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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM2927 STM3747 STM0413 STM1749 STM2463 STM4275 STM3554 STM4568 STM4570 STM1511 STM3709 STM2283 STM1620 STM2167 STM3553 STM0974 STM0152 STM1211 STM2317 STM2338 STM2466 STM4452 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.241314 (mmol/gDw/h)
  Minimum Production Rate : 0.200433 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.334594
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.461043
  EX_pi_e : 0.815302
  EX_k_e : 0.042857
  EX_so4_e : 0.029436
  EX_mg2_e : 0.001905
  EX_fe2_e : 0.001769
  EX_ca2_e : 0.001143
  EX_cl_e : 0.001143
  EX_cobalt2_e : 0.000762
  EX_cu2_e : 0.000762
  EX_mn2_e : 0.000762
  EX_mobd_e : 0.000762
  EX_zn2_e : 0.000762

Product: (mmol/gDw/h)
  EX_h2o_e : 26.119782
  EX_co2_e : 16.861541
  EX_h_e : 3.346367
  EX_ac_e : 0.887669
  Auxiliary production reaction : 0.200433
  EX_glyclt_e : 0.012066
  DM_hmfurn_c : 0.000108

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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