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 : pg140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM0620 STM1756 STM2285 STM3526 STM1290 STM4326 STM0840 STM0842 STM3709 STM1620 STM4408 STM1291 STM0518 STM4184 STM4484 STM0399 STM3179 STM1480 STM4126 STM2338 STM2466 STM3218 STM0977 STM1124 STM0733 STM0402 STM0608 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.110531 (mmol/gDw/h)
  Minimum Production Rate : 0.005448 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.370772
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.218062
  EX_pi_e : 0.103470
  EX_k_e : 0.019630
  EX_so4_e : 0.013483
  EX_mg2_e : 0.000873
  EX_fe2_e : 0.000810
  EX_ca2_e : 0.000524
  EX_cl_e : 0.000524
  EX_cobalt2_e : 0.000349
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000349
  EX_mobd_e : 0.000349
  EX_zn2_e : 0.000349

Product: (mmol/gDw/h)
  EX_h2o_e : 13.466573
  EX_co2_e : 10.408537
  EX_h_e : 8.496888
  EX_ac_e : 7.559774
  EX_glyclt_e : 0.005527
  Auxiliary production reaction : 0.005448
  DM_hmfurn_c : 0.000049

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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