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 : methf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (121 of 126: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3010 STM2927 STM1463 STM3747 STM2421 STM1749 STM2463 STM4275 STM0598 STM4568 STM1511 STM3709 STM0974 STM0152 STM0150 STM3279 STM2502 STM2501 STM4569 STM2338 STM2466 STM2196 STM3240 STM2970 STM3243 STM2467 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.251693 (mmol/gDw/h)
  Minimum Production Rate : 0.377322 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.702981
  EX_nh4_e : 5.447841
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.223207
  EX_k_e : 0.044701
  EX_so4_e : 0.030702
  EX_mg2_e : 0.001987
  EX_fe3_e : 0.001845
  EX_ca2_e : 0.001192
  EX_cl_e : 0.001192
  EX_cu2_e : 0.000795
  EX_mn2_e : 0.000795
  EX_mobd_e : 0.000795
  EX_zn2_e : 0.000795
  EX_cobalt2_e : 0.000795

Product: (mmol/gDw/h)
  EX_h2o_e : 25.032800
  EX_co2_e : 10.482741
  EX_h_e : 6.287954
  EX_ac_e : 1.100880
  Auxiliary production reaction : 0.377322
  EX_gua_e : 0.006579
  DM_hmfurn_c : 0.000112

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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