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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b1478 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b0937 b1982 b2210 b2799 b3945 b1602 b0529 b2492 b0904 b1380 b2660 b3662 b1518 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300020 (mmol/gDw/h)
  Minimum Production Rate : 0.769460 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.829129
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.549579
  EX_pi_e : 1.828321
  EX_so4_e : 0.075551
  EX_k_e : 0.058562
  EX_fe2_e : 0.004819
  EX_mg2_e : 0.002603
  EX_ca2_e : 0.001562
  EX_cl_e : 0.001562
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 46.196159
  EX_co2_e : 31.346304
  EX_h_e : 9.002850
  EX_glyclt_e : 4.706218
  Auxiliary production reaction : 0.769460
  EX_ade_e : 0.000202
  DM_mththf_c : 0.000134
  DM_5drib_c : 0.000068
  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.

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Last updated: 21-Sep-2023
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