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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM0158 STM2285 STM3526 STM0169 STM0861 STM4326 STM0321 STM2947 STM3709 STM3068 STM2141 STM1620 STM1448 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.221203 (mmol/gDw/h)
  Minimum Production Rate : 0.175726 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.437684
  EX_pi_e : 0.196168
  EX_k_e : 0.039286
  EX_so4_e : 0.026983
  EX_mg2_e : 0.001746
  EX_fe2_e : 0.001621
  EX_ca2_e : 0.001048
  EX_cl_e : 0.001048
  EX_cobalt2_e : 0.000699
  EX_cu2_e : 0.000699
  EX_mn2_e : 0.000699
  EX_mobd_e : 0.000699
  EX_zn2_e : 0.000699

Product: (mmol/gDw/h)
  EX_h2o_e : 25.410642
  EX_co2_e : 19.312458
  EX_h_e : 2.062059
  Auxiliary production reaction : 0.175726
  EX_glyclt_e : 0.011060
  DM_hmfurn_c : 0.000099

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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