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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 100: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM2927 STM2421 STM1749 STM2463 STM4275 STM2009 STM4567 STM4568 STM1511 STM3709 STM1620 STM2167 STM0974 STM0152 STM3069 STM1211 STM2317 STM1480 STM2338 STM2466 STM0208 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.214020 (mmol/gDw/h)
  Minimum Production Rate : 0.095787 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.251895
  EX_pi_e : 0.285585
  EX_k_e : 0.038010
  EX_so4_e : 0.026107
  EX_mg2_e : 0.001690
  EX_fe2_e : 0.001569
  EX_ca2_e : 0.001014
  EX_cl_e : 0.001014
  EX_cobalt2_e : 0.000676
  EX_cu2_e : 0.000676
  EX_mn2_e : 0.000676
  EX_mobd_e : 0.000676
  EX_zn2_e : 0.000676

Product: (mmol/gDw/h)
  EX_h2o_e : 26.026641
  EX_co2_e : 18.523970
  EX_h_e : 2.863549
  EX_etoh_e : 0.471591
  EX_ac_e : 0.240890
  EX_his__L_e : 0.126163
  Auxiliary production reaction : 0.095787
  EX_glyclt_e : 0.010701
  EX_ade_e : 0.007187
  DM_hmfurn_c : 0.000095

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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