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 : 1tdecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 125: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM1463 STM1749 STM2463 STM4108 STM2285 STM3526 STM1290 STM4326 STM1884 STM2947 STM3709 STM3529 STM1570 STM1620 STM4036 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.228402 (mmol/gDw/h)
  Minimum Production Rate : 0.041522 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.517016
  EX_pi_e : 0.244073
  EX_k_e : 0.040564
  EX_so4_e : 0.027861
  EX_mg2_e : 0.001803
  EX_fe2_e : 0.001674
  EX_cl_e : 0.001082
  EX_ca2_e : 0.001082
  EX_cu2_e : 0.000721
  EX_mn2_e : 0.000721
  EX_mobd_e : 0.000721
  EX_zn2_e : 0.000721
  EX_cobalt2_e : 0.000721

Product: (mmol/gDw/h)
  EX_h2o_e : 25.331083
  EX_co2_e : 18.992919
  EX_h_e : 2.086376
  EX_acald_e : 0.582705
  EX_ac_e : 0.138654
  Auxiliary production reaction : 0.041522
  EX_glyclt_e : 0.011420
  EX_glyald_e : 0.000158
  DM_hmfurn_c : 0.000102

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