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 : 1tdecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 125: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM2285 STM3526 STM4567 STM4326 STM1511 STM1884 STM0321 STM0840 STM0842 STM0517 STM2947 STM3709 STM1135 STM4183 STM0370 STM1448 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.253661 (mmol/gDw/h)
  Minimum Production Rate : 0.020894 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.795377
  EX_pi_e : 0.245847
  EX_k_e : 0.045050
  EX_so4_e : 0.030942
  EX_mg2_e : 0.002003
  EX_fe2_e : 0.001859
  EX_ca2_e : 0.001202
  EX_cl_e : 0.001202
  EX_cobalt2_e : 0.000801
  EX_cu2_e : 0.000801
  EX_mn2_e : 0.000801
  EX_mobd_e : 0.000801
  EX_zn2_e : 0.000801

Product: (mmol/gDw/h)
  EX_h2o_e : 25.573826
  EX_co2_e : 18.559934
  EX_h_e : 2.786732
  EX_ac_e : 0.623609
  Auxiliary production reaction : 0.020894
  EX_glyclt_e : 0.012683
  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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