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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b3617 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b3665 b3945 b2406 b0114 b2366 b2492 b0904 b1533 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.630214 (mmol/gDw/h)
  Minimum Production Rate : 0.086883 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.479135
  EX_o2_e : 272.255938
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.959242
  EX_pi_e : 0.868557
  EX_so4_e : 0.788267
  EX_k_e : 0.123013
  EX_mg2_e : 0.005467
  EX_ca2_e : 0.003280
  EX_cl_e : 0.003280
  EX_cu2_e : 0.000447
  EX_mn2_e : 0.000435
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989878
  EX_h2o_e : 545.367221
  EX_co2_e : 25.902806
  EX_acald_e : 1.800716
  EX_met__L_e : 0.542684
  Auxiliary production reaction : 0.086883
  EX_ade_e : 0.000424
  DM_mththf_c : 0.000282
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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