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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM2009 STM3526 STM1290 STM4326 STM1511 STM1884 STM2947 STM3709 STM1135 STM1570 STM4036 STM0370 STM1448 STM1326 STM4062 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1933 STM1124 STM3063 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 : 0.040663 (mmol/gDw/h)
  Minimum Production Rate : 0.003483 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 8.838689
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.541836
  EX_pi_e : 0.129784
  EX_k_e : 0.007222
  EX_so4_e : 0.004960
  EX_mg2_e : 0.000321
  EX_fe2_e : 0.000297
  EX_ca2_e : 0.000193
  EX_cl_e : 0.000193
  EX_cobalt2_e : 0.000128
  EX_cu2_e : 0.000128
  EX_mn2_e : 0.000128
  EX_mobd_e : 0.000128
  EX_zn2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 11.605636
  EX_co2_e : 9.875423
  EX_dha_e : 4.802952
  EX_h_e : 0.535656
  EX_acald_e : 0.071843
  EX_kdo2lipid4_e : 0.046862
  Auxiliary production reaction : 0.003483
  DM_hmfurn_c : 0.000018

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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