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 (64 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM2285 STM3526 STM0322 STM1290 STM0169 STM0861 STM4326 STM1511 STM3068 STM2141 STM1135 STM0370 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0007 STM2473 STM0402 STM0608 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.229795 (mmol/gDw/h)
  Minimum Production Rate : 0.142321 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.532375
  EX_pi_e : 0.203788
  EX_k_e : 0.040812
  EX_so4_e : 0.028031
  EX_mg2_e : 0.001814
  EX_fe2_e : 0.001684
  EX_ca2_e : 0.001089
  EX_cl_e : 0.001089
  EX_cobalt2_e : 0.000726
  EX_cu2_e : 0.000726
  EX_mn2_e : 0.000726
  EX_mobd_e : 0.000726
  EX_zn2_e : 0.000726

Product: (mmol/gDw/h)
  EX_h2o_e : 25.483675
  EX_co2_e : 19.148609
  EX_h_e : 2.217660
  Auxiliary production reaction : 0.142321
  EX_ac_e : 0.127222
  DM_hmfurn_c : 0.000102

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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