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 : 5drib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 34: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2927 STM4482 STM0413 STM2451 STM2555 STM2285 STM4567 STM3512 STM3541 STM1750 STM1620 STM0974 STM3359 STM1566 STM2472 STM0785 STM0542 STM1211 STM2317 STM3179 STM4301 STM3599 STM4325 STM0627 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.180598 (mmol/gDw/h)
  Minimum Production Rate : 0.054125 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 6.457131
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.276654
  EX_pi_e : 0.160158
  EX_k_e : 0.032074
  EX_fe2_e : 0.028386
  EX_so4_e : 0.022030
  EX_mg2_e : 0.001426
  EX_ca2_e : 0.000855
  EX_cl_e : 0.000855
  EX_cobalt2_e : 0.000570
  EX_cu2_e : 0.000570
  EX_mn2_e : 0.000570
  EX_mobd_e : 0.000570
  EX_zn2_e : 0.000570

Product: (mmol/gDw/h)
  EX_h2o_e : 13.092141
  EX_h_e : 9.166969
  EX_ac_e : 6.753707
  EX_co2_e : 6.449811
  EX_4abz_e : 0.178195
  EX_succ_e : 0.150153
  DM_5drib_c : 0.054125
  EX_pheme_e : 0.027062
  EX_glyclt_e : 0.009030
  DM_hmfurn_c : 0.000081

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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