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 : pa140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (10 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM1290 STM0169 STM0861 STM4570 STM4326 STM0321 STM2947 STM3068 STM2141 STM1620 STM0370 STM1448 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.191338 (mmol/gDw/h)
  Minimum Production Rate : 0.086285 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.108566
  EX_pi_e : 0.255967
  EX_k_e : 0.033982
  EX_so4_e : 0.023340
  EX_mg2_e : 0.001511
  EX_fe2_e : 0.001402
  EX_cl_e : 0.000906
  EX_ca2_e : 0.000906
  EX_cobalt2_e : 0.000604
  EX_cu2_e : 0.000604
  EX_mn2_e : 0.000604
  EX_mobd_e : 0.000604
  EX_zn2_e : 0.000604

Product: (mmol/gDw/h)
  EX_h2o_e : 25.045397
  EX_co2_e : 19.597975
  EX_h_e : 1.631655
  EX_acald_e : 0.153311
  Auxiliary production reaction : 0.086285
  EX_glyclt_e : 0.009567
  DM_hmfurn_c : 0.000085

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