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 : ocdca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4326 STM1884 STM0517 STM2947 STM3709 STM1135 STM4183 STM0491 STM0369 STM1448 STM1326 STM4062 STM2403 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3661 STM1933 STM3063 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.023711 (mmol/gDw/h)
  Minimum Production Rate : 0.083176 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.249201
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.315951
  EX_pi_e : 0.075679
  EX_k_e : 0.004211
  EX_so4_e : 0.002892
  EX_mg2_e : 0.000187
  EX_fe2_e : 0.000174
  EX_ca2_e : 0.000112
  EX_cl_e : 0.000112
  EX_cobalt2_e : 0.000075
  EX_cu2_e : 0.000075
  EX_mn2_e : 0.000075
  EX_mobd_e : 0.000075
  EX_zn2_e : 0.000075

Product: (mmol/gDw/h)
  EX_h2o_e : 11.520513
  EX_co2_e : 10.511605
  EX_dha_e : 4.885099
  EX_h_e : 0.394679
  Auxiliary production reaction : 0.083176
  EX_acald_e : 0.060493
  EX_kdo2lipid4_e : 0.027326
  EX_glyclt_e : 0.001186
  DM_hmfurn_c : 0.000011

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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