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 : pa180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM1511 STM1884 STM0321 STM2947 STM3709 STM1620 STM0491 STM1326 STM4062 STM2403 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3241 STM0973 STM3661 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.174378 (mmol/gDw/h)
  Minimum Production Rate : 0.010733 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 40.127620
  EX_h_e : 38.639309
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.921673
  EX_pi_e : 0.165376
  EX_k_e : 0.030970
  EX_so4_e : 0.021271
  EX_mg2_e : 0.001377
  EX_ca2_e : 0.000826
  EX_cl_e : 0.000826
  EX_cobalt2_e : 0.000551
  EX_cu2_e : 0.000551
  EX_mn2_e : 0.000551
  EX_mobd_e : 0.000551
  EX_zn2_e : 0.000551

Product: (mmol/gDw/h)
  EX_fe3_e : 40.126342
  EX_h2o_e : 33.707732
  EX_co2_e : 8.815780
  EX_dha_e : 4.371009
  EX_acald_e : 0.444879
  Auxiliary production reaction : 0.010733
  EX_glyclt_e : 0.008719
  DM_hmfurn_c : 0.000078

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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