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 (31 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM0620 STM4482 STM2792 STM1749 STM2463 STM0737 STM2654 STM0441 STM1756 STM3512 STM3541 STM1511 STM3866 STM1620 STM2167 STM0785 STM0150 STM4184 STM0568 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 : 0.015423 (mmol/gDw/h)
  Minimum Production Rate : 0.010596 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 54.320422
  EX_h_e : 44.426000
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.169960
  EX_pi_e : 0.013675
  EX_k_e : 0.002739
  EX_so4_e : 0.001880
  EX_mg2_e : 0.000122
  EX_ca2_e : 0.000073
  EX_cl_e : 0.000073
  EX_cobalt2_e : 0.000049
  EX_cu2_e : 0.000049
  EX_mn2_e : 0.000049
  EX_mobd_e : 0.000049
  EX_zn2_e : 0.000049

Product: (mmol/gDw/h)
  EX_fe3_e : 54.320309
  EX_h2o_e : 37.440439
  EX_pyr_e : 9.731296
  EX_co2_e : 0.049656
  EX_ac_e : 0.020898
  Auxiliary production reaction : 0.010594
  EX_glyclt_e : 0.000771

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.

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Last updated: 27-Sep-2023
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