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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2779 b2925 b2097 b3617 b0030 b2407 b3236 b0907 b2690 b1982 b2210 b3665 b3945 b2406 b0112 b0114 b0529 b2492 b0904 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300766 (mmol/gDw/h)
  Minimum Production Rate : 1.153222 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.927530
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.708925
  EX_pi_e : 0.290121
  EX_so4_e : 0.075739
  EX_k_e : 0.058707
  EX_fe2_e : 0.004831
  EX_mg2_e : 0.002609
  EX_cl_e : 0.001565
  EX_ca2_e : 0.001565
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 45.432584
  EX_co2_e : 29.415609
  EX_h_e : 10.153526
  EX_ac_e : 3.929223
  Auxiliary production reaction : 1.153222
  EX_ade_e : 0.000202
  DM_mththf_c : 0.000135
  DM_5drib_c : 0.000068
  EX_glyc__R_e : 0.000067
  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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