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 (37 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b3752 b0871 b2297 b2458 b2925 b2097 b2407 b3236 b0517 b2690 b1982 b3616 b3589 b2210 b3945 b0507 b4388 b4381 b2406 b0112 b0114 b0755 b3612 b0529 b2492 b0904 b3662 b1813 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.275983 (mmol/gDw/h)
  Minimum Production Rate : 1.058200 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.913016
  EX_o2_e : 278.960009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.155941
  EX_pi_e : 2.382615
  EX_so4_e : 0.069498
  EX_k_e : 0.053870
  EX_mg2_e : 0.002394
  EX_ca2_e : 0.001436
  EX_cl_e : 0.001436
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000191
  EX_zn2_e : 0.000094
  EX_ni2_e : 0.000089

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995567
  EX_h2o_e : 547.098704
  EX_co2_e : 26.694585
  EX_pyr_e : 3.593275
  Auxiliary production reaction : 1.058200
  EX_ac_e : 0.836103
  EX_alltn_e : 0.000186
  EX_glyclt_e : 0.000185
  EX_mththf_e : 0.000124
  DM_5drib_c : 0.000062
  DM_4crsol_c : 0.000062

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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