1. 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

2. http://www.genome.jp/kegg/soap/ KEGG API reference manual –Http://www.genome.jp/kegg/soap/doc/keggapi_ manual.html

3. 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

4. KEGG API SOAP/WSDL interface for the KEGG system http://soap.genome.jp/KEGG.wsdl Meta information list_pathways – list_databases, list_organisms, list_pathways PATHWAY – mark_pathway_by_objects, color_pathway_by_objects get_reactions_by_pathway – get_genes_by_pathway, get_enzymes_by_pathway, get_compounds_by_pathway, get_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

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

6. path:eco00510 rn:R06238 path:eco00511 path:eco00512 path: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

7. reaction.list R04208 R02439 R00118 R04132 R01901 R01719 R05902 R02957 R00289 R02617 R01316 R04738 R00931 R00022 R00837 R03277 R01874

8. use SOAP::Lite; http://soap.genome.jp/KEGG.wsdl $wsdl = 'http://soap.genome.jp/KEGG.wsdl'; $serv = SOAP::Lite->service($wsdl); open(FP,"reaction.list"); while($in= ){ chomp($in); print $in."\n"; bget $reaction=$serv->bget('rn:'.$in); open(OUT,">",'rn/'.$in); print OUT $reaction."\n"; close(OUT); }

9. EnsEMBL[/workspace/tcs/kegg/rn]-root- more R02738 ENTRY R02738 NAME Protein-N(pai)-phosphohistidine:sugar N(pai)- phosphotransferase DEFINITION Protein N(pai)-phosphohistidine + D-Glucose Protein histidine + alpha-D-Glucose 6-phosphate EQUATION C04085 + C00031 C00615 + C00668 RPAIR A00029 A02452 A07162 PATHWAY PATH: rn00010 Glycolysis / Gluconeogenesis ENZYME 2.7.1.69 ///

10. grep EQUATION *|sed s/:EQUATION// R02735 C00666 C00680 R02736 C01172 + C00006 C01236 + C00005 + C00080 R02737 C00029 + C00668 C00015 + C00689 R02738 C04085 + C00031 C00615 + C00668 R02739 C00668 C01172 R02740 C00668 C05345 R02746 C04230 + C00001 C00670 + C00162 R02747 C04233 + C00001 C00670 + C00162 R02748 C05512 + C00009 C00262 + C00672

11. C03785: - R01069 + R03236 + R03237 + R03238 + R03239 = 0 C03793: - R04313 = 0 C03794: - R01083 + R01135 = 0 C03838: + R04144 - R04325 - R04326 = 0 C03892: + R01801 - R02029 = 0 C03912: - R00707 - R00708 + R01248 + R01251 + R01253 = 0

12. glpsol lpt_read_prob: reading LP data from `lp.lpt'... lpt_read_prob: 1125 variables, 679 constraints lpt_read_prob: 897 lines were read lpx_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 SOLUTION Time used: 0.0 secs Memory used: 0.8M (825532 bytes)

13. Ethanol Maximize R04779 Subject To C00001: + R00658 - R00710 >= 0 C00002: - R00200 - R00235 - R01512 - R04779 >= 0 C00003: - R00710 - R00754 - R01061 >= 0 C00004: + R00710 + R00754 + R01061 >= 0 C00008: + R00200 + R01512 + R04779 >= 0 C00010: - R00235 + R02569 >= 0 C00022: + R00014 - R00200 >= 0 C00024: + R00235 - R02569 >= 0 C00033: - R00235 + R00710 >= 0 C00068: + R00014 + R03270 >= 0 C00074: + R00200 + R00658 >= 0 C00080: + R00710 + R00754 + R01061 > 0 C00084: - R00710 + R00754 >= 0 C00118: - R01061 + R01070 >= 0 C00197: - R01512 + R01518 >= 0 C00236: + R01061 + R01512 >= 0 C00631: - R00658 - R01518 >= 0 C00668: + R02738 - R02740 >= 0 C01136: + R02569 + R03270 >= 0 C05125: - R00014 - R03270 >= 0 C05345: + R02740 - R04779 >= 0 C05378: - R01070 + R04779 >= 0 P99999: + R02738 >= 100 Bounds R02378 > 0 R04779 > 0 R00200 < 0 End

15. Maximize x5 Subject To x4 - x5 =0 - x3 - x4 =0 x2 + x3 =0 x1 - x2 =0 x1 = 100 End =========================================================== Maximize x5 Subject To x4 - x5 =0 x3 - x4 =0 x2 - x3 =0 x1 - x2 =0 x1 = 100 End

17. 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

18. crt E: GGPP synthase crt B: phytoene synthase crt I: lycopene synthase from E.uredovora gps:ggpp synthase from A.fulgidus

19. Red : E.coli Blue : A.fulgidus Green: E.uredovora

21. Error & Result Files....