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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b1479 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b0030 b2407 b3236 b2690 b2463 b2210 b3945 b2406 b2943 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b3437 b4268 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.533841 (mmol/gDw/h)
  Minimum Production Rate : 0.072439 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 988.380587
  EX_o2_e : 274.929997
  EX_nh4_e : 11.835845
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.732263
  EX_so4_e : 0.134432
  EX_k_e : 0.104202
  EX_mg2_e : 0.004631
  EX_ca2_e : 0.002779
  EX_cl_e : 0.002779
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000369
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991426
  EX_h2o_e : 550.619737
  EX_co2_e : 24.023750
  EX_his__L_e : 1.975178
  EX_ac_e : 0.780165
  Auxiliary production reaction : 0.072439
  EX_mththf_e : 0.000239
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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