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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (117 of 118: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM0051 STM2421 STM1749 STM2463 STM4275 STM0661 STM2391 STM2285 STM2009 STM3526 STM1511 STM3709 STM1620 STM2167 STM0974 STM0152 STM1211 STM2317 STM3179 STM4569 STM2338 STM2466 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826 STM3334 STM2392 STM2393   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.073717 (mmol/gDw/h)
  Minimum Production Rate : 0.056648 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 11.629238
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.097803
  EX_pi_e : 0.122021
  EX_k_e : 0.013092
  EX_so4_e : 0.008992
  EX_mg2_e : 0.000582
  EX_fe2_e : 0.000540
  EX_ca2_e : 0.000349
  EX_cl_e : 0.000349
  EX_cobalt2_e : 0.000233
  EX_cu2_e : 0.000233
  EX_mn2_e : 0.000233
  EX_mobd_e : 0.000233
  EX_zn2_e : 0.000233

Product: (mmol/gDw/h)
  EX_h2o_e : 14.237801
  EX_co2_e : 11.652814
  EX_h_e : 8.128312
  EX_ac_e : 7.100953
  EX_etoh_e : 0.245265
  Auxiliary production reaction : 0.056648
  EX_glyclt_e : 0.003686
  EX_hxan_e : 0.000549
  DM_hmfurn_c : 0.000033

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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