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 : pg160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3646 STM1463 STM2285 STM3526 STM4326 STM1885 STM2952 STM0321 STM3709 STM3068 STM2141 STM1135 STM4183 STM0370 STM1448 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM0007 STM2473 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.253876 (mmol/gDw/h)
  Minimum Production Rate : 0.027396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.797752
  EX_pi_e : 0.252540
  EX_k_e : 0.045088
  EX_so4_e : 0.030968
  EX_mg2_e : 0.002004
  EX_fe2_e : 0.001861
  EX_ca2_e : 0.001203
  EX_cl_e : 0.001203
  EX_cu2_e : 0.000802
  EX_mn2_e : 0.000802
  EX_mobd_e : 0.000802
  EX_zn2_e : 0.000802
  EX_cobalt2_e : 0.000802

Product: (mmol/gDw/h)
  EX_h2o_e : 25.891908
  EX_co2_e : 18.838174
  EX_h_e : 2.271772
  EX_ac_e : 0.140554
  Auxiliary production reaction : 0.027396
  EX_glyc__R_e : 0.006347
  DM_hmfurn_c : 0.000113

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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