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 (38 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM4326 STM2947 STM3068 STM2141 STM1135 STM3542 STM4485 STM0491 STM0368 STM3597 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM1933 STM1124 STM3063 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.094073 (mmol/gDw/h)
  Minimum Production Rate : 0.100053 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.802150
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.253510
  EX_pi_e : 0.300249
  EX_k_e : 0.016707
  EX_so4_e : 0.011475
  EX_mg2_e : 0.000743
  EX_fe2_e : 0.000689
  EX_ca2_e : 0.000446
  EX_cl_e : 0.000446
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000297
  EX_mobd_e : 0.000297
  EX_zn2_e : 0.000297
  EX_cobalt2_e : 0.000297

Product: (mmol/gDw/h)
  EX_h2o_e : 18.976208
  EX_co2_e : 14.973449
  EX_h_e : 1.331208
  EX_acald_e : 0.239999
  EX_kdo2lipid4_e : 0.108412
  Auxiliary production reaction : 0.100053
  DM_hmfurn_c : 0.000042

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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