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 : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: STM3646 STM0158 STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM1884 STM2952 STM2947 STM1135 STM4183 STM3597 STM0974 STM1326 STM4062 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977 STM1933 STM3063 STM4467 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.039890 (mmol/gDw/h)
  Minimum Production Rate : 0.003523 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 38.500615
  EX_h_e : 37.974752
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.531527
  EX_pi_e : 0.127315
  EX_k_e : 0.007084
  EX_so4_e : 0.004866
  EX_mg2_e : 0.000315
  EX_ca2_e : 0.000189
  EX_cl_e : 0.000189
  EX_cobalt2_e : 0.000126
  EX_cu2_e : 0.000126
  EX_mn2_e : 0.000126
  EX_mobd_e : 0.000126
  EX_zn2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 38.500323
  EX_h2o_e : 30.855881
  EX_co2_e : 9.908425
  EX_dha_e : 4.806701
  EX_acald_e : 0.101767
  EX_kdo2lipid4_e : 0.045970
  Auxiliary production reaction : 0.003523
  DM_hmfurn_c : 0.000018

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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