Biosynthesis of

生科系博士班 884234 李曉青資工系博士班 914338 張君天資工系博士班 928307 林沿妊

Group 3

http://www.genome.jp/kegg/soap/

• KEGG API reference manual – Http://www.genome.jp/kegg/soap/doc/

keggapi_manual.html

Install SOAP::Lite

# perl -MCPAN -e shell

cpan shell -- CPAN exploration and modules installation (v1.61)

ReadLine support available (try 'install Bundle::CPAN')

cpan> install SOAP::Lite

KEGG APISOAP/WSDL interface for the KEGG system

• http://soap.genome.jp/KEGG.wsdl• Meta information

– list_databases, list_organisms, list_pathwayslist_pathways • PATHWAY

– mark_pathway_by_objects, color_pathway_by_objects – get_genes_by_pathway, get_enzymes_by_pathway,

get_compounds_by_pathway, get_reactions_by_pathwayget_reactions_by_pathway – get_pathways_by_genes, get_pathways_by_enzymes,

get_pathways_by_compounds, get_pathways_by_reactions – get_linked_pathways – get_genes_by_enzyme, get_enzymes_by_gene – get_enzymes_by_compound, get_enzymes_by_reaction,

get_compounds_by_enzyme, get_compounds_by_reaction, get_reactions_by_enzyme, get_reactions_by_compound

use SOAP::Lite;$wsdl = 'http://soap.genome.jp/KEGG.wsdl'http://soap.genome.jp/KEGG.wsdl';$serv = SOAP::Lite->service($wsdl);$pathways=$serv->list_pathwayslist_pathways("eco");foreach $i (@{$pathways}) { print $i->{entry_id}."\n"; $reactions=$serv->get_reactions_by_pathwayget_reactions_by_pathway($i-

>{entry_id}); foreach $j (@{$reactions}){ print "\t".$j."\n"; $j=~ /rn:(.+)/; $reaction{$1}++; }}open(FP,">","reaction.list");foreach $i (keys %reaction){ print FP $i."\n";}

path:eco00510 rn:R06238path:eco00511 path:eco00512path:eco00520 rn:R00286 rn:R00289 rn:R00291 rn:R00501 rn:R00502 rn:R02328 rn:R02771 rn:R02774 rn:R02775 rn:R02777 rn:R02983 rn:R02984 rn:R04778 rn:R04937 rn:R04938

reaction.listR04208R02439R00118R04132R01901R01719R05902R02957R00289R02617R01316R04738R00931R00022R00837R03277R01874

use SOAP::Lite;

$wsdl = 'http://soap.genome.jp/KEGG.wsdlhttp://soap.genome.jp/KEGG.wsdl';

$serv = SOAP::Lite->service($wsdl);open(FP,"reaction.list");while($in=<FP>){chomp($in); print $in."\n"; $reaction=$serv->bgetbget('rn:'.$in); open(OUT,">",'rn/'.$in); print OUT $reaction."\n"; close(OUT);}

EnsEMBL[/workspace/tcs/kegg/rn]-root- more R02738ENTRY R02738NAME Protein-N(pai)-phosphohistidine:sugar

N(pai)-phosphotransferaseDEFINITION Protein N(pai)-phosphohistidine + D-

Glucose <=> Protein histidine + alpha-D-Glucose 6-phosphate

EQUATION C04085 + C00031 <=> C00615 + C00668

RPAIR A00029 A02452 A07162PATHWAY PATH: rn00010 Glycolysis /

GluconeogenesisENZYME 2.7.1.69///

grep EQUATION *|sed s/:EQUATION//

R02735 C00666 <=> C00680R02736 C01172 + C00006 <=> C01236 + C00005 + C00080R02737 C00029 + C00668 <=> C00015 + C00689R02738 C04085 + C00031 <=> C00615 + C00668R02739 C00668 <=> C01172R02740 C00668 <=> C05345R02746 C04230 + C00001 <=> C00670 + C00162R02747 C04233 + C00001 <=> C00670 + C00162R02748 C05512 + C00009 <=> C00262 + C00672

C03785: - R01069 + R03236 + R03237 + R03238 + R03239 = 0

C03793: - R04313 = 0C03794: - R01083 + R01135 = 0C03838: + R04144 - R04325 - R04326 = 0C03892: + R01801 - R02029 = 0C03912: - R00707 - R00708 + R01248 +

R01251 + R01253 = 0

glpsol

lpt_read_prob: reading LP data from `lp.lpt'...lpt_read_prob: 1125 variables, 679 constraintslpt_read_prob: 897 lines were readlpx_adv_basis: size of triangular part = 679 0: objval = -1.000000000e+02 infeas =

1.000000000e+00 (0) 11: objval = -1.000000000e+02 infeas =

3.333333333e-01 (0)PROBLEM HAS NO FEASIBLE SOLUTIONPROBLEM HAS NO FEASIBLE SOLUTIONTime used: 0.0 secsMemory used: 0.8M (825532 bytes)

EthanolMaximize R04779Subject ToC00001: + R00658 - R00710 >= 0

C00002: - R00200 - R00235 - R01512 - R04779 >= 0C00003: - R00710 - R00754 - R01061 >= 0C00004: + R00710 + R00754 + R01061 >= 0

C00008: + R00200 + R01512 + R04779 >= 0C00010: - R00235 + R02569 >= 0C00022: + R00014 - R00200 >= 0C00024: + R00235 - R02569 >= 0C00033: - R00235 + R00710 >= 0C00068: + R00014 + R03270 >= 0C00074: + R00200 + R00658 >= 0C00080: + R00710 + R00754 + R01061 > 0C00084: - R00710 + R00754 >= 0C00118: - R01061 + R01070 >= 0C00197: - R01512 + R01518 >= 0C00236: + R01061 + R01512 >= 0C00631: - R00658 - R01518 >= 0

C00668: + R02738 - R02740 >= 0C01136: + R02569 + R03270 >= 0C05125: - R00014 - R03270 >= 0

C05345: + R02740 - R04779 >= 0C05378: - R01070 + R04779 >= 0P99999: + R02738 >= 100BoundsR02378 > 0R04779 > 0R00200 < 0End

Maximize x5Subject To x4 - x5 =0 - x3 - x4 =0 x2 + x3 =0 x1 - x2 =0 x1 = 100End

===========================================================Maximize x5Subject To x4 - x5 =0 x3 - x4 =0 x2 - x3 =0 x1 - x2 =0 x1 = 100End

Lycopene

•R02061 C00448 + C00129 <=> C00013 + C00353

•R02065 2 C00353 <=> C00013 + C03427 + C00080

•R04218 C03427 + C00080 + C00005 <=> C00013 + C05421 + C00006

http://www.genome.jp/dbget-bin/show_pathway?rn00100

•R04786 C05413 <=> C05414 + C00282

crt E: GGPP synthasecrt B: phytoene synthasecrt I: lycopene synthase from E.uredovora gps:ggpp synthase

from A.fulgidus

Red : E.coli

Blue : A.fulgidus

Green: E.uredovora

Error & Result

• Files....