bio 1.4.0 → 1.4.1

data/test/data/KEGG/M00118.module

@@ -0,0 +1,44 @@
+ENTRY       M00118            Pathway   Module
+NAME        Pentose interconversion, arabinose/ribulose/xylulose/xylose
+DEFINITION  K00011 K01804 K00853 (K01786,K03080) K03331 K05351 K00854 K00011
+            K01805 K01783 (K00853,K00875) K00039
+CLASS       Metabolism; Central metabolism; Other carbohydrate metabolism
+PATHWAY     ko00040(K00011+K01804+K00853+K01786+K03080+K03331+K05351+K00854+K00011+K01805+K01783+K00853+K00875+K00039)  Pentose and glucuronate interconversions
+ORTHOLOGY   K00011  aldehyde reductase [EC:1.1.1.21] [RN:R01758 R01759]
+            K01804  L-arabinose isomerase [EC:5.3.1.4] [RN:R01761]
+            K00853  L-ribulokinase [EC:2.7.1.16] [RN:R02439]
+            K01786,K03080  L-ribulose-5-phosphate 4-epimerase [EC:5.1.3.4]
+                    [RN:R05850]
+            K03331  L-xylulose reductase [EC:1.1.1.10] [RN:R01904]
+            K05351  D-xylulose reductase [EC:1.1.1.9] [RN:R01896]
+            K00854  xylulokinase [EC:2.7.1.17] [RN:R01639]
+            K00011  aldehyde reductase [EC:1.1.1.21] [RN:R01431]
+            K01805  xylose isomerase [EC:5.3.1.5] [RN:R01432]
+            K01783  ribulose-phosphate 3-epimerase [EC:5.1.3.1] [RN:R01529]
+            K00853,K00875  ribulokinase [EC:2.7.1.16 2.7.1.47] [RN:R01526]
+            K00039  ribitol 2-dehydrogenase [EC:1.1.1.56] [RN:R01895]
+REACTION    R01903  C00312 -> C00532
+            R01758,R01759  C00532 -> C00259
+            R01761  C00259 -> C00508
+            R02439  C00508 -> C01101
+            R05850  C01101 -> C00231
+            R01904  C00312 -> C00379
+            R01896  C00379 -> C00310
+            R01639  C00310 -> C00231
+            R01431  C00379 -> C00181
+            R01432  C00181 -> C00310
+            R01529  C00199 -> C00231
+            R01526  C00231 -> C00309
+            R01895  C00309 -> C00474
+COMPOUND    C00312  L-Xylulose
+            C00532  L-Arabitol
+            C00259  L-Arabinose
+            C00508  L-Ribulose
+            C01101  L-Ribulose 5-phosphate
+            C00231  D-Xylulose 5-phosphate
+            C00379  Xylitol
+            C00310  D-Xylulose
+            C00181  D-Xylose
+            C00199  D-Ribulose 5-phosphate
+            C00309  D-Ribulose
+            C00474  Ribitol

