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 : pa161_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM1290 STM4567 STM4326 STM2947 STM1620 STM3542 STM4485 STM0491 STM0369 STM1326 STM4062 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM1124 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.136124 (mmol/gDw/h)
  Minimum Production Rate : 0.231733 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 12.654208
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.500103
  EX_pi_e : 0.352451
  EX_k_e : 0.024176
  EX_so4_e : 0.016605
  EX_mg2_e : 0.001075
  EX_fe2_e : 0.000998
  EX_ca2_e : 0.000645
  EX_cl_e : 0.000645
  EX_cobalt2_e : 0.000430
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000430
  EX_mobd_e : 0.000430
  EX_zn2_e : 0.000430

Product: (mmol/gDw/h)
  EX_h2o_e : 20.595162
  EX_co2_e : 15.915528
  EX_h_e : 1.160812
  EX_acald_e : 0.347283
  Auxiliary production reaction : 0.231733
  EX_glyclt_e : 0.006806
  DM_hmfurn_c : 0.000061

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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