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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b0871 b2297 b2458 b2925 b2097 b2926 b1982 b3616 b3589 b3946 b0825 b0675 b2361 b2291 b4388 b0112 b0114 b0529 b2492 b0904 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.292242 (mmol/gDw/h)
  Minimum Production Rate : 1.118651 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.608179
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.398052
  EX_pi_e : 2.519200
  EX_so4_e : 0.073592
  EX_k_e : 0.057044
  EX_fe2_e : 0.004694
  EX_mg2_e : 0.002535
  EX_cl_e : 0.001521
  EX_ca2_e : 0.001521
  EX_cu2_e : 0.000207
  EX_mn2_e : 0.000202
  EX_zn2_e : 0.000100
  EX_ni2_e : 0.000094

Product: (mmol/gDw/h)
  EX_h2o_e : 46.393231
  EX_co2_e : 26.500902
  EX_h_e : 7.912589
  EX_pyr_e : 3.217837
  Auxiliary production reaction : 1.118651
  EX_ac_e : 0.886303
  EX_alltn_e : 0.001141
  DM_mththf_c : 0.000945
  DM_5drib_c : 0.000196
  DM_4crsol_c : 0.000065

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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