data/test/data/KEGG/T00005.genome

@@ -0,0 +1,140 @@
+ENTRY       T00005            Complete  Genome
+NAME        sce, S.cerevisiae, YEAST, 4932
+DEFINITION  Saccharomyces cerevisiae S288C
+ANNOTATION  manual
+TAXONOMY    TAX:4932
+  LINEAGE   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
+            Saccharomycetes; Saccharomycetales; Saccharomycetaceae;
+            Saccharomyces
+DATA_SOURCE RefSeq
+ORIGINAL_DB SGD
+            MIPS
+CHROMOSOME  I
+  SEQUENCE  RS:NC_001133
+  LENGTH    230208
+CHROMOSOME  II
+  SEQUENCE  RS:NC_001134
+  LENGTH    813178
+CHROMOSOME  III
+  SEQUENCE  RS:NC_001135
+  LENGTH    316617
+CHROMOSOME  IV
+  SEQUENCE  RS:NC_001136
+  LENGTH    1531919
+CHROMOSOME  V
+  SEQUENCE  RS:NC_001137
+  LENGTH    576869
+CHROMOSOME  VI
+  SEQUENCE  RS:NC_001138
+  LENGTH    270148
+CHROMOSOME  VII
+  SEQUENCE  RS:NC_001139
+  LENGTH    1090947
+CHROMOSOME  VIII
+  SEQUENCE  RS:NC_001140
+  LENGTH    562643
+CHROMOSOME  IX
+  SEQUENCE  RS:NC_001141
+  LENGTH    439885
+CHROMOSOME  X
+  SEQUENCE  RS:NC_001142
+  LENGTH    745741
+CHROMOSOME  XI
+  SEQUENCE  RS:NC_001143
+  LENGTH    666454
+CHROMOSOME  XII
+  SEQUENCE  RS:NC_001144
+  LENGTH    1078175
+CHROMOSOME  XIII
+  SEQUENCE  RS:NC_001145
+  LENGTH    924429
+CHROMOSOME  XIV
+  SEQUENCE  RS:NC_001146
+  LENGTH    784333
+CHROMOSOME  XV
+  SEQUENCE  RS:NC_001147
+  LENGTH    1091289
+CHROMOSOME  XVI
+  SEQUENCE  RS:NC_001148
+  LENGTH    948062
+CHROMOSOME  MT (mitochondrion); Circular
+  SEQUENCE  RS:NC_001224
+  LENGTH    85779
+STATISTICS  Number of nucleotides:      12156676
+            Number of protein genes:        5881
+            Number of RNA genes:             414
+REFERENCE   PMID:8849441
+  AUTHORS   Goffeau A, et al.
+  TITLE     Life with 6000 genes.
+  JOURNAL   Science 274:546-67 (1996)
+REFERENCE   PMID:7731988 (chromosome I)
+  AUTHORS   Bussey H, et al.
+  TITLE     The nucleotide sequence of chromosome I from Saccharomyces
+            cerevisiae.
+  JOURNAL   Proc Natl Acad Sci U S A 92:3809-13 (1995)
+REFERENCE   PMID:7813418 (chromosome II)
+  AUTHORS   Feldmann,H., et al.
+  TITLE     Complete DNA sequence of yeast chromosome II.
+  JOURNAL   EMBO J 13:5795-809 (1994)
+REFERENCE   PMID:1574125 (chromosome III)
+  AUTHORS   Oliver,S.G., et al.
+  TITLE     The complete DNA sequence of yeast chromosome III.
+  JOURNAL   Nature 357:38-46 (1992)
+REFERENCE   PMID:9169867 (chromosome IV)
+  AUTHORS   Jacq C, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.
+  JOURNAL   Nature 387(6632 Suppl):75-8 (1997)
+REFERENCE   PMID:9169868 (chromosome V)
+  AUTHORS   Dietrich FS, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome V.
+  JOURNAL   Nature 387(6632 Suppl):78-81 (1997)
+REFERENCE   PMID:7670463 (chromosome VI)
+  AUTHORS   Murakami,Y., et al.
+  TITLE     Analysis of the nucleotide sequence of chromosome VI from
+            Saccharomyces cerevisiae.
+  JOURNAL   Nat Genet 10:261-8 (1995)
+REFERENCE   PMID:9169869 (chromosome VII)
+  AUTHORS   Tettelin H, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.
+  JOURNAL   Nature 387(6632 Suppl):81-4 (1997)
+REFERENCE   PMID:8091229 (chromosome VIII)
+  AUTHORS   Johnston,M., et al.
+  TITLE     Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
+            VIII.
+  JOURNAL   Science 265:2077-82 (1994)
+REFERENCE   PMID:9169870 (chromosome IX)
+  AUTHORS   Churcher C, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.
+  JOURNAL   Nature 387(6632 Suppl):84-7 (1997)
+REFERENCE   PMID:8641269 (chromosome X)
+  AUTHORS   Galibert,F., et al.
+  TITLE     Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
+            X.
+  JOURNAL   EMBO J 15:2031-49 (1996)
+REFERENCE   PMID:8196765 (chromosome XI)
+  AUTHORS   Dujon,B., et al.
+  TITLE     Complete DNA sequence of yeast chromosome XI.
+  JOURNAL   Nature 369:371-8 (1994)
+REFERENCE   PMID:9169871 (chromosome XII)
+  AUTHORS   Johnston M, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.
+  JOURNAL   Nature 387(6632 Suppl):87-90 (1997)
+REFERENCE   PMID:9169872 (chromosome XIII)
+  AUTHORS   Bowman S, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome
+            XIII.
+  JOURNAL   Nature 387(6632 Suppl):90-3 (1997)
+REFERENCE   PMID:9169873 (chromosome XIV)
+  AUTHORS   Philippsen P, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV
+            and its evolutionary implications.
+  JOURNAL   Nature 387(6632 Suppl):93-8 (1997)
+REFERENCE   PMID:9169874 (chromosome XV)
+  AUTHORS   Dujon B, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.
+  JOURNAL   Nature 387(6632 Suppl):98-102 (1997)
+REFERENCE   PMID:9169875 (chromosome XVI)
+  AUTHORS   Bussey H, et al.
+  TITLE     The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.
+  JOURNAL   Nature 387(6632 Suppl):103-5 (1997)
+///

