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 : dhna_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM0620 STM1597 STM1749 STM2463 STM0737 STM2654 STM0441 STM1511 STM3866 STM0517 STM1135 STM2167 STM2081 STM4183 STM0150 STM0568 STM0542 STM1211 STM2317 STM0935 STM2338 STM2466 STM1937 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014549 (mmol/gDw/h)
  Minimum Production Rate : 0.009993 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.160323
  EX_o2_e : 0.027533
  EX_pi_e : 0.012899
  EX_k_e : 0.002584
  EX_so4_e : 0.001774
  EX_mg2_e : 0.000115
  EX_fe2_e : 0.000107
  EX_ca2_e : 0.000069
  EX_cl_e : 0.000069
  EX_cobalt2_e : 0.000046
  EX_cu2_e : 0.000046
  EX_mn2_e : 0.000046
  EX_mobd_e : 0.000046
  EX_zn2_e : 0.000046

Product: (mmol/gDw/h)
  EX_h_e : 9.914348
  EX_lac__D_e : 9.737681
  EX_h2o_e : 0.498621
  EX_ac_e : 0.033758
  EX_co2_e : 0.018749
  Auxiliary production reaction : 0.009994
  EX_pyr_e : 0.008852
  EX_glyclt_e : 0.000727

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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