A Short Note on Mapping PEGs to Subsystems

You can use

svr_all_features 83333.1 peg | svr_ids_to_subsystems 2> /dev/null > E.coli.pegs.in.subsystems

to get a 2-column file [PEG,Subsystem] for the PEGs in the genome with ID 83333.1

(which happens to be E.coli). If you also want the function of the PEGs, use

svr_all_features 83333.1 peg | svr_ids_to_subsystems 2> /dev/null | svr_function_of -c 1 > E.coli.pegs.in.subsystems

The

svr_function_of -c 1

command takes as input a file in which each line is a tab-separated set of fields. The

-c 1

says that the PEG ids for which functions are to be appended occur in the first column.

This produces output like

fig|83333.1.peg.2 CBSS-216591.1.peg.168 Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)

fig|83333.1.peg.2 Lysine Biosynthesis DAP Pathway Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)

fig|83333.1.peg.2 Threonine and Homoserine Biosynthesis Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)

fig|83333.1.peg.2 Methionine Biosynthesis Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)

fig|83333.1.peg.3 Threonine and Homoserine Biosynthesis Homoserine kinase (EC 2.7.1.39)

fig|83333.1.peg.3 Methionine Biosynthesis Homoserine kinase (EC 2.7.1.39)

fig|83333.1.peg.3 CBSS-269482.1.peg.1294 Homoserine kinase (EC 2.7.1.39)

fig|83333.1.peg.4 Threonine and Homoserine Biosynthesis Threonine synthase (EC 4.2.3.1)

fig|83333.1.peg.6 YaaA UPF0246 protein YaaA