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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (123 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM3091 STM4326 STM1884 STM2952 STM2947 STM3709 STM1135 STM4183 STM0491 STM0369 STM1448 STM1326 STM4062 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM2332 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826 STM4559_S   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.128108 (mmol/gDw/h)
  Minimum Production Rate : 0.035320 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 13.115482
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.411767
  EX_pi_e : 0.184249
  EX_k_e : 0.022752
  EX_so4_e : 0.015627
  EX_mg2_e : 0.001011
  EX_fe2_e : 0.000939
  EX_cl_e : 0.000607
  EX_ca2_e : 0.000607
  EX_cobalt2_e : 0.000405
  EX_cu2_e : 0.000405
  EX_mn2_e : 0.000405
  EX_mobd_e : 0.000405
  EX_zn2_e : 0.000405

Product: (mmol/gDw/h)
  EX_h2o_e : 17.366601
  EX_co2_e : 13.728922
  EX_dha_e : 3.204660
  EX_h_e : 1.057136
  EX_acald_e : 0.102647
  Auxiliary production reaction : 0.035320
  EX_glyclt_e : 0.006405
  DM_hmfurn_c : 0.000057

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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