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 : ppp9_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (2 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 19
  Gene deletion: STM3646 STM1469 STM0761 STM1468 STM4300 STM2285 STM4568 STM1135 STM1570 STM4036 STM1211 STM2317 STM3179 STM1933 STM3063 STM4301 STM3599 STM4325 STM0627   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.095930 (mmol/gDw/h)
  Minimum Production Rate : 0.012776 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 5.396408
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.329363
  EX_pi_e : 0.306178
  EX_k_e : 0.017037
  EX_so4_e : 0.011702
  EX_mg2_e : 0.000757
  EX_fe2_e : 0.000703
  EX_ca2_e : 0.000454
  EX_cl_e : 0.000454
  EX_cu2_e : 0.000303
  EX_mn2_e : 0.000303
  EX_mobd_e : 0.000303
  EX_zn2_e : 0.000303
  EX_cobalt2_e : 0.000303

Product: (mmol/gDw/h)
  EX_h2o_e : 12.110782
  EX_co2_e : 7.655396
  EX_h_e : 5.829771
  EX_ac_e : 4.255807
  EX_kdo2lipid4_e : 0.110553
  EX_for_e : 0.082335
  EX_succ_e : 0.079756
  Auxiliary production reaction : 0.012775
  DM_hmfurn_c : 0.000043

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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