MetNetComp Database [1] / Minimal gene deletions

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

Model : STM_v1_0 [2].
Target metabolite : prfp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (119 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2421 STM1749 STM2463 STM4275 STM2009 STM4567 STM1750 STM4570 STM1511 STM2952 STM3709 STM0974 STM0152 STM0150 STM2317 STM2338 STM2466 STM2422 STM3885 STM3793 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.207060 (mmol/gDw/h)
  Minimum Production Rate : 0.159114 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.085111
  EX_pi_e : 0.501854
  EX_k_e : 0.036774
  EX_so4_e : 0.025258
  EX_mg2_e : 0.001635
  EX_fe2_e : 0.001518
  EX_cl_e : 0.000981
  EX_ca2_e : 0.000981
  EX_cobalt2_e : 0.000654
  EX_cu2_e : 0.000654
  EX_mn2_e : 0.000654
  EX_mobd_e : 0.000654
  EX_zn2_e : 0.000654

Product: (mmol/gDw/h)
  EX_h2o_e : 25.831209
  EX_co2_e : 18.079725
  EX_h_e : 3.273459
  EX_ac_e : 0.709625
  Auxiliary production reaction : 0.159114
  EX_etoh_e : 0.040716
  EX_glyc__R_e : 0.005177
  EX_ade_e : 0.001542
  DM_hmfurn_c : 0.000092

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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