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 (57 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM0255 STM3165 STM1288 STM2285 STM3526 STM0322 STM4326 STM1511 STM1885 STM2952 STM0840 STM0842 STM1135 STM2081 STM4183 STM3597 STM4408 STM3062 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0007 STM2473 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.243237 (mmol/gDw/h)
  Minimum Production Rate : 0.004841 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.847611
  EX_pi_e : 0.225390
  EX_k_e : 0.043199
  EX_so4_e : 0.029671
  EX_mg2_e : 0.001920
  EX_fe2_e : 0.001783
  EX_ca2_e : 0.001152
  EX_cl_e : 0.001152
  EX_cu2_e : 0.000768
  EX_mn2_e : 0.000768
  EX_mobd_e : 0.000768
  EX_zn2_e : 0.000768
  EX_cobalt2_e : 0.000768

Product: (mmol/gDw/h)
  EX_h2o_e : 26.151801
  EX_co2_e : 18.596121
  EX_h_e : 2.365081
  EX_tyr__L_e : 0.167104
  EX_ac_e : 0.134664
  EX_glyc__R_e : 0.006081
  Auxiliary production reaction : 0.004841
  DM_hmfurn_c : 0.000108

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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