Finding Metabolic Pathway

Question

[glady]

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

Answer 1

[EagleEye]

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

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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

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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)

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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...