data/test/data/KEGG/T00070.genome

@@ -0,0 +1,34 @@
+ENTRY       T00070            Complete  Genome
+NAME        atu, A.tumefaciens, AGRT5, 176299
+DEFINITION  Agrobacterium tumefaciens C58
+ANNOTATION  manual
+TAXONOMY    TAX:176299
+  LINEAGE   Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
+            Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium
+DATA_SOURCE RefSeq
+ORIGINAL_DB UWash
+DISEASE     Crown gall disease in plants
+COMMENT     Originally called Agrobacterium tumefaciens C58
+            (U.Washington/Dupont) to distinguish from Agrobacterium tumefaciens
+            C58 (Cereon) [GN:atc]
+CHROMOSOME  Circular
+  SEQUENCE  RS:NC_003062
+  LENGTH    2841580
+CHROMOSOME  L (linear chromosome)
+  SEQUENCE  RS:NC_003063
+  LENGTH    2075577
+PLASMID  Ti; Circular
+  SEQUENCE  RS:NC_003065
+  LENGTH    214233
+PLASMID  AT; Circular
+  SEQUENCE  RS:NC_003064
+  LENGTH    542868
+STATISTICS  Number of nucleotides:       5674258
+            Number of protein genes:        5355
+            Number of RNA genes:              74
+REFERENCE   PMID:11743193
+  AUTHORS   Wood DW, et al.
+  TITLE     The genome of the natural genetic engineer Agrobacterium
+            tumefaciens C58.
+  JOURNAL   Science 294:2317-23 (2001)
+///

