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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3399 b3942 b1732 b2744 b3708 b3008 b1479 b0871 b2779 b2925 b2097 b3844 b3236 b2883 b2690 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b0261 b0411 b3945 b4219 b1832 b1778 b4381 b2406 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b1710 b2480 b2413 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393350 (mmol/gDw/h)
  Minimum Production Rate : 0.048080 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.622741
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.574149
  EX_pi_e : 0.427491
  EX_so4_e : 0.099054
  EX_k_e : 0.076779
  EX_fe2_e : 0.006319
  EX_mg2_e : 0.003412
  EX_ca2_e : 0.002047
  EX_cl_e : 0.002047
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 39.170854
  EX_co2_e : 27.498991
  EX_h_e : 9.424883
  EX_glyc__R_e : 4.524368
  EX_mal__L_e : 0.527424
  Auxiliary production reaction : 0.048064
  EX_xan_e : 0.009021
  DM_oxam_c : 0.001536
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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