Metabolic Reconstructions Provided for Complete Prokaryotic Genomes

By The SEED Team on June 3, 2010 2:35 PM
Given a set of functional roles, one often wishes to understand what subsystems can be inferred from the set. This example reads as input a set of functional roles and constructs a table of subsystems, along with their variation codes, that can be identified. The data displayed in this simple example could form the start of a research project to gather the functional roles not connected to subsystems, to determine whether they were not connected because a small set of functional roles were not present in the input, and to seek candidates for such "missing functional roles". The ability to easily map functional roles into subsystems will improve over time, as the SEED annotation effort improves its collection of encoded subsystems [PMID: 16214803].

Example 2 Discussion

With the server packages installed, the code in example 2 can be run as follows
> perl server_paper_example2.pl < Buchnera_roles.tbl
The work of this routine is in two parts. First, we use the Subsystem Server to construct the list of role-id pairs for use later on.
	    my $sapObject = SAPserver->new();
	    my @pairs;
	    while () {
	        chomp;
	        my ($id, $role) = split(/\t/, $_);
	        push @pairs, [$role, $id];
	    }
  Then, we call the Subsystem Server method metabolic_reconstruction and process the results to produce the output table.
	    my $reconstruction = 
	        $ssObject->metabolic_reconstruction(-roles => \@pairs);
	    for my $record (@$reconstruction) {
	        my ($variantID, $role, $id) = @$record;
	        my ($subsysID, $code) = $variantID =~ /^(.+):(.+)$/;
	        print join("\t", $subsysID, $code, $role, $id) . "\n";
	    }

Example 2 Input File (Truncated)

fig|107806.1.peg.1      Anthranilate synthase, aminase component (EC 4.1.3.27) # TrpAa          82
fig|107806.1.peg.2      Anthranilate synthase, amidotransferase component (EC 4.1.3.27) # TrpAb Buchnera aphidicola str. APS (Acyrthosiphon pisum)      167
fig|107806.1.peg.3      Anthranilate synthase, amidotransferase component (EC 4.1.3.27) # TrpAb Buchnera aphidicola str. APS (Acyrthosiphon pisum)      167
fig|107806.1.peg.7      2-isopropylmalate synthase (EC 2.3.3.13)        Buchnera aphidicola str. APS (Acyrthosiphon pisum)      508
fig|107806.1.peg.8      3-isopropylmalate dehydrogenase (EC 1.1.1.85)   Buchnera aphidicola str. APS (Acyrthosiphon pisum)      353
fig|107806.1.peg.9      3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)       Buchnera aphidicola str. APS (Acyrthosiphon pisum)      462
fig|107806.1.peg.10     3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)               28
fig|107806.1.peg.11     tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA        Buchnera aphidicola str. APS (Acyrthosiphon pisum)      150
fig|107806.1.peg.12     ATP synthase A chain (EC 3.6.3.14)      Buchnera aphidicola str. APS (Acyrthosiphon pisum)      264
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Example 2 Output Table (Truncated)

tRNA processing	1	Ribonuclease P protein component (EC 3.1.26.5)	fig|107806.1.peg.24
tRNA processing	1	tRNA(Ile)-lysidine synthetase	fig|107806.1.peg.111
tRNA processing	1	tRNA-specific adenosine-34 deaminase (EC 3.5.4.-)	fig|107806.1.peg.247
tRNA processing	1	tRNA delta(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8)	fig|107806.1.peg.541
tRNA processing	1	tRNA-i(6)A37 methylthiotransferase	fig|107806.1.peg.421
tRNA processing	1	Ribonuclease T (EC 3.1.13.-)	fig|107806.1.peg.187
tRNA processing	1	tRNA pseudouridine synthase B (EC 4.2.1.70)	fig|107806.1.peg.361
tRNA processing	1	tRNA pseudouridine synthase A (EC 4.2.1.70)	fig|107806.1.peg.198
tRNA aminoacylation, Arg	1.00	Arginyl-tRNA synthetase (EC 6.1.1.19)	fig|107806.1.peg.239
Experimental-EFP	1	Translation elongation factor P	fig|107806.1.peg.29
mnm5U34 biosynthesis bacteria	1	tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA	fig|107806.1.peg.11
mnm5U34 biosynthesis bacteria	1	tRNA 5-methylaminomethyl-2-thiouridine synthase TusD	fig|107806.1.peg.507
mnm5U34 biosynthesis bacteria	1	tRNA 5-methylaminomethyl-2-thiouridine synthase TusA	fig|107806.1.peg.427
mnm5U34 biosynthesis bacteria	1	tRNA 5-methylaminomethyl-2-thiouridine synthase TusC	fig|107806.1.peg.506
mnm5U34 biosynthesis bacteria	1	GTPase and tRNA-U34 5-formylation enzyme TrmE	fig|107806.1.peg.26
mnm5U34 biosynthesis bacteria	1	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (EC 2.1.1.61)	fig|107806.1.peg.253
mnm5U34 biosynthesis bacteria	1	Cysteine desulfurase (EC 2.8.1.7)	fig|107806.1.peg.568
mnm5U34 biosynthesis bacteria	1	tRNA 5-methylaminomethyl-2-thiouridine synthase TusB	fig|107806.1.peg.505
Ribosome LSU bacterial	1	LSU ribosomal protein L18p (L5e)	fig|107806.1.peg.483
Ribosome LSU bacterial	1	LSU ribosomal protein L11p (L12e)	fig|107806.1.peg.47
Ribosome LSU bacterial	1	LSU ribosomal protein L23p (L23Ae)	fig|107806.1.peg.497
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