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 : pe140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM3646 STM0158 STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4326 STM1511 STM1884 STM2947 STM3709 STM1135 STM1448 STM1326 STM4062 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM4467 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.069024 (mmol/gDw/h)
  Minimum Production Rate : 0.060059 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.203786
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.820702
  EX_pi_e : 0.121270
  EX_k_e : 0.012259
  EX_so4_e : 0.008420
  EX_mg2_e : 0.000545
  EX_fe2_e : 0.000506
  EX_ca2_e : 0.000327
  EX_cl_e : 0.000327
  EX_cobalt2_e : 0.000218
  EX_cu2_e : 0.000218
  EX_mn2_e : 0.000218
  EX_mobd_e : 0.000218
  EX_zn2_e : 0.000218

Product: (mmol/gDw/h)
  EX_h2o_e : 12.166738
  EX_co2_e : 10.083716
  EX_dha_e : 4.930673
  EX_h_e : 0.525091
  EX_acald_e : 0.236153
  Auxiliary production reaction : 0.060059
  DM_hmfurn_c : 0.000031

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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