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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b4382 b3846 b2341 b1241 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b2799 b3945 b1602 b2913 b3915 b1539 b2492 b0904 b1380 b1518 b0606 b2285 b1008 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462377 (mmol/gDw/h)
  Minimum Production Rate : 0.257110 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.776054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.280663
  EX_pi_e : 1.217295
  EX_so4_e : 0.116437
  EX_k_e : 0.090253
  EX_fe3_e : 0.007428
  EX_mg2_e : 0.004011
  EX_cl_e : 0.002407
  EX_ca2_e : 0.002407
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.838510
  EX_co2_e : 37.029685
  EX_h_e : 5.737932
  EX_glyclt_e : 0.439968
  EX_ac_e : 0.269190
  Auxiliary production reaction : 0.257094
  EX_ade_e : 0.000311
  EX_mththf_e : 0.000207
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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