data/test/data/KEGG/b0529.gene

@@ -0,0 +1,47 @@
+ENTRY       b0529             CDS       E.coli
+NAME        folD, ads, ECK0522, JW0518
+DEFINITION  bifunctional 5,10-methylene-tetrahydrofolate
+            dehydrogenase/5,10-methylene-tetrahydrofolate cyclohydrolase
+            (EC:1.5.1.5 3.5.4.9)
+ORTHOLOGY   K01491  methylenetetrahydrofolate dehydrogenase (NADP+) /
+                    methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]
+PATHWAY     eco00630  Glyoxylate and dicarboxylate metabolism
+            eco00670  One carbon pool by folate
+            eco01100  Metabolic pathways
+CLASS       Metabolism; Carbohydrate Metabolism; Glyoxylate and dicarboxylate
+            metabolism [PATH:eco00630]
+            Metabolism; Metabolism of Cofactors and Vitamins; One carbon pool by
+            folate [PATH:eco00670]
+POSITION    complement(556098..556964)
+MOTIF       Pfam: THF_DHG_CYH_C THF_DHG_CYH Amidohydro_1
+            PROSITE: THF_DHG_CYH_1 THF_DHG_CYH_2
+DBLINKS     NCBI-GI: 16128513
+            NCBI-GeneID: 945221
+            RegulonDB: B0529
+            EcoGene: EG10328
+            ECOCYC: EG10328
+            UniProt: P24186
+STRUCTURE   PDB: 1B0A
+AASEQ       288
+            MAAKIIDGKTIAQQVRSEVAQKVQARIAAGLRAPGLAVVLVGSNPASQIYVASKRKACEE
+            VGFVSRSYDLPETTSEAELLELIDTLNADNTIDGILVQLPLPAGIDNVKVLERIHPDKDV
+            DGFHPYNVGRLCQRAPRLRPCTPRGIVTLLERYNIDTFGLNAVVIGASNIVGRPMSMELL
+            LAGCTTTVTHRFTKNLRHHVENADLLIVAVGKPGFIPGDWIKEGAIVIDVGINRLENGKV
+            VGDVVFEDAAKRASYITPVPGGVGPMTVATLIENTLQACVEYHDPQDE
+NTSEQ       867
+            atggcagcaaagattattgacggtaaaacgattgcgcagcaggtgcgctctgaagttgct
+            caaaaagttcaggcgcgtattgcagccggactgcgggcaccaggactggccgttgtgctg
+            gtgggtagtaaccctgcatcgcaaatttatgtcgcaagcaaacgcaaggcttgtgaagaa
+            gtcgggttcgtctcccgctcttatgacctcccggaaaccaccagcgaagcggagctgctg
+            gagcttatcgatacgctgaatgccgacaacaccatcgatggcattctggttcaactgccg
+            ttaccggcgggtattgataacgtcaaagtgctggaacgtattcatccggacaaagacgtg
+            gacggtttccatccttacaacgtcggtcgtctgtgccagcgcgcgccgcgtctgcgtccc
+            tgcaccccgcgcggtatcgtcacgctgcttgagcgttacaacattgataccttcggcctc
+            aacgccgtggtgattggcgcatcgaatatcgttggccgcccgatgagcatggaactgctg
+            ctggcaggttgcaccactacagtgactcaccgcttcactaaaaatctgcgtcatcacgta
+            gaaaatgccgatctattgatcgttgccgttggcaagccaggctttattcccggtgactgg
+            atcaaagaaggcgcaattgtgattgatgtcggcatcaaccgtctggaaaatggcaaagtt
+            gtgggcgacgtcgtgtttgaagacgcggctaaacgcgcctcatacattacgcctgttccc
+            ggcggcgttggcccgatgacggttgccacgctgattgaaaacacgctacaggcgtgcgtt
+            gaatatcatgatccacaggatgagtaa
+///

data/test/data/KEGG/ec00072.pathway

@@ -0,0 +1,23 @@
+ENTRY       ec00072                     Pathway
+NAME        Synthesis and degradation of ketone bodies
+CLASS       Metabolism; Lipid Metabolism
+PATHWAY_MAP ec00072  Synthesis and degradation of ketone bodies
+MODULE      M00177  Ketone body biosynthesis, acetyl-CoA => acetoacetate/3-hydroxybutyrate/acetone [PATH:ec00072]
+ENZYME      1.1.1.30
+            2.3.1.9
+            2.3.3.10
+            2.8.3.5
+            4.1.1.4
+            4.1.3.4
+COMPOUND    C00024  Acetyl-CoA
+            C00164  Acetoacetate
+            C00207  Acetone
+            C00332  Acetoacetyl-CoA
+            C00356  (S)-3-Hydroxy-3-methylglutaryl-CoA
+            C01089  (R)-3-Hydroxybutanoate
+REL_PATHWAY ec00010  Glycolysis / Gluconeogenesis
+            ec00071  Fatty acid metabolism
+            ec00620  Pyruvate metabolism
+            ec00650  Butanoate metabolism
+KO_PATHWAY  ko00072
+///

