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 : ppp9_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM3680 STM2285 STM1886 STM1290 STM1135 STM0974 STM3359 STM1566 STM2472 STM0772 STM4585 STM3704 STM4184 STM0542 STM1211 STM2317 STM3179 STM1480 STM1933 STM3063 STM4301 STM3599 STM4325 STM0627   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.036671 (mmol/gDw/h)
  Minimum Production Rate : 0.004884 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 8.966200
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.508168
  EX_pi_e : 0.117041
  EX_k_e : 0.006513
  EX_so4_e : 0.004473
  EX_mg2_e : 0.000290
  EX_fe2_e : 0.000269
  EX_ca2_e : 0.000174
  EX_cl_e : 0.000174
  EX_cu2_e : 0.000116
  EX_mn2_e : 0.000116
  EX_mobd_e : 0.000116
  EX_zn2_e : 0.000116
  EX_cobalt2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 12.445963
  EX_co2_e : 8.948106
  EX_h_e : 8.467952
  EX_ac_e : 4.308311
  EX_succ_e : 1.825210
  EX_kdo2lipid4_e : 0.042260
  Auxiliary production reaction : 0.004884
  DM_hmfurn_c : 0.000016

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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