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 : ichor_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM1203 STM1832 STM3646 STM4482 STM1749 STM2463 STM3680 STM2285 STM1884 STM1465 STM0840 STM0842 STM4085 STM4415 STM1135 STM1647 STM2167 STM0974 STM1566 STM2472 STM1076 STM1211 STM2317 STM3179 STM1480 STM2338 STM2466 STM1378 STM1888 STM4301 STM3599 STM4325 STM0627 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.095429 (mmol/gDw/h)
  Minimum Production Rate : 0.125593 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.542324
  EX_so4_e : 1.417064
  EX_h_e : 0.684464
  EX_pi_e : 0.084627
  EX_k_e : 0.016948
  EX_mg2_e : 0.000753
  EX_fe2_e : 0.000699
  EX_ca2_e : 0.000452
  EX_cl_e : 0.000452
  EX_cobalt2_e : 0.000301
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000301
  EX_mobd_e : 0.000301
  EX_zn2_e : 0.000301

Product: (mmol/gDw/h)
  EX_h2o_e : 26.953510
  EX_co2_e : 21.281997
  EX_h2s_e : 1.405423
  EX_4abz_e : 0.490687
  Auxiliary production reaction : 0.125593
  EX_etoh_e : 0.081905
  EX_succ_e : 0.041214
  EX_glyc__R_e : 0.002386
  DM_hmfurn_c : 0.000043

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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