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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3616 b3589 b1033 b0411 b2406 b0114 b0529 b2492 b0904 b1380 b0516 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449431 (mmol/gDw/h)
  Minimum Production Rate : 0.729346 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.297804
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.507669
  EX_pi_e : 0.433524
  EX_so4_e : 0.113176
  EX_k_e : 0.087726
  EX_fe2_e : 0.007218
  EX_mg2_e : 0.003899
  EX_ca2_e : 0.002339
  EX_cl_e : 0.002339
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.895279
  EX_co2_e : 31.991550
  EX_h_e : 7.783403
  EX_acald_e : 1.126255
  Auxiliary production reaction : 0.729446
  EX_alltn_e : 0.001654
  DM_mththf_c : 0.001353
  DM_5drib_c : 0.000302
  DM_4crsol_c : 0.000100

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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