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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM2952 STM2947 STM3709 STM3068 STM2141 STM1620 STM0370 STM0974 STM1448 STM3062 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 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 : 0.278624 (mmol/gDw/h)
  Minimum Production Rate : 0.010422 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_fe2_e : 4.708756
  EX_nh4_e : 3.070471
  EX_h_e : 2.320295
  EX_pi_e : 0.247090
  EX_k_e : 0.049484
  EX_so4_e : 0.033987
  EX_mg2_e : 0.002200
  EX_ca2_e : 0.001320
  EX_cl_e : 0.001320
  EX_cobalt2_e : 0.000880
  EX_cu2_e : 0.000880
  EX_mn2_e : 0.000880
  EX_mobd_e : 0.000880
  EX_zn2_e : 0.000880

Product: (mmol/gDw/h)
  EX_h2o_e : 27.682039
  EX_co2_e : 17.647500
  EX_fe3_e : 4.706714
  EX_acald_e : 0.710833
  EX_glyclt_e : 0.013931
  Auxiliary production reaction : 0.010422
  DM_hmfurn_c : 0.000124

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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