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 : clpn160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (113 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM4108 STM2285 STM3526 STM1290 STM4326 STM1884 STM2947 STM0525 STM3247 STM2959 STM2492 STM1135 STM4183 STM1326 STM4062 STM2403 STM0393 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3241 STM0973 STM1933 STM1124 STM3063 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.022522 (mmol/gDw/h)
  Minimum Production Rate : 0.014018 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.194851
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.300105
  EX_pi_e : 0.099919
  EX_k_e : 0.004000
  EX_so4_e : 0.002747
  EX_mg2_e : 0.000178
  EX_fe2_e : 0.000165
  EX_ca2_e : 0.000107
  EX_cl_e : 0.000107
  EX_cu2_e : 0.000071
  EX_mn2_e : 0.000071
  EX_mobd_e : 0.000071
  EX_zn2_e : 0.000071
  EX_cobalt2_e : 0.000071

Product: (mmol/gDw/h)
  EX_h2o_e : 11.541528
  EX_co2_e : 10.461221
  EX_dha_e : 4.890862
  EX_h_e : 0.267280
  EX_acald_e : 0.057459
  EX_lipa_e : 0.025955
  Auxiliary production reaction : 0.014018
  EX_glyc__R_e : 0.000563
  DM_hmfurn_c : 0.000010

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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