data/test/data/KEGG/hsa00790.pathway

@@ -0,0 +1,59 @@
+ENTRY       hsa00790                    Pathway
+NAME        Folate biosynthesis - Homo sapiens (human)
+CLASS       Metabolism; Metabolism of Cofactors and Vitamins
+PATHWAY_MAP hsa00790  Folate biosynthesis
+MODULE      M00251  Folate biosynthesis, GTP => THF [PATH:hsa00790]
+            M00304  Methanogenesis [PATH:hsa00790]
+DISEASE     H00167  Phenylketonuria (PKU)
+            H00213  Hypophosphatasia
+DRUG        D00142  Methotrexate (JP15/USP/INN)
+            D02115  Methotrexate sodium
+            D06238  Trimetrexate (USAN/INN)
+            D06239  Trimetrexate glucuronate (USAN)
+DBLINKS     GO: 0046656
+ORGANISM    Homo sapiens (human) [GN:hsa]
+GENE        2643  GCH1, DYT14, DYT5, DYT5a, GCH, GTP-CH-1, GTPCH1, HPABH4B [KO:K01495] [EC:3.5.4.16]
+            248  ALPI, IAP [KO:K01077] [EC:3.1.3.1]
+            249  ALPL, AP-TNAP, APTNAP, FLJ40094, FLJ93059, HOPS, MGC161443, MGC167935, TNAP, TNSALP [KO:K01077] [EC:3.1.3.1]
+            250  ALPP, ALP, FLJ61142, PALP, PLAP [KO:K01077] [EC:3.1.3.1]
+            251  ALPPL2, ALPG, ALPPL, GCAP [KO:K01077] [EC:3.1.3.1]
+            1719  DHFR, DHFRP1, DYR [KO:K00287] [EC:1.5.1.3]
+            2356  FPGS [KO:K01930] [EC:6.3.2.17]
+            8836  GGH, GH [KO:K01307] [EC:3.4.19.9]
+            5805  PTS, FLJ97081, PTPS [KO:K01737] [EC:4.2.3.12]
+            6697  SPR, SDR38C1 [KO:K00072] [EC:1.1.1.153]
+            5860  QDPR, DHPR, FLJ42391, PKU2, SDR33C1 [KO:K00357] [EC:1.5.1.34]
+COMPOUND    C00044  GTP
+            C00101  Tetrahydrofolate
+            C00251  Chorismate
+            C00266  Glycolaldehyde
+            C00268  Dihydrobiopterin
+            C00272  Tetrahydrobiopterin
+            C00415  Dihydrofolate
+            C00504  Folate
+            C00568  4-Aminobenzoate
+            C00921  Dihydropteroate
+            C01217  5,6,7,8-Tetrahydromethanopterin
+            C01300  2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine
+            C03541  Tetrahydrofolyl-[Glu](n)
+            C03684  6-Pyruvoyltetrahydropterin
+            C04244  6-Lactoyl-5,6,7,8-tetrahydropterin
+            C04807  2-Amino-7,8-dihydro-4-hydroxy-6-(diphosphooxymethyl)pteridine
+            C04874  2-Amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine
+            C04895  2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate
+            C05922  Formamidopyrimidine nucleoside triphosphate
+            C05923  2,5-Diaminopyrimidine nucleoside triphosphate
+            C05924  Molybdopterin
+            C05925  Dihydroneopterin phosphate
+            C05926  Neopterin
+            C05927  7,8-Dihydromethanopterin
+            C06148  2,5-Diamino-6-(5'-triphosphoryl-3',4'-trihydroxy-2'-oxopentyl)-amino-4-oxopyrimidine
+            C06149  6-(3'-Triphosphoryl-1'-methylglyceryl)-7-methyl-7,8-dihydrobiopterin
+            C09332  Tetrahydrofolyl-[Glu](2)
+            C11355  4-Amino-4-deoxychorismate
+REL_PATHWAY hsa00230  Purine metabolism
+            hsa00400  Phenylalanine, tyrosine and tryptophan biosynthesis
+            hsa00670  One carbon pool by folate
+            hsa00680  Methane metabolism
+KO_PATHWAY  ko00790
+///

