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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM0158 STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM2947 STM3709 STM3068 STM2141 STM1135 STM3542 STM4485 STM3597 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.190459 (mmol/gDw/h)
  Minimum Production Rate : 0.064462 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.098883
  EX_pi_e : 0.297827
  EX_k_e : 0.033826
  EX_so4_e : 0.023233
  EX_mg2_e : 0.001504
  EX_fe2_e : 0.001396
  EX_ca2_e : 0.000902
  EX_cl_e : 0.000902
  EX_cobalt2_e : 0.000601
  EX_cu2_e : 0.000601
  EX_mn2_e : 0.000601
  EX_mobd_e : 0.000601
  EX_zn2_e : 0.000601

Product: (mmol/gDw/h)
  EX_h2o_e : 25.063952
  EX_co2_e : 19.619939
  EX_h_e : 1.550177
  EX_acald_e : 0.152607
  Auxiliary production reaction : 0.064462
  DM_hmfurn_c : 0.000085

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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