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 : 1odec11eg3p_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (128 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM1511 STM1884 STM1299 STM2947 STM3709 STM1135 STM0141 STM2081 STM4183 STM0491 STM0974 STM1448 STM1326 STM4062 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM3218 STM1124 STM4467 STM2196 STM3240 STM2051 STM0007 STM2473 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.048505 (mmol/gDw/h)
  Minimum Production Rate : 0.113973 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.285696
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.567847
  EX_pi_e : 0.156991
  EX_k_e : 0.008614
  EX_so4_e : 0.005917
  EX_mg2_e : 0.000383
  EX_fe3_e : 0.000355
  EX_ca2_e : 0.000230
  EX_cl_e : 0.000230
  EX_cobalt2_e : 0.000153
  EX_cu2_e : 0.000153
  EX_mn2_e : 0.000153
  EX_mobd_e : 0.000153
  EX_zn2_e : 0.000153

Product: (mmol/gDw/h)
  EX_h2o_e : 12.012361
  EX_co2_e : 10.280798
  EX_dha_e : 4.940175
  EX_h_e : 0.447381
  EX_acald_e : 0.161795
  Auxiliary production reaction : 0.113976
  EX_tyr__L_e : 0.033321
  EX_glyclt_e : 0.002425
  EX_hxa_e : 0.000078
  EX_glyald_e : 0.000034
  DM_hmfurn_c : 0.000022

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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