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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM3091 STM4570 STM4326 STM1884 STM2947 STM3709 STM3068 STM2141 STM1620 STM0369 STM1448 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM3968 STM1124 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 : 0.176001 (mmol/gDw/h)
  Minimum Production Rate : 0.036838 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 8.385377
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.939555
  EX_pi_e : 0.156082
  EX_k_e : 0.031258
  EX_so4_e : 0.021469
  EX_mg2_e : 0.001390
  EX_fe2_e : 0.001290
  EX_ca2_e : 0.000834
  EX_cl_e : 0.000834
  EX_cu2_e : 0.000556
  EX_mn2_e : 0.000556
  EX_mobd_e : 0.000556
  EX_zn2_e : 0.000556
  EX_cobalt2_e : 0.000556

Product: (mmol/gDw/h)
  EX_h2o_e : 13.634961
  EX_co2_e : 8.782911
  EX_dha_e : 4.368767
  EX_h_e : 1.537708
  EX_acald_e : 0.310956
  Auxiliary production reaction : 0.036838
  EX_glyclt_e : 0.008800
  DM_hmfurn_c : 0.000078

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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