MetNetComp Database [1] / Core Genes A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : iYO844 [2].
Target metabolite : 2mop_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 245
  Remaining genes: BSU36850 BSU36830 BSU36800 BSU36820 BSU36860 BSU36870 BSU36880 BSU19310 BSU24340 BSU29200 BSU22440 BSU24350 BSU29210 BSU11210 BSU11200 BSU28300 BSU28310 BSU11230 BSU11240 BSU16920 BSU02270 BSU32820 BSU18000 BSU11220 BSU00500 BSU35740 BSU22830 BSU29750 BSU22710 BSU39060 BSU00760 BSU38770 BSU00740 BSU00750 BSU36590 BSU01370 BSU31350 BSU29140 BSU37150 BSU14900 BSU14190 BSU14910 BSU14920 BSU14890 BSU22540 BSU35670 BSU22560 BSU22550 BSU27250 BSU27260 BSU33940 BSU06440 BSU02230 BSU01780 BSU40420 BSU36900 BSU09540 BSU11190 BSU06520 BSU06420 BSU06430 BSU10520 BSU17460 BSU23380 BSU32170 BSU07570 BSU15680 BSU05740 BSU04560 BSU21870 BSU22490 BSU04640 BSU16770 BSU31400 BSU21810 BSU28080 BSU00780 BSU15540 BSU15530 BSU15500 BSU00770 BSU23080 BSU22700 BSU22670 BSU22680 BSU00280 BSU06490 BSU14180 BSU28390 BSU15570 BSU14000 BSU28540 BSU33900 BSU17000 BSU10360 BSU39670 BSU29440 BSU29450 BSU28680 BSU09290 BSU06360 BSU22780 BSU08450 BSU08460 BSU08440 BSU16750 BSU24850 BSU30540 BSU07990 BSU15490 BSU16760 BSU34910 BSU29620 BSU27870 BSU22370 BSU34920 BSU36810 BSU36840 BSU38500 BSU38530 BSU38510 BSU38520 BSU00790 BSU32260 BG12900 BSU32240 BSU21910 BSU22600 BSU02290 BSU10020 BSU34890 BSU04740 BSU29130 BSU34870 BSU34900 BSU29180 BSU22660 BSU24080 BSU02390 BSU27850 BSU00090 BSU29120 BSU29220 BSU17370 BSU17390 BSU28270 BSU28260 BSU17380 BSU28250 BSU28280 BSU15790 BSU28290 BSU15590 BSU36370 BSU13180 BSU15910 BSU21690 BSU10170 BSU08650 BSU15900 BSU24740 BSU11340 BSU25660 BSU03150 BSU11870 BSU26640 BSU01580 BSU24310 BSU11010 BSU28430 BSU28440 BSU28450 BSU16090 BSU32200 BSU16100 BSU11610 BSU03130 BSU33440 BSU37110 BSU35710 BSU35760 BSU22730 BSU35720 BSU36510 BSU35700 BSU25640 BSU27860 BSU35530 BSU35750 BSU35730 BSU35690 BSU35680 BSU16990 BSU11250 BSU32250 BSU24030 BSU17890 BSU24060 BSU24050 BSU17680 BSU24040 BSU15550 BSU40340 BSU15560 BSU18670 BSU33920 BSU12910 BSU15190 BSU32110 BSU22640 BSU14860 BSU22630 BSU15180 BSU35660 BSU29190 BSU30870 BSU01770 BSU23070 BSU23860 BSU36760 BSU33930 BSU15220 BSU15200 BSU33910 BSU16540 BSU29790 BSU15230 BSU31150 BSU04570 BSU21920 BSU12840 BSU40550 BSU22610 BSU27900 BSU16510 BSU06530 BSU22650 BSU06500 BSU34860 BSU06450 BSU06470 BSU06480 BSU06460 BSU34880 BSU00510   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.003252 (mmol/gDw/h)
  Minimum Production Rate : 1.664968 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 3.316209
  EX_glc__D_e : 1.700000
  EX_nh4_e : 0.046374
  EX_pi_e : 0.016085
  EX_k_e : 0.002297
  EX_so4_e : 0.000554
  EX_mg2_e : 0.000331
  EX_fe3_e : 0.000011
  EX_ca2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 5.074447
  EX_co2_e : 3.306532
  EX_h_e : 1.722589
  Auxiliary production reaction : 1.664968
  EX_gly_e : 0.010955
  EX_6pgc_e : 0.009348
  EX_fum_e : 0.002405
  EX_cmp_e : 0.001746
  EX_ac_e : 0.001389
  EX_fol_e : 0.000590

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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