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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4326 STM0517 STM2947 STM3068 STM2141 STM1135 STM4183 STM0491 STM0974 STM4408 STM1291 STM3069 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1124 STM2041 STM0402 STM0608 STM3708 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.174868 (mmol/gDw/h)
  Minimum Production Rate : 0.235181 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.927069
  EX_pi_e : 0.155077
  EX_k_e : 0.031057
  EX_so4_e : 0.021331
  EX_mg2_e : 0.001381
  EX_fe2_e : 0.001282
  EX_ca2_e : 0.000828
  EX_cl_e : 0.000828
  EX_cobalt2_e : 0.000552
  EX_cu2_e : 0.000552
  EX_mn2_e : 0.000552
  EX_mobd_e : 0.000552
  EX_zn2_e : 0.000552

Product: (mmol/gDw/h)
  EX_h2o_e : 24.598886
  EX_co2_e : 19.778072
  EX_h_e : 1.726389
  EX_acald_e : 0.308954
  Auxiliary production reaction : 0.235181
  EX_glyclt_e : 0.008743
  DM_hmfurn_c : 0.000078

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