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 : pa160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2947 STM3709 STM1135 STM4183 STM0974 STM1448 STM1326 STM4062 STM3069 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM3248 STM0519 STM1124 STM4467 STM3802 STM2196 STM3240 STM2041 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.064470 (mmol/gDw/h)
  Minimum Production Rate : 0.061524 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.382898
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.710465
  EX_pi_e : 0.118699
  EX_k_e : 0.011450
  EX_so4_e : 0.007864
  EX_mg2_e : 0.000509
  EX_fe2_e : 0.000473
  EX_ca2_e : 0.000305
  EX_cl_e : 0.000305
  EX_cobalt2_e : 0.000204
  EX_cu2_e : 0.000204
  EX_mn2_e : 0.000204
  EX_mobd_e : 0.000204
  EX_zn2_e : 0.000204

Product: (mmol/gDw/h)
  EX_h2o_e : 12.213076
  EX_co2_e : 10.312704
  EX_dha_e : 4.935247
  EX_h_e : 0.549773
  EX_acald_e : 0.113904
  Auxiliary production reaction : 0.061527
  EX_glyclt_e : 0.003224
  DM_hmfurn_c : 0.000029

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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