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 : pg140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM0620 STM2285 STM3526 STM1290 STM4326 STM1511 STM2952 STM4109 STM1620 STM4183 STM4408 STM1291 STM0518 STM4484 STM0399 STM0935 STM3179 STM1480 STM4126 STM2338 STM2466 STM3218 STM1124 STM0733 STM0402 STM0608 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.082299 (mmol/gDw/h)
  Minimum Production Rate : 0.196490 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.138162
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.906934
  EX_pi_e : 0.269474
  EX_k_e : 0.014616
  EX_so4_e : 0.010039
  EX_mg2_e : 0.000650
  EX_fe2_e : 0.000603
  EX_ca2_e : 0.000390
  EX_cl_e : 0.000390
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000260
  EX_mobd_e : 0.000260
  EX_zn2_e : 0.000260
  EX_cobalt2_e : 0.000260

Product: (mmol/gDw/h)
  EX_h2o_e : 16.382344
  EX_co2_e : 11.615312
  EX_h_e : 4.761354
  EX_succ_e : 2.105238
  Auxiliary production reaction : 0.196491
  EX_ac_e : 0.045563
  EX_glyclt_e : 0.004115
  EX_glyald_e : 0.000057
  DM_hmfurn_c : 0.000037

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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