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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM0158 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4326 STM2947 STM3709 STM3068 STM2141 STM1620 STM3542 STM4485 STM0491 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.190063 (mmol/gDw/h)
  Minimum Production Rate : 0.064491 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.094525
  EX_pi_e : 0.297535
  EX_k_e : 0.033755
  EX_so4_e : 0.023184
  EX_mg2_e : 0.001501
  EX_fe2_e : 0.001393
  EX_ca2_e : 0.000900
  EX_cl_e : 0.000900
  EX_cu2_e : 0.000600
  EX_mn2_e : 0.000600
  EX_mobd_e : 0.000600
  EX_zn2_e : 0.000600
  EX_cobalt2_e : 0.000600

Product: (mmol/gDw/h)
  EX_h2o_e : 25.048834
  EX_co2_e : 19.615634
  EX_h_e : 1.556298
  EX_acald_e : 0.152290
  Auxiliary production reaction : 0.064491
  EX_glyclt_e : 0.009503
  DM_hmfurn_c : 0.000085

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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