Finding Metabolic Pathway
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7.6 years ago
glady ▴ 320

I am looking to find the a pathway for the genome - "Pseudomonas aeruginosa AF137358". Where can I get a complete pathway for this organism.

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7.6 years ago
EagleEye 7.5k

This seems like more specific... Do you have any of the strains specified below is closest to 'Pseudomonas aeruginosa AF137358' ?,


T00035 pae Pseudomonas aeruginosa PAO1 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03097 paev Pseudomonas aeruginosa PAO1-VE13 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03170 paei Pseudomonas aeruginosa PAO1-VE2 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T00401 pau Pseudomonas aeruginosa UCBPP-PA14 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T00569 pap Pseudomonas aeruginosa PA7 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T00818 pag Pseudomonas aeruginosa LESB58 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T01973 paf Pseudomonas aeruginosa M18 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T01974 pnc Pseudomonas aeruginosa NCGM2.S1 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03789 paeb Pseudomonas aeruginosa NCGM 1900 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02161 pdk Pseudomonas aeruginosa DK2 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02627 psg Pseudomonas aeruginosa B136-33 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02711 prp Pseudomonas aeruginosa RP73 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02928 paep Pseudomonas aeruginosa PA1 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02929 paer Pseudomonas aeruginosa PA1R Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02951 paem Pseudomonas aeruginosa MTB-1 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02970 pael Pseudomonas aeruginosa LES431 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T02971 paes Pseudomonas aeruginosa SCV20265 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03031 paeu Pseudomonas aeruginosa PA38182 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03035 paeg Pseudomonas aeruginosa YL84 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03098 paec Pseudomonas aeruginosa c7447m Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas

T03171 paeo Pseudomonas aeruginosa PAO581 Prokaryotes;Bacteria;Gammaproteobacteria - Others;Pseudomonas


If so you can have a look at GeneSCF,

A: focus on specific pathway

For example: If I need pathways for 'Pseudomonas aeruginosa PAO1' the first strain/species from the list, use GeneSCF 'prepare_module' feature to extract all pathways from the species.

./prepare_database -db=KEGG -org=pae

The pathways and the genes will be downloaded in the following directory in the tool,

geneSCF-master_xxx/class/lib/db/pae/

The output file will look like this (TAB-delimitted)


pae00010~Glycolysis_/_Gluconeogenesis <tab> PA0552,PA0555,PA0887,PA1027,PA1498,PA1587,PA1982,PA1984,PA2250,PA2323,PA2555,PA3001....

pae00020~Citrate_cycle_(TCA_cycle) <tab> PA0854,PA1562,PA1580,PA1581,PA1582,PA1583,PA1584,PA1585,PA1586,PA1587,PA1588,PA1589....

pae00030~Pentose_phosphate_pathway <tab> PA0330,PA0548,PA0555,PA0607,PA1950,PA2261,PA2263,PA2264,PA2265,PA2290,PA2321,PA2323,PA2796,PA3131,PA3181...

pae00040~Pentose_and_glucuronate_interconversions <tab> PA0607,PA1027,PA2022,PA2023,PA2343,PA3559,PA4899...

pae00051~Fructose_and_mannose_metabolism <tab> PA0555,PA2232,PA2342,PA2344,PA3540,PA3541,PA3542,PA3545...

pae00052~Galactose_metabolism <tab> PA1384,PA2023,PA3193,PA4068,PA5322...

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