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 : pe140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM3091 STM4570 STM4326 STM1511 STM1884 STM2947 STM3709 STM1135 STM0974 STM1448 STM1326 STM4062 STM3069 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1933 STM3063 STM4467 STM2196 STM3240 STM2041 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014505 (mmol/gDw/h)
  Minimum Production Rate : 0.053200 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.445536
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.247009
  EX_pi_e : 0.099491
  EX_k_e : 0.002576
  EX_so4_e : 0.001768
  EX_mg2_e : 0.000115
  EX_fe2_e : 0.000106
  EX_ca2_e : 0.000069
  EX_cl_e : 0.000069
  EX_cobalt2_e : 0.000046
  EX_cu2_e : 0.000046
  EX_mn2_e : 0.000046
  EX_mobd_e : 0.000046
  EX_zn2_e : 0.000046

Product: (mmol/gDw/h)
  EX_h2o_e : 11.556476
  EX_co2_e : 10.745215
  EX_dha_e : 4.929715
  EX_acald_e : 0.154889
  EX_h_e : 0.137164
  Auxiliary production reaction : 0.053200
  EX_lipa_e : 0.016715
  EX_ade_e : 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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