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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM0051 STM0413 STM1749 STM2463 STM4275 STM3680 STM2009 STM1290 STM1511 STM1884 STM1620 STM2167 STM0694 STM3045 STM0974 STM0152 STM1211 STM2317 STM4569 STM1480 STM2338 STM2466 STM3968 STM2196 STM3240 STM2970 STM3243 STM2051 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.190343 (mmol/gDw/h)
  Minimum Production Rate : 0.101137 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.729999
  EX_pi_e : 0.269938
  EX_k_e : 0.033805
  EX_so4_e : 0.023218
  EX_mg2_e : 0.001503
  EX_fe2_e : 0.001395
  EX_ca2_e : 0.000902
  EX_cl_e : 0.000902
  EX_cu2_e : 0.000601
  EX_mn2_e : 0.000601
  EX_mobd_e : 0.000601
  EX_zn2_e : 0.000601
  EX_cobalt2_e : 0.000601

Product: (mmol/gDw/h)
  EX_h2o_e : 24.844557
  EX_co2_e : 19.055897
  EX_h_e : 2.109759
  EX_etoh_e : 0.694276
  EX_12ppd__R_e : 0.237952
  Auxiliary production reaction : 0.101137
  EX_ac_e : 0.056467
  EX_glyclt_e : 0.009517
  EX_hxan_e : 0.006392
  DM_hmfurn_c : 0.000085

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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