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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM3646 STM2927 STM1749 STM2463 STM2285 STM3526 STM1290 STM4326 STM1511 STM0321 STM0517 STM2947 STM3709 STM1135 STM4183 STM0369 STM1326 STM4062 STM4408 STM1291 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM4467 STM2196 STM3240 STM0007 STM2473 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.284919 (mmol/gDw/h)
  Minimum Production Rate : 0.012897 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.998842
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.139844
  EX_pi_e : 0.252673
  EX_k_e : 0.050602
  EX_so4_e : 0.034755
  EX_mg2_e : 0.002249
  EX_fe2_e : 0.002088
  EX_ca2_e : 0.001350
  EX_cl_e : 0.001350
  EX_cobalt2_e : 0.000900
  EX_cu2_e : 0.000900
  EX_mn2_e : 0.000900
  EX_mobd_e : 0.000900
  EX_zn2_e : 0.000900

Product: (mmol/gDw/h)
  EX_h2o_e : 25.196269
  EX_co2_e : 17.341542
  EX_h_e : 2.442576
  EX_acald_e : 0.726894
  EX_glyclt_e : 0.014246
  Auxiliary production reaction : 0.012897
  DM_hmfurn_c : 0.000127

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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