MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iNF517 [2].
Target metabolite : PG_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 201: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 10
  Gene deletion: LLMG_RS01925 LLMG_RS01930 LLMG_RS11565 LLMG_RS11585 LLMG_RS06560 LLMG_RS04455 LLMG_RS04645 LLMG_RS05395 LLMG_RS03310 LLMG_RS06770   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.025323 (mmol/gDw/h)
  Minimum Production Rate : 0.001679 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 2.120000
  EX_h2o_e : 0.754133
  EX_glu__L_e : 0.050000
  EX_ser__L_e : 0.040000
  EX_thr__L_e : 0.020000
  EX_pi_e : 0.017458
  EX_lys__L_e : 0.010282
  EX_arg__L_e : 0.010000
  EX_asp__L_e : 0.010000
  EX_ile__L_e : 0.010000
  EX_leu__L_e : 0.010000
  EX_val__L_e : 0.010000
  EX_cys__L_e : 0.004817
  EX_orot_e : 0.004390
  EX_xan_e : 0.003003
  EX_ade_e : 0.002822
  EX_met__L_e : 0.002529
  EX_his__L_e : 0.001915
  EX_nac_e : 0.000051
  EX_ura_e : 0.000046

Product: (mmol/gDw/h)
  EX_h_e : 5.242122
  EX_for_e : 3.748826
  EX_acald_e : 1.563402
  EX_ac_e : 1.149980
  EX_etoh_e : 1.020000
  EX_lac__L_e : 0.400000
  EX_pro__L_e : 0.034562
  EX_co2_e : 0.021546
  EX_2h3mp_e : 0.003830
  EX_phe__L_e : 0.002865
  EX_2h3mb_e : 0.002234
  Auxiliary production reaction : 0.001679
  EX_2hxic__L_e : 0.000638

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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