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 : ser__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM2285 STM3526 STM4326 STM1511 STM1135 STM1570 STM4036 STM2167 STM0368 STM3597 STM0152 STM4408 STM1291 STM4184 STM4484 STM0399 STM1211 STM2317 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.058272 (mmol/gDw/h)
  Minimum Production Rate : 0.510038 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 4.108435
  EX_nh4_e : 1.152193
  EX_pi_e : 0.051675
  EX_k_e : 0.010349
  EX_so4_e : 0.007108
  EX_mg2_e : 0.000460
  EX_fe2_e : 0.000427
  EX_ca2_e : 0.000276
  EX_cl_e : 0.000276
  EX_cu2_e : 0.000184
  EX_mn2_e : 0.000184
  EX_mobd_e : 0.000184
  EX_zn2_e : 0.000184
  EX_cobalt2_e : 0.000184

Product: (mmol/gDw/h)
  EX_h_e : 9.274135
  EX_for_e : 8.252810
  EX_etoh_e : 6.072460
  EX_co2_e : 5.783498
  EX_h2o_e : 1.827509
  EX_ser__L_e : 0.510038
  EX_ac_e : 0.017287
  DM_hmfurn_c : 0.000026

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