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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b2291 b0822 b2406 b0112 b2868 b1727 b0114 b2366 b2492 b0904 b1533 b1912 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.630007 (mmol/gDw/h)
  Minimum Production Rate : 0.614551 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.808145
  EX_o2_e : 272.485472
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.101735
  EX_so4_e : 0.611015
  EX_pi_e : 0.607708
  EX_k_e : 0.122973
  EX_mg2_e : 0.005465
  EX_ca2_e : 0.003279
  EX_cl_e : 0.003279
  EX_cu2_e : 0.000447
  EX_mn2_e : 0.000435
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989881
  EX_h2o_e : 546.343426
  EX_co2_e : 25.115892
  EX_acald_e : 1.536276
  Auxiliary production reaction : 0.614551
  EX_met__L_e : 0.452366
  EX_hxan_e : 0.000424
  EX_mththf_e : 0.000282
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000140

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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