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 (2 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM3526 STM1290 STM4570 STM4326 STM1511 STM1884 STM0321 STM2947 STM1620 STM3597 STM0974 STM1326 STM4062 STM2403 STM4408 STM1291 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3661 STM1933 STM3063 STM4467 STM2196 STM3240 STM2051 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.016843 (mmol/gDw/h)
  Minimum Production Rate : 0.116793 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.448126
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.224427
  EX_pi_e : 0.053753
  EX_k_e : 0.002991
  EX_so4_e : 0.002054
  EX_mg2_e : 0.000133
  EX_fe2_e : 0.000123
  EX_cl_e : 0.000080
  EX_ca2_e : 0.000080
  EX_cobalt2_e : 0.000053
  EX_cu2_e : 0.000053
  EX_mn2_e : 0.000053
  EX_mobd_e : 0.000053
  EX_zn2_e : 0.000053

Product: (mmol/gDw/h)
  EX_h2o_e : 11.516411
  EX_co2_e : 10.799768
  EX_dha_e : 4.918384
  EX_h_e : 0.338044
  Auxiliary production reaction : 0.116775
  EX_acald_e : 0.029758
  EX_kdo2lipid4_e : 0.019410
  EX_glyclt_e : 0.000842

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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