
  EX_so4_e : 0.085164
  EX_k_e : 0.066013
  EX_mg2_e : 0.002934
  EX_fe2_e : 0.002791
  EX_fe3_e : 0.002641
  EX_ca2_e : 0.001760
  EX_cl_e : 0.001760
  EX_cu2_e : 0.000240
  EX_mn2_e : 0.000234
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 46.304504
  EX_co2_e : 26.845069
  EX_h_e : 8.981976
  EX_pyr_e : 3.080385
  EX_thymd_e : 0.630629
  Auxiliary production reaction : 0.333051
  EX_ac_e : 0.196892
  EX_ade_e : 0.000228
  EX_mththf_e : 0.000152
  DM_5drib_c : 0.000076
  DM_4crsol_c : 0.000075

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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