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 : 12dgr160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM0620 STM2792 STM2285 STM3526 STM1290 STM4326 STM1511 STM4109 STM0517 STM1620 STM4183 STM1448 STM0772 STM4585 STM3704 STM4484 STM0399 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM1124 STM0733   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.102850 (mmol/gDw/h)
  Minimum Production Rate : 0.004436 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.639403
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.133420
  EX_pi_e : 0.091210
  EX_k_e : 0.018266
  EX_so4_e : 0.012546
  EX_mg2_e : 0.000812
  EX_fe2_e : 0.000754
  EX_ca2_e : 0.000487
  EX_cl_e : 0.000487
  EX_cobalt2_e : 0.000325
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000325
  EX_mobd_e : 0.000325
  EX_zn2_e : 0.000325

Product: (mmol/gDw/h)
  EX_h2o_e : 14.512793
  EX_co2_e : 11.672960
  EX_h_e : 7.968450
  EX_ac_e : 7.091385
  EX_glyclt_e : 0.005142
  Auxiliary production reaction : 0.004436
  EX_glyald_e : 0.000071
  DM_hmfurn_c : 0.000046

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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