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 : pap_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 100: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2927 STM1463 STM3747 STM0051 STM2421 STM1749 STM2463 STM4275 STM0661 STM1290 STM1511 STM3709 STM0974 STM0152 STM0150 STM2317 STM4569 STM2338 STM2466 STM3968 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 : 0.212208 (mmol/gDw/h)
  Minimum Production Rate : 0.025886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.024631
  EX_pi_e : 0.239963
  EX_k_e : 0.037688
  EX_so4_e : 0.025886
  EX_mg2_e : 0.001675
  EX_fe2_e : 0.001555
  EX_ca2_e : 0.001005
  EX_cl_e : 0.001005
  EX_cu2_e : 0.000670
  EX_mn2_e : 0.000670
  EX_mobd_e : 0.000670
  EX_zn2_e : 0.000670
  EX_cobalt2_e : 0.000670

Product: (mmol/gDw/h)
  EX_h2o_e : 25.672383
  EX_co2_e : 18.622435
  EX_h_e : 2.592467
  EX_etoh_e : 0.568858
  EX_thym_e : 0.274368
  EX_ac_e : 0.062954
  EX_5dglcn_e : 0.044426
  Auxiliary production reaction : 0.025886
  EX_gua_e : 0.001580
  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
Contact