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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM4108 STM2285 STM3526 STM1290 STM0169 STM0861 STM4326 STM1511 STM0321 STM0517 STM2947 STM3709 STM3529 STM1135 STM4183 STM3597 STM0974 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.227670 (mmol/gDw/h)
  Minimum Production Rate : 0.016182 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.508949
  EX_pi_e : 0.234267
  EX_k_e : 0.040434
  EX_so4_e : 0.027772
  EX_mg2_e : 0.001797
  EX_fe2_e : 0.001669
  EX_ca2_e : 0.001078
  EX_cl_e : 0.001078
  EX_cu2_e : 0.000719
  EX_mn2_e : 0.000719
  EX_mobd_e : 0.000719
  EX_zn2_e : 0.000719
  EX_cobalt2_e : 0.000719

Product: (mmol/gDw/h)
  EX_h2o_e : 25.322420
  EX_co2_e : 18.997412
  EX_h_e : 2.090874
  EX_acald_e : 0.580837
  EX_ac_e : 0.165577
  Auxiliary production reaction : 0.016182
  EX_glyclt_e : 0.011383
  EX_glyald_e : 0.000158
  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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