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 : 6hmhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b0030 b2883 b1982 b3616 b3589 b1623 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.515435 (mmol/gDw/h)
  Minimum Production Rate : 0.505740 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.906543
  EX_nh4_e : 11.031423
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.497192
  EX_so4_e : 0.129797
  EX_k_e : 0.100609
  EX_fe2_e : 0.008278
  EX_mg2_e : 0.004471
  EX_ca2_e : 0.002683
  EX_cl_e : 0.002683
  EX_cu2_e : 0.000365
  EX_mn2_e : 0.000356
  EX_zn2_e : 0.000176
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.486989
  EX_co2_e : 20.007879
  EX_h_e : 10.504318
  EX_thymd_e : 1.467025
  Auxiliary production reaction : 0.505740
  EX_ac_e : 0.300079
  DM_oxam_c : 0.002012
  DM_5drib_c : 0.001781
  DM_4crsol_c : 0.001550
  EX_glyclt_e : 0.001435

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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