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 : ichor_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM1203 STM1832 STM1749 STM2463 STM4340 STM3680 STM1884 STM1465 STM0840 STM0842 STM3068 STM2141 STM1620 STM1647 STM2167 STM0974 STM1566 STM2472 STM1076 STM4484 STM1211 STM2317 STM1480 STM2338 STM2466 STM1378 STM1888 STM4301 STM3599 STM4325 STM0627 STM0054 STM3353   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.094806 (mmol/gDw/h)
  Minimum Production Rate : 0.143553 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.532242
  EX_so4_e : 1.426787
  EX_h_e : 0.759403
  EX_pi_e : 0.084074
  EX_k_e : 0.016837
  EX_mg2_e : 0.000748
  EX_fe2_e : 0.000695
  EX_cl_e : 0.000449
  EX_ca2_e : 0.000449
  EX_cobalt2_e : 0.000299
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000299
  EX_mobd_e : 0.000299
  EX_zn2_e : 0.000299

Product: (mmol/gDw/h)
  EX_h2o_e : 26.999209
  EX_co2_e : 21.311552
  EX_h2s_e : 1.415223
  EX_4abz_e : 0.487480
  Auxiliary production reaction : 0.143553
  EX_etoh_e : 0.081370
  EX_glyclt_e : 0.004740
  EX_succ_e : 0.000259
  DM_hmfurn_c : 0.000042

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
Contact