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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM1749 STM2463 STM4275 STM2009 STM1750 STM4570 STM1511 STM3709 STM2081 STM0506 STM3553 STM0694 STM3045 STM0974 STM0152 STM2338 STM2466 STM2422 STM2196 STM3240 STM2970 STM3243 STM0007 STM2473 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.154758 (mmol/gDw/h)
  Minimum Production Rate : 0.049486 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 6.699099
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.114452
  EX_pi_e : 0.137243
  EX_k_e : 0.027485
  EX_so4_e : 0.018878
  EX_mg2_e : 0.001222
  EX_fe2_e : 0.001134
  EX_ca2_e : 0.000733
  EX_cl_e : 0.000733
  EX_cobalt2_e : 0.000489
  EX_cu2_e : 0.000489
  EX_mn2_e : 0.000489
  EX_mobd_e : 0.000489
  EX_zn2_e : 0.000489

Product: (mmol/gDw/h)
  EX_h2o_e : 12.262352
  EX_h_e : 9.523648
  EX_ac_e : 7.802671
  EX_co2_e : 6.349530
  EX_enter_e : 0.051835
  Auxiliary production reaction : 0.049486
  EX_ade_e : 0.001152
  EX_23dhbzs3_e : 0.000100
  DM_hmfurn_c : 0.000069

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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