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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (2 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM1463 STM4482 STM1749 STM2463 STM2285 STM3526 STM1290 STM3512 STM3541 STM4326 STM1511 STM3709 STM1620 STM0368 STM1448 STM1326 STM4062 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.224467 (mmol/gDw/h)
  Minimum Production Rate : 0.092772 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.473661
  EX_pi_e : 0.199063
  EX_k_e : 0.039865
  EX_so4_e : 0.027381
  EX_mg2_e : 0.001772
  EX_fe2_e : 0.001645
  EX_ca2_e : 0.001063
  EX_cl_e : 0.001063
  EX_cobalt2_e : 0.000709
  EX_cu2_e : 0.000709
  EX_mn2_e : 0.000709
  EX_mobd_e : 0.000709
  EX_zn2_e : 0.000709

Product: (mmol/gDw/h)
  EX_h2o_e : 25.453138
  EX_co2_e : 19.264954
  EX_h_e : 2.006944
  EX_acald_e : 0.179856
  Auxiliary production reaction : 0.092772
  EX_glyclt_e : 0.011223
  DM_hmfurn_c : 0.000100

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
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