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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM1463 STM3747 STM2421 STM1749 STM2463 STM4275 STM1750 STM3709 STM0506 STM3553 STM0974 STM0152 STM0150 STM2502 STM2501 STM4569 STM2338 STM2466 STM3802 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 : 0.317313 (mmol/gDw/h)
  Minimum Production Rate : 0.164133 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.409428
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.645758
  EX_pi_e : 0.773798
  EX_so4_e : 0.202839
  EX_k_e : 0.056355
  EX_mg2_e : 0.002505
  EX_fe2_e : 0.002326
  EX_ca2_e : 0.001503
  EX_cl_e : 0.001503
  EX_cu2_e : 0.001002
  EX_mn2_e : 0.001002
  EX_mobd_e : 0.001002
  EX_zn2_e : 0.001002
  EX_cobalt2_e : 0.001002

Product: (mmol/gDw/h)
  EX_h2o_e : 23.352865
  EX_co2_e : 11.486573
  EX_h_e : 4.578525
  EX_ac_e : 1.396070
  Auxiliary production reaction : 0.164133
  DM_hmfurn_c : 0.000142

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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