MetNetComp Database / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iHN637 [2].
Target metabolite : lac__D_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 247
  Remaining genes: CLJU_RS18335 CLJU_RS10115 CLJU_RS20750 CLJU_RS17225 CLJU_RS20760 CLJU_RS04205 CLJU_RS10110 CLJU_RS18540 CLJU_RS19990 CLJU_RS15825 CLJU_RS19995 CLJU_RS20585 CLJU_RS19890 CLJU_RS10450 CLJU_RS02195 CLJU_RS06280 CLJU_RS12245 CLJU_RS06125 CLJU_RS05870 CLJU_RS02950 CLJU_RS17490 CLJU_RS20745 CLJU_RS20755 CLJU_RS20740 CLJU_RS20735 CLJU_RS10565 CLJU_RS10570 CLJU_RS06580 CLJU_RS04225 CLJU_RS11515 CLJU_RS07885 CLJU_RS10025 CLJU_RS07875 CLJU_RS07880 CLJU_RS19905 CLJU_RS05640 CLJU_RS20780 CLJU_RS06285 CLJU_RS20670 CLJU_RS02945 CLJU_RS01300 CLJU_RS03255 CLJU_RS10560 CLJU_RS04215 CLJU_RS20665 CLJU_RS02190 CLJU_RS06575 CLJU_RS03300 CLJU_RS15775 CLJU_RS15780 CLJU_RS03295 CLJU_RS05835 CLJU_RS18300 CLJU_RS17045 CLJU_RS20110 CLJU_RS17495 CLJU_RS16620 CLJU_RS06565 CLJU_RS20860 CLJU_RS19340 CLJU_RS10575 CLJU_RS05255 CLJU_RS03265 CLJU_RS10900 CLJU_RS13170 CLJU_RS17595 CLJU_RS17590 CLJU_RS18875 CLJU_RS12015 CLJU_RS05725 CLJU_RS06595 CLJU_RS12040 CLJU_RS15680 CLJU_RS05730 CLJU_RS01975 CLJU_RS05795 CLJU_RS15760 CLJU_RS11705 CLJU_RS04950 CLJU_RS05750 CLJU_RS03645 CLJU_RS15740 CLJU_RS01030 CLJU_RS14395 CLJU_RS14375 CLJU_RS12010 CLJU_RS14325 CLJU_RS13835 CLJU_RS15715 CLJU_RS17585 CLJU_RS15700 CLJU_RS15710 CLJU_RS15705 CLJU_RS17570 CLJU_RS03260 CLJU_RS15730 CLJU_RS05755 CLJU_RS15720 CLJU_RS15725 CLJU_RS18405 CLJU_RS05740 CLJU_RS15690 CLJU_RS05735 CLJU_RS15735 CLJU_RS05200 CLJU_RS07890 CLJU_RS18410 CLJU_RS04620 CLJU_RS03250 CLJU_RS19915 CLJU_RS18305 CLJU_RS04475 CLJU_RS04470 CLJU_RS01075 CLJU_RS04465 CLJU_RS15745 CLJU_RS04460 CLJU_RS19355 CLJU_RS10010 CLJU_RS15095 CLJU_RS19470 CLJU_RS19480 CLJU_RS19475 CLJU_RS19270 CLJU_RS19260 CLJU_RS15865 CLJU_RS06515 CLJU_RS10470 CLJU_RS02275 CLJU_RS06110 CLJU_RS18870 CLJU_RS05285 CLJU_RS19495 CLJU_RS19490 CLJU_RS20455 CLJU_RS07005 CLJU_RS04605 CLJU_RS20770 CLJU_RS06465 CLJU_RS16730 CLJU_RS05135 CLJU_RS15750 CLJU_RS06155 CLJU_RS05525 CLJU_RS02910 CLJU_RS06145 CLJU_RS10015 CLJU_RS14390 CLJU_RS08870 CLJU_RS12565 CLJU_RS04235 CLJU_RS06430 CLJU_RS07895 CLJU_RS00770 CLJU_RS02100 CLJU_RS12050 CLJU_RS04220 CLJU_RS20335 CLJU_RS05760 CLJU_RS04210 CLJU_RS05765 CLJU_RS05660 CLJU_RS11580 CLJU_RS05745 CLJU_RS03270 CLJU_RS17580 CLJU_RS17575 CLJU_RS20580 CLJU_RS14380 CLJU_RS18360 CLJU_RS00340 CLJU_RS00465 CLJU_RS14190 CLJU_RS04500 CLJU_RS14385 CLJU_RS10625 CLJU_RS01425 CLJU_RS05465 CLJU_RS10465 CLJU_RS16560 CLJU_RS06240 CLJU_RS08690 CLJU_RS00680 CLJU_RS12820 CLJU_RS02395 CLJU_RS12020 CLJU_RS06420 CLJU_RS05470 CLJU_RS20775 CLJU_RS11545 CLJU_RS19255 CLJU_RS01315 CLJU_RS01375 CLJU_RS18520 CLJU_RS14330 CLJU_RS18525 CLJU_RS05480 CLJU_RS03400 CLJU_c20040 CLJU_RS05590 CLJU_RS05575 CLJU_RS05195 CLJU_RS05580 CLJU_RS06855 CLJU_RS05570 CLJU_RS06400 CLJU_RS05595 CLJU_RS05585 CLJU_RS06865 CLJU_RS15755 CLJU_RS00895 CLJU_RS06475 CLJU_RS06205 CLJU_RS01130 CLJU_RS17500 CLJU_RS11225 CLJU_RS11215 CLJU_RS19350 CLJU_RS07395 CLJU_RS15665 CLJU_RS15695 CLJU_RS15670 CLJU_RS18655 CLJU_RS14365 CLJU_RS14360 CLJU_RS03010 CLJU_RS12555 CLJU_RS12550 CLJU_RS19520 CLJU_RS12895 CLJU_RS15770 CLJU_RS12725 CLJU_RS12720 CLJU_RS19265 CLJU_RS19940 CLJU_RS07900 CLJU_RS07905 CLJU_RS05190 CLJU_RS05215 CLJU_RS16795 CLJU_RS01205 CLJU_RS01055 CLJU_RS20420 CLJU_RS20600 CLJU_RS01560 CLJU_RS03055 CLJU_RS17465   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.063677 (mmol/gDw/h)
  Minimum Production Rate : 1.646182 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fru_e : 5.000000
  EX_nh4_e : 0.541287
  EX_pi_e : 0.074361
  EX_so4_e : 0.068312
  EX_k_e : 0.012174
  EX_fe2_e : 0.000880
  EX_mg2_e : 0.000541
  EX_ca2_e : 0.000325
  EX_cl_e : 0.000325
  EX_fol_e : 0.000057
  EX_cu2_e : 0.000044
  EX_mn2_e : 0.000043
  EX_ribflv_e : 0.000028
  EX_zn2_e : 0.000021
  EX_ni2_e : 0.000020
  EX_cobalt2_e : 0.000016
  EX_thm_e : 0.000014

Product: (mmol/gDw/h)
  EX_co2_e : 7.687347
  EX_etoh_e : 7.072606
  EX_h_e : 2.016964
  EX_h2o_e : 1.951841
  Auxiliary production reaction : 1.651531
  EX_ac_e : 0.068042
  EX_met__L_e : 0.056288
  DM_succ_c : 0.008052
  EX_ala__D_e : 0.001809
  EX_glyc_e : 0.001464
  EX_udcpdp_e : 0.000291
  DM_mththf_c : 0.000142

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] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[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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