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 : pa140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: STM3646 STM4482 STM2285 STM3526 STM4567 STM3512 STM3541 STM4326 STM1511 STM2952 STM0840 STM0842 STM2947 STM1135 STM0370 STM4408 STM3062 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM1124 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 : 0.254963 (mmol/gDw/h)
  Minimum Production Rate : 0.008925 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.809726
  EX_pi_e : 0.235033
  EX_k_e : 0.045281
  EX_so4_e : 0.031101
  EX_mg2_e : 0.002013
  EX_fe2_e : 0.001869
  EX_cl_e : 0.001208
  EX_ca2_e : 0.001208
  EX_cobalt2_e : 0.000805
  EX_cu2_e : 0.000805
  EX_mn2_e : 0.000805
  EX_mobd_e : 0.000805
  EX_zn2_e : 0.000805

Product: (mmol/gDw/h)
  EX_h2o_e : 25.588417
  EX_co2_e : 18.541672
  EX_h_e : 2.820977
  EX_ac_e : 0.659498
  Auxiliary production reaction : 0.008925
  DM_hmfurn_c : 0.000114

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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