data/test/data/KEGG/ko00312.pathway

@@ -0,0 +1,16 @@
+ENTRY       ko00312                     Pathway
+NAME        beta-Lactam resistance
+CLASS       Metabolism; Biosynthesis of Other Secondary Metabolites
+PATHWAY_MAP ko00312  beta-Lactam resistance
+DRUG        D00660  Tazobactam (JAN/USAN/INN)
+ORTHOLOGY   K02172  bla regulator protein blaR1
+            K02171  penicillinase repressor
+            K01467  beta-lactamase [EC:3.5.2.6]
+            K02352  drp35
+            K02547  methicillin resistance protein
+            K02546  methicillin resistance regulatory protein
+            K02545  penicillin-binding protein 2 prime
+COMPOUND    C00039  DNA
+            C03438  beta-Lactam antibiotics
+REL_PATHWAY ko00311  Penicillin and cephalosporin biosynthesis
+///

data/test/data/KEGG/map00030.pathway

@@ -0,0 +1,37 @@
+ENTRY       map00030                    Pathway
+NAME        Pentose phosphate pathway
+DESCRIPTION The pentose phosphate pathway is a process of glucose turnover that produces NADPH as reducing equivalents and pentoses as essential parts of nucleotides. There are two different phases in the pathway. One is irreversible oxidative phase in which glucose-6P is converted to ribulose-5P by oxidative decarboxylation, and NADPH is generated [MD:M00006]. The other is reversible non-oxidative phase in which phosphorylated sugars are interconverted to generate xylulose-5P, ribulose-5P, and ribose-5P [MD:M00007]. Phosphoribosyl pyrophosphate (PRPP) formed from ribose-5P [MD:M00005] is an activated compound used in the biosynthesis of histidine and purine/pyrimidine nucleotides. This pathway map also shows the Entner-Doudoroff pathway where 6-P-gluconate is dehydrated and then cleaved into pyruvate and glyceraldehyde-3P [MD:M00008].
+CLASS       Metabolism; Carbohydrate Metabolism
+PATHWAY_MAP map00030  Pentose phosphate pathway
+MODULE      M00004  Pentose phosphate pathway (Pentose phosphate cycle) [PATH:map00030]
+            M00005  PRPP biosynthesis, ribose 5P -> PRPP [PATH:map00030]
+            M00006  Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P [PATH:map00030]
+            M00007  Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P [PATH:map00030]
+            M00008  Entner-Doudoroff pathway, glucose-6P => glyceraldehyde-3P + pyruvate [PATH:map00030]
+            M00680  Semi-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde-3P + pyruvate [PATH:map00030]
+            M00681  Non-phosphorylative Entner-Doudoroff pathway, gluconate => glyceraldehyde + pyruvate [PATH:map00030]
+DISEASE     H00196  Phosphoribosylpyrophosphate synthetase I superactivity
+DBLINKS     GO: 0006098
+REFERENCE   (map 3)
+  AUTHORS   Nishizuka Y (ed).
+  TITLE     [Metabolic Maps] (In Japanese)
+  JOURNAL   Tokyo Kagaku Dojin (1980)
+REFERENCE   (map 4)
+  AUTHORS   Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
+  TITLE     [Cellular Functions and Metabolic Maps] (In Japanese)
+  JOURNAL   Tokyo Kagaku Dojin (1997)
+REFERENCE   
+  AUTHORS   Michal G.
+  TITLE     Biochemical Pathways
+  JOURNAL   Wiley (1999)
+REFERENCE   PMID:12700258
+  AUTHORS   Hove-Jensen B, Rosenkrantz TJ, Haldimann A, Wanner BL.
+  TITLE     Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways.
+  JOURNAL   J Bacteriol 185:2793-801 (2003)
+REL_PATHWAY map00010  Glycolysis / Gluconeogenesis
+            map00040  Pentose and glucuronate interconversions
+            map00230  Purine metabolism
+            map00240  Pyrimidine metabolism
+            map00340  Histidine metabolism
+KO_PATHWAY  ko00030
+///

data/test/data/KEGG/map00052.pathway

@@ -0,0 +1,13 @@
+ENTRY       map00052                    Pathway
+NAME        Galactose metabolism
+CLASS       Metabolism; Carbohydrate Metabolism
+PATHWAY_MAP map00052  Galactose metabolism
+MODULE      M00097  UDP-glucose and UDP-galactose biosynthesis, Glc-1P/Gal-1P => UDP-Glc/UDP-Gal
+            M00614  PTS system, N-acetylgalactosamine-specific II component
+            M00616  PTS system, galactitol-specific II component
+            M00618  PTS system, lactose-specific II component
+            M00624  PTS system, galactosamine-specific II component
+REL_PATHWAY map00010  Glycolysis / Gluconeogenesis
+            map00040  Pentose and glucuronate interconversions
+            map00051  Fructose and mannose metabolism
+            map00520  Amino sugar and nucleotide sugar metabolism

data/test/data/KEGG/rn00250.pathway

@@ -0,0 +1,114 @@
+ENTRY       rn00250                     Pathway
+NAME        Alanine, aspartate and glutamate metabolism
+CLASS       Metabolism; Amino Acid Metabolism
+PATHWAY_MAP rn00250  Alanine, aspartate and glutamate metabolism
+MODULE      M00017  Glutamate biosynthesis, oxoglutarate => glutamate (glutamate dehydrogenase) [PATH:rn00250]
+            M00018  Glutamine biosynthesis, glutamate => glutamine [PATH:rn00250]
+            M00019  Glutamate biosynthesis, oxoglutarete => glutamate (glutamate synthase) [PATH:rn00250]
+            M00021  Aspartate biosynthesis, oxaloacetate => aspartate [PATH:rn00250]
+            M00022  Asparagine biosynthesis, aspartate => asparagine [PATH:rn00250]
+            M00026  Alanine biosynthesis, pyruvate => alanine [PATH:rn00250]
+            M00038  Glutamine degradation, glutamine => glutamate + NH3 [PATH:rn00250]
+            M00040  GABA (gamma-Aminobutyrate) shunt [PATH:rn00250]
+            M00044  Aspartate degradation, aspartate => fumarate [PATH:rn00250]
+            M00045  Aspartate degradation, aspartate => oxaloacetate [PATH:rn00250]
+            M00046  Asparagine degradation, asparagine => aspartate +NH3 [PATH:rn00250]
+DISEASE     H00074  Canavan disease (CD)
+            H00185  Citrullinemia (CTLN)
+            H00197  Adenylosuccinate lyase deficiency
+DBLINKS     GO: 0006522 0006531 0006536
+REACTION    R00093  L-glutamate:NAD+ oxidoreductase (transaminating)
+            R00114  L-Glutamate:NADP+ oxidoreductase (transaminating)
+            R00149  Carbon-dioxide:ammonia ligase (ADP-forming,carbamate-phosphorylating)
+            R00243  L-Glutamate:NAD+ oxidoreductase (deaminating)
+            R00248  L-Glutamate:NADP+ oxidoreductase (deaminating)
+            R00253  L-Glutamate:ammonia ligase (ADP-forming)
+            R00256  L-Glutamine amidohydrolase
+            R00258  L-Alanine:2-oxoglutarate aminotransferase
+            R00261  L-glutamate 1-carboxy-lyase (4-aminobutanoate-forming)
+            R00269  2-Oxoglutaramate amidohydrolase
+            R00348  2-Oxosuccinamate amidohydrolase
+            R00355  L-Aspartate:2-oxoglutarate aminotransferase
+            R00357  L-Aspartic acid:oxygen oxidoreductase (deaminating)
+            R00359  D-Aspartate:oxygen oxidoreductase (deaminating)
+            R00369  L-Alanine:glyoxylate aminotransferase
+            R00396  L-Alanine:NAD+ oxidoreductase (deaminating)
+            R00397  L-aspartate 4-carboxy-lyase (L-alanine-forming)
+            R00400  L-alanine:oxaloacetate aminotransferase
+            R00483  L-aspartate:ammonia ligase (AMP-forming)
+            R00484  N-Carbamoyl-L-aspartate amidohydrolase
+            R00485  L-Asparagine amidohydrolase
+            R00487  Acetyl-CoA:L-aspartate N-acetyltransferase
+            R00488  N-Acetyl-L-aspartate amidohydrolase
+            R00490  L-Aspartate ammonia-lyase
+            R00491  aspartate racemase
+            R00575  hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)
+            R00576  L-Glutamine:pyruvate aminotransferase
+            R00578  L-aspartate:L-glutamine amido-ligase (AMP-forming)
+            R00707  (S)-1-pyrroline-5-carboxylate:NAD+ oxidoreductase
+            R00708  (S)-1-pyrroline-5-carboxylate:NADP+ oxidoreductase
+            R00713  Succinate-semialdehyde:NAD+ oxidoreductase
+            R00714  Succinate-semialdehyde:NADP+ oxidoreductase
+            R00768  L-glutamine:D-fructose-6-phosphate isomerase (deaminating)
+            R01072  5-phosphoribosylamine:diphosphate phospho-alpha-D-ribosyltransferase (glutamate-amidating)
+            R01083  N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming)
+            R01086  2-(Nomega-L-arginino)succinate arginine-lyase (fumarate-forming)
+            R01135  IMP:L-aspartate ligase (GDP-forming)
+            R01346  L-Asparagine:2-oxo-acid aminotransferase
+            R01397  carbamoyl-phosphate:L-aspartate carbamoyltransferase
+            R01648  4-Aminobutanoate:2-oxoglutarate aminotransferase
+            R01954  L-Citrulline:L-aspartate ligase (AMP-forming)
+COMPOUND    C00014  NH3
+            C00022  Pyruvate
+            C00025  L-Glutamate
+            C00026  2-Oxoglutarate
+            C00036  Oxaloacetate
+            C00041  L-Alanine
+            C00042  Succinate
+            C00049  L-Aspartate
+            C00064  L-Glutamine
+            C00122  Fumarate
+            C00152  L-Asparagine
+            C00169  Carbamoyl phosphate
+            C00232  Succinate semialdehyde
+            C00334  4-Aminobutanoate
+            C00352  D-Glucosamine 6-phosphate
+            C00402  D-Aspartate
+            C00438  N-Carbamoyl-L-aspartate
+            C00940  2-Oxoglutaramate
+            C01042  N-Acetyl-L-aspartate
+            C02362  2-Oxosuccinamate
+            C03090  5-Phosphoribosylamine
+            C03406  N-(L-Arginino)succinate
+            C03794  N6-(1,2-Dicarboxyethyl)-AMP
+            C03912  (S)-1-Pyrroline-5-carboxylate
+REFERENCE   
+  AUTHORS   Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
+  TITLE     [Cellular Functions and Metabolic Maps] (In Japanese)
+  JOURNAL   Tokyo Kagaku Dojin (1997)
+REFERENCE   PMID:9687539
+  AUTHORS   Wu G
+  TITLE     Intestinal mucosal amino acid catabolism.
+  JOURNAL   J Nutr 128:1249-52 (1998)
+REL_PATHWAY rn00010  Glycolysis / Gluconeogenesis
+            rn00020  Citrate cycle (TCA cycle)
+            rn00230  Purine metabolism
+            rn00240  Pyrimidine metabolism
+            rn00253  Tetracycline biosynthesis
+            rn00260  Glycine, serine and threonine metabolism
+            rn00300  Lysine biosynthesis
+            rn00330  Arginine and proline metabolism
+            rn00340  Histidine metabolism
+            rn00410  beta-Alanine metabolism
+            rn00460  Cyanoamino acid metabolism
+            rn00471  D-Glutamine and D-glutamate metabolism
+            rn00473  D-Alanine metabolism
+            rn00480  Glutathione metabolism
+            rn00650  Butanoate metabolism
+            rn00660  C5-Branched dibasic acid metabolism
+            rn00760  Nicotinate and nicotinamide metabolism
+            rn00770  Pantothenate and CoA biosynthesis
+            rn00860  Porphyrin and chlorophyll metabolism
+            rn00910  Nitrogen metabolism
+KO_PATHWAY  ko00250
+///