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 (111 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM2927 STM1463 STM3747 STM2421 STM0413 STM1749 STM2463 STM4275 STM4567 STM4568 STM0506 STM3553 STM0974 STM0152 STM0150 STM2338 STM2466 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318746 (mmol/gDw/h)
  Minimum Production Rate : 0.159320 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.443480
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.661188
  EX_pi_e : 0.760631
  EX_so4_e : 0.198201
  EX_k_e : 0.056609
  EX_mg2_e : 0.002516
  EX_fe2_e : 0.002336
  EX_ca2_e : 0.001510
  EX_cl_e : 0.001510
  EX_cobalt2_e : 0.001007
  EX_cu2_e : 0.001007
  EX_mn2_e : 0.001007
  EX_mobd_e : 0.001007
  EX_zn2_e : 0.001007

Product: (mmol/gDw/h)
  EX_h2o_e : 23.383935
  EX_co2_e : 11.494591
  EX_h_e : 4.607536
  EX_ac_e : 1.394045
  Auxiliary production reaction : 0.159320
  EX_hxan_e : 0.008331
  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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