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 : clpn160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM1290 STM4567 STM4326 STM1511 STM2947 STM1570 STM1620 STM4036 STM0369 STM3597 STM1326 STM4062 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.278490 (mmol/gDw/h)
  Minimum Production Rate : 0.001854 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.316425
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.069000
  EX_pi_e : 0.250680
  EX_k_e : 0.049460
  EX_so4_e : 0.033971
  EX_mg2_e : 0.002199
  EX_fe2_e : 0.002041
  EX_ca2_e : 0.001319
  EX_cl_e : 0.001319
  EX_cobalt2_e : 0.000879
  EX_cu2_e : 0.000879
  EX_mn2_e : 0.000879
  EX_mobd_e : 0.000879
  EX_zn2_e : 0.000879

Product: (mmol/gDw/h)
  EX_h2o_e : 25.329837
  EX_co2_e : 17.643063
  EX_h_e : 2.371151
  EX_acald_e : 0.710493
  EX_glyclt_e : 0.013925
  Auxiliary production reaction : 0.001854
  DM_hmfurn_c : 0.000124

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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