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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (110 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2927 STM2421 STM1749 STM2463 STM4275 STM2009 STM1290 STM1750 STM1511 STM3709 STM1620 STM2167 STM0974 STM0152 STM1211 STM2317 STM4569 STM2338 STM2466 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 : 0.215650 (mmol/gDw/h)
  Minimum Production Rate : 0.325658 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.374322
  EX_pi_e : 0.191244
  EX_k_e : 0.038300
  EX_so4_e : 0.026305
  EX_mg2_e : 0.001703
  EX_fe2_e : 0.001581
  EX_ca2_e : 0.001022
  EX_cl_e : 0.001022
  EX_cu2_e : 0.000681
  EX_mn2_e : 0.000681
  EX_mobd_e : 0.000681
  EX_zn2_e : 0.000681
  EX_cobalt2_e : 0.000681

Product: (mmol/gDw/h)
  EX_h2o_e : 26.039531
  EX_co2_e : 18.422819
  EX_h_e : 3.129792
  EX_ac_e : 0.618640
  Auxiliary production reaction : 0.325658
  EX_glyclt_e : 0.010783
  EX_gua_e : 0.002886
  EX_hxan_e : 0.001606
  DM_hmfurn_c : 0.000096

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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