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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM2009 STM3526 STM1290 STM4326 STM1511 STM0321 STM0517 STM2947 STM3709 STM3068 STM2141 STM1135 STM4183 STM0369 STM0974 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM2332 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.277275 (mmol/gDw/h)
  Minimum Production Rate : 0.013445 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.332452
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.055602
  EX_pi_e : 0.245894
  EX_k_e : 0.049244
  EX_so4_e : 0.033823
  EX_mg2_e : 0.002189
  EX_fe2_e : 0.002032
  EX_ca2_e : 0.001313
  EX_cl_e : 0.001313
  EX_cobalt2_e : 0.000876
  EX_cu2_e : 0.000876
  EX_mn2_e : 0.000876
  EX_mobd_e : 0.000876
  EX_zn2_e : 0.000876

Product: (mmol/gDw/h)
  EX_h2o_e : 25.314417
  EX_co2_e : 17.670430
  EX_h_e : 2.377937
  EX_acald_e : 0.707391
  EX_glyclt_e : 0.013864
  Auxiliary production reaction : 0.013445
  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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