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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (122 of 122: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM2927 STM2421 STM1749 STM2463 STM4275 STM3680 STM2009 STM4568 STM1511 STM1620 STM2167 STM0974 STM0152 STM3069 STM1211 STM2317 STM2338 STM2466 STM4452 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM1627 STM1567 STM2461   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.212504 (mmol/gDw/h)
  Minimum Production Rate : 0.231475 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.279315
  EX_pi_e : 0.419928
  EX_k_e : 0.037741
  EX_so4_e : 0.025922
  EX_mg2_e : 0.001678
  EX_fe2_e : 0.001557
  EX_ca2_e : 0.001007
  EX_cl_e : 0.001007
  EX_cobalt2_e : 0.000671
  EX_cu2_e : 0.000671
  EX_mn2_e : 0.000671
  EX_mobd_e : 0.000671
  EX_zn2_e : 0.000671

Product: (mmol/gDw/h)
  EX_h2o_e : 26.409689
  EX_co2_e : 18.615564
  EX_h_e : 2.581212
  EX_acald_e : 0.662098
  Auxiliary production reaction : 0.231475
  EX_ac_e : 0.063042
  EX_hxan_e : 0.060767
  EX_glyclt_e : 0.010625
  DM_hmfurn_c : 0.000095

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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