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 : pa160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: STM3646 STM4482 STM4108 STM2285 STM3526 STM1290 STM3512 STM3541 STM4326 STM1511 STM0517 STM2947 STM3529 STM1135 STM4183 STM0368 STM3597 STM4408 STM1291 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM1124 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.254429 (mmol/gDw/h)
  Minimum Production Rate : 0.008522 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.803837
  EX_pi_e : 0.234155
  EX_k_e : 0.045187
  EX_so4_e : 0.031036
  EX_mg2_e : 0.002009
  EX_fe2_e : 0.001865
  EX_ca2_e : 0.001205
  EX_cl_e : 0.001205
  EX_cobalt2_e : 0.000803
  EX_cu2_e : 0.000803
  EX_mn2_e : 0.000803
  EX_mobd_e : 0.000803
  EX_zn2_e : 0.000803

Product: (mmol/gDw/h)
  EX_h2o_e : 25.578659
  EX_co2_e : 18.547453
  EX_h_e : 2.812843
  EX_ac_e : 0.643172
  EX_glyclt_e : 0.012721
  Auxiliary production reaction : 0.008522
  EX_glyald_e : 0.000176
  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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