[Bioperl-l] Is Bio::KEGG:Enzyme implemented?

[Bryan Bishop]

On Wed, Feb 25, 2009 at 8:31 AM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Bio::SeqIO::kegg parses the database format and creates Seq objects, I show
> an example of the format below.

That doesn't look like the same thing. In the ligand/enzyme file, you
see data like this:

---------
ENTRY       EC 1.1.1.1                  Enzyme
NAME        alcohol dehydrogenase;
            aldehyde reductase;
            ADH;
            alcohol dehydrogenase (NAD);
            aliphatic alcohol dehydrogenase;
            ethanol dehydrogenase;
            NAD-dependent alcohol dehydrogenase;
            NAD-specific aromatic alcohol dehydrogenase;
            NADH-alcohol dehydrogenase;
            NADH-aldehyde dehydrogenase;
            primary alcohol dehydrogenase;
            yeast alcohol dehydrogenase
CLASS       Oxidoreductases;
            Acting on the CH-OH group of donors;
            With NAD+ or NADP+ as acceptor
SYSNAME     alcohol:NAD+ oxidoreductase
REACTION    an alcohol + NAD+ = an aldehyde or ketone + NADH + H+ [RN:R07326
            R07327]
ALL_REAC    R07326 > R00623 R00754 R02124 R04805 R04880 R06917 R06927 R08281
            R08306 R08557 R08558;
            R07327 > R00624 R08310;
            (other) R01041 R05233 R05234 R07105
SUBSTRATE   alcohol [CPD:C00069];
            NAD+ [CPD:C00003]
PRODUCT     aldehyde [CPD:C00071];
            ketone [CPD:C00709];
            NADH [CPD:C00004];
            H+ [CPD:C00080]
COFACTOR    Zinc [CPD:C00038]
COMMENT     A zinc protein. Acts on primary or secondary alcohols or
            hemi-acetals; the animal, but not the yeast, enzyme acts also on
            cyclic secondary alcohols.
REFERENCE   1
  AUTHORS   Branden, G.-I., Jornvall, H., Eklund, H. and Furugren, B.
  TITLE     Alcohol dehydrogenase.
  JOURNAL   In: Boyer, P.D. (Ed.), The Enzymes, 3rd ed., vol. 11, Academic
            Press, New York, 1975, p. 103-190.
  ORGANISM  horse, human [GN:hsa], rat [GN:rno], Saccharomyces cerevisiae
            [GN:sce]
REFERENCE   2  [PMID:320001]
  AUTHORS   Jornvall H.
  TITLE     Differences between alcohol dehydrogenases. Structural properties
            and evolutionary aspects.
  JOURNAL   Eur. J. Biochem. 72 (1977) 443-52.
  ORGANISM  horse, human [GN:hsa], rat [GN:rno], Bacillus stearotherrnophilus,
            