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 : pg160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (109 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: STM3646 STM0158 STM1463 STM1749 STM2463 STM2285 STM3526 STM4326 STM1511 STM2947 STM3709 STM3247 STM1135 STM4183 STM0974 STM1326 STM4062 STM4408 STM1291 STM0772 STM4585 STM3704 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1124 STM4467 STM2196 STM3240 STM0007 STM2473 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.270517 (mmol/gDw/h)
  Minimum Production Rate : 0.014795 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.100321
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.981137
  EX_pi_e : 0.254696
  EX_k_e : 0.048044
  EX_so4_e : 0.032998
  EX_mg2_e : 0.002136
  EX_fe2_e : 0.001983
  EX_cl_e : 0.001281
  EX_ca2_e : 0.001281
  EX_cu2_e : 0.000854
  EX_mn2_e : 0.000854
  EX_mobd_e : 0.000854
  EX_zn2_e : 0.000854
  EX_cobalt2_e : 0.000854

Product: (mmol/gDw/h)
  EX_h2o_e : 25.080452
  EX_co2_e : 17.593161
  EX_h_e : 2.278548
  EX_acald_e : 0.690152
  Auxiliary production reaction : 0.014795
  DM_hmfurn_c : 0.000121

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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