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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b1479 b0871 b3617 b0030 b2407 b3844 b3236 b2463 b1982 b2210 b3551 b4219 b1832 b1778 b4381 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b1511 b3662 b1206 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.414415 (mmol/gDw/h)
  Minimum Production Rate : 1.347719 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.117683
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.519918
  EX_pi_e : 4.442904
  EX_so4_e : 0.104358
  EX_k_e : 0.080891
  EX_fe2_e : 0.006656
  EX_mg2_e : 0.003595
  EX_ca2_e : 0.002157
  EX_cl_e : 0.002157
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.690161
  EX_co2_e : 28.404732
  EX_h_e : 6.018821
  Auxiliary production reaction : 1.347719
  EX_fum_e : 0.431088
  EX_acald_e : 0.364646
  EX_xan_e : 0.000279
  DM_mththf_c : 0.000186
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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.

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Last updated: 21-Sep-2023
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