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 : 1odec11eg3p_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM4326 STM0321 STM1299 STM2947 STM3709 STM3068 STM2141 STM1570 STM1620 STM4036 STM0369 STM1448 STM3069 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM0007 STM2473 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.259102 (mmol/gDw/h)
  Minimum Production Rate : 0.013255 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.855338
  EX_pi_e : 0.243033
  EX_k_e : 0.046016
  EX_so4_e : 0.031606
  EX_mg2_e : 0.002046
  EX_fe2_e : 0.001899
  EX_cl_e : 0.001227
  EX_ca2_e : 0.001227
  EX_cobalt2_e : 0.000818
  EX_cu2_e : 0.000818
  EX_mn2_e : 0.000818
  EX_mobd_e : 0.000818
  EX_zn2_e : 0.000818

Product: (mmol/gDw/h)
  EX_h2o_e : 25.926932
  EX_co2_e : 18.757423
  EX_h_e : 2.209522
  EX_acald_e : 0.457778
  Auxiliary production reaction : 0.013255
  EX_glyclt_e : 0.012955
  DM_hmfurn_c : 0.000116

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.

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Last updated: 27-Sep-2023
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