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 : 4abut_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM0620 STM2792 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM2952 STM4109 STM1135 STM4183 STM1448 STM3359 STM3062 STM4484 STM0399 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM0733 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.077381 (mmol/gDw/h)
  Minimum Production Rate : 1.041970 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.567357
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.894710
  EX_pi_e : 0.068622
  EX_k_e : 0.013743
  EX_so4_e : 0.009439
  EX_mg2_e : 0.000611
  EX_fe2_e : 0.000567
  EX_ca2_e : 0.000367
  EX_cl_e : 0.000367
  EX_cobalt2_e : 0.000244
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000244
  EX_mobd_e : 0.000244
  EX_zn2_e : 0.000244

Product: (mmol/gDw/h)
  EX_h2o_e : 14.802163
  EX_co2_e : 8.833790
  EX_h_e : 8.371033
  EX_succ_e : 2.793160
  EX_ac_e : 1.084808
  Auxiliary production reaction : 1.041968
  EX_acald_e : 0.328416
  EX_glyc__R_e : 0.001935
  EX_glyald_e : 0.000054
  DM_hmfurn_c : 0.000035

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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