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 : camp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (99 of 100: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM2927 STM1463 STM3747 STM0413 STM1749 STM2463 STM4275 STM1290 STM1750 STM1620 STM2167 STM0694 STM3045 STM0974 STM0152 STM1211 STM2317 STM4569 STM1480 STM2338 STM2466 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.211551 (mmol/gDw/h)
  Minimum Production Rate : 0.121335 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.264254
  EX_pi_e : 0.308943
  EX_k_e : 0.037571
  EX_so4_e : 0.025805
  EX_mg2_e : 0.001670
  EX_fe2_e : 0.001550
  EX_cl_e : 0.001002
  EX_ca2_e : 0.001002
  EX_cobalt2_e : 0.000668
  EX_cu2_e : 0.000668
  EX_mn2_e : 0.000668
  EX_mobd_e : 0.000668
  EX_zn2_e : 0.000668

Product: (mmol/gDw/h)
  EX_h2o_e : 26.086595
  EX_co2_e : 18.482014
  EX_h_e : 2.882045
  EX_etoh_e : 0.457389
  EX_ac_e : 0.266419
  Auxiliary production reaction : 0.121335
  EX_his__L_e : 0.108754
  EX_glyclt_e : 0.010578
  DM_hmfurn_c : 0.000094

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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