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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b0238 b0125 b1241 b0351 b4069 b2744 b2297 b2458 b3617 b2883 b1982 b0477 b4374 b0675 b2361 b2291 b0261 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524850 (mmol/gDw/h)
  Minimum Production Rate : 2.011722 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.706988
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.691779
  EX_pi_e : 4.529718
  EX_so4_e : 0.132168
  EX_k_e : 0.102447
  EX_fe2_e : 0.008430
  EX_mg2_e : 0.004553
  EX_ca2_e : 0.002732
  EX_cl_e : 0.002732
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.769038
  EX_co2_e : 18.815424
  EX_h_e : 7.601866
  Auxiliary production reaction : 2.011722
  EX_ac_e : 0.767613
  DM_5drib_c : 0.000352
  DM_4crsol_c : 0.000117

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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