Downloading a Subsystem

In this tutorial we will show how to use command-line scripts to get the roles and features of a subsystem.

The roles of a subsystem can be listed using the svr_subsystem_roles command. This takes the subsystem name from the command line. Since many subsystem names contain spaces, this means you'll usually need to use quotes. For example, the following invocation lists the roles for the Alanine biosynthesis subsystem.

   svr_subsystem_roles "Alanine biosynthesis" >roles.tbl

The output file will be two columns tab-delimited, containing the roles in order--one per line--with each line having the role abbreviation in the first column and the full role name in the second, as shown below.

IlvY    HTH-type transcriptional regulator IlvY
IlvE    Branched-chain amino acid aminotransferase (EC
AvtA    Valine--pyruvate aminotransferase (EC
IscS    Cysteine desulfurase (EC, IscS subfamily
AlaR    Alanine racemase (EC
AlaR_b  Alanine racemase, biosynthetic (EC
AlaR_c  Alanine racemase, catabolic (EC
AlaB    Glutamate-pyruvate aminotransferase (EC
CDSe    Cysteine desulfurase, mitochondrial precursor (EC
prAvtA  Probable valine-pyruvate aminotransferase (EC
SufS    Cysteine desulfurase (EC, SufS subfamily
CDS     Cysteine desulfurase (EC
NifS    Cysteine desulfurase (EC, NifS subfamily
CsdA    Cysteine desulfurase CsdA-CsdE (EC, main protein CsdA

To get a complete list of the genes in the subsystem organized in the form of a spreadsheet, use the svr_subsystem_spreadsheet command.

    svr_subsystem_spreadsheet "Alanine biosynthesis" >

The output from this command is also a tab-delimited file. Each line of the output corresponds to a single genome. The first column is the genome ID, the second is the variant code, and the remaining columns correspond one-for-one with the roles of the subsystem, in order. If the role is used by the relevant genome, the IDs of the features performing the role will be placed in the column as a comma-separated list.

217.1     C                   fig|217.1.peg.1434                      fig|217.1.peg.1516                                                              fig|217.1.peg.1682, fig|217.1.peg.362
354.1     C                   fig|354.1.peg.1665            fig|354.1.peg.1435  fig|354.1.peg.136                                                               fig|354.1.peg.3056, fig|354.1.peg.4190, fig|354.1.peg.548   fig|354.1.peg.2228  fig|354.1.peg.1319
394.5     B                                                                                                                                 fig|394.5.peg.466
486.1     A.123               fig|486.1.peg.1242  fig|486.1.peg.2140  fig|486.1.peg.37    fig|486.1.peg.134
487.2     A.123               fig|487.2.peg.19    fig|487.2.peg.1204  fig|487.2.peg.615   fig|487.2.peg.2183
521.1     A.123               fig|521.1.peg.653, fig|521.1.peg.882              fig|521.1.peg.1841                      fig|521.1.peg.60
573.2     A.123     fig|573.2.peg.6483  fig|573.2.peg.6476  fig|573.2.peg.5593, fig|573.2.peg.5594, fig|573.2.peg.5595, fig|573.2.peg.5596  fig|573.2.peg.3180, fig|573.2.peg.3181  fig|573.2.peg.386   fig|573.2.peg.8193, fig|573.2.peg.8195                                          fig|573.2.peg.4552, fig|573.2.peg.4553                      fig|573.2.peg.3987, fig|573.2.peg.3988
584.1     A.123     fig|584.1.peg.1190  fig|584.1.peg.1187  fig|584.1.peg.2624  fig|584.1.peg.1841  fig|584.1.peg.2528  fig|584.1.peg.2464  fig|584.1.peg.374                                 fig|584.1.peg.1022                      fig|584.1.peg.3026
592.2     A.123     fig|592.2.peg.1979  fig|592.2.peg.4101  fig|592.2.peg.2030  fig|592.2.peg.3094  fig|592.2.peg.2326  fig|592.2.peg.1366  fig|592.2.peg.3978                                fig|592.2.peg.1572  fig|592.2.peg.611             fig|592.2.peg.3925
594.1     A.123     fig|594.1.peg.674   fig|594.1.peg.679   fig|594.1.peg.3397  fig|594.1.peg.2823  fig|594.1.peg.4236  fig|594.1.peg.617                                           fig|594.1.peg.4423                      fig|594.1.peg.1453

About this Entry

This page contains a single entry by The SEED Team published on August 11, 2010 3:43 PM.

Downloading a Genome was the previous entry in this blog.

Video Tutorial: Creating a RAST Account is the next entry in this blog.

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