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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b0517 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522557 (mmol/gDw/h)
  Minimum Production Rate : 0.521230 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.432466
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.294516
  EX_pi_e : 1.546521
  EX_so4_e : 0.652820
  EX_k_e : 0.101999
  EX_fe2_e : 0.008393
  EX_mg2_e : 0.004533
  EX_ca2_e : 0.002720
  EX_cl_e : 0.002720
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.252539
  EX_co2_e : 22.067030
  EX_h_e : 9.135031
  EX_ac_e : 2.767192
  Auxiliary production reaction : 0.521230
  EX_alltn_e : 0.000585
  DM_5drib_c : 0.000351
  EX_glyclt_e : 0.000350
  DM_4crsol_c : 0.000117

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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