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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3916 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b1982 b1200 b2797 b3117 b1814 b4471 b3616 b3589 b2440 b4374 b0675 b2361 b2291 b0261 b0112 b0452 b2868 b0114 b0509 b3125 b2366 b1723 b2492 b0904 b1533 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504479 (mmol/gDw/h)
  Minimum Production Rate : 0.244193 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.640157
  EX_o2_e : 272.990011
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.202312
  EX_pi_e : 1.219203
  EX_so4_e : 1.103811
  EX_mobd_e : 0.244197
  EX_k_e : 0.098471
  EX_mg2_e : 0.004376
  EX_ca2_e : 0.002626
  EX_cl_e : 0.002626
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991898
  EX_h2o_e : 548.134549
  EX_co2_e : 23.800768
  EX_ac_e : 3.870231
  Auxiliary production reaction : 0.244193
  EX_hxan_e : 0.022761
  DM_5drib_c : 0.022535
  EX_glyclt_e : 0.022534
  DM_4crsol_c : 0.022309
  EX_etha_e : 0.000041

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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