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 : pa160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM3068 STM2141 STM1135 STM3542 STM4485 STM0974 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2196 STM3240 STM2041 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.212102 (mmol/gDw/h)
  Minimum Production Rate : 0.067747 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.337396
  EX_pi_e : 0.255844
  EX_k_e : 0.037669
  EX_so4_e : 0.025873
  EX_mg2_e : 0.001675
  EX_fe2_e : 0.001554
  EX_ca2_e : 0.001005
  EX_cl_e : 0.001005
  EX_cobalt2_e : 0.000670
  EX_cu2_e : 0.000670
  EX_mn2_e : 0.000670
  EX_mobd_e : 0.000670
  EX_zn2_e : 0.000670

Product: (mmol/gDw/h)
  EX_h2o_e : 25.406975
  EX_co2_e : 19.424182
  EX_h_e : 1.798123
  Auxiliary production reaction : 0.067747
  DM_hmfurn_c : 0.000095

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.

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Last updated: 27-Sep-2023
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