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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b3752 b0871 b2297 b2458 b2925 b2097 b2407 b3236 b2690 b2463 b3616 b3589 b2210 b3665 b4374 b2361 b2291 b3551 b0261 b3945 b2913 b4219 b1832 b1778 b0114 b0755 b3612 b0529 b2492 b0904 b1710 b2480 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.280675 (mmol/gDw/h)
  Minimum Production Rate : 1.076063 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.635126
  EX_o2_e : 278.710940
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.184338
  EX_pi_e : 1.346804
  EX_so4_e : 0.070680
  EX_k_e : 0.054786
  EX_mg2_e : 0.002435
  EX_ca2_e : 0.001461
  EX_cl_e : 0.001461
  EX_cu2_e : 0.000199
  EX_mn2_e : 0.000194
  EX_zn2_e : 0.000096
  EX_ni2_e : 0.000091

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995492
  EX_h2o_e : 545.067441
  EX_co2_e : 26.345487
  EX_pyr_e : 3.191896
  Auxiliary production reaction : 1.076063
  EX_ac_e : 0.850316
  EX_fum_e : 0.293064
  EX_ade_e : 0.000189
  DM_5drib_c : 0.000063
  DM_4crsol_c : 0.000063

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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