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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3010 STM3747 STM2421 STM1749 STM2463 STM4275 STM4568 STM4570 STM3709 STM0974 STM0152 STM0150 STM0597 STM2338 STM2466 STM2422 STM3885 STM3793 STM3802 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 : 0.305109 (mmol/gDw/h)
  Minimum Production Rate : 0.473461 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 12.518969
  EX_nh4_e : 5.729644
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.744038
  EX_k_e : 0.054187
  EX_so4_e : 0.037218
  EX_mg2_e : 0.002409
  EX_fe2_e : 0.002236
  EX_ca2_e : 0.001445
  EX_cl_e : 0.001445
  EX_cobalt2_e : 0.000964
  EX_cu2_e : 0.000964
  EX_mn2_e : 0.000964
  EX_mobd_e : 0.000964
  EX_zn2_e : 0.000964

Product: (mmol/gDw/h)
  EX_h2o_e : 24.871074
  EX_co2_e : 11.251675
  EX_h_e : 6.296277
  EX_ac_e : 1.342378
  Auxiliary production reaction : 0.473461
  DM_hmfurn_c : 0.000136

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.

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Last updated: 27-Sep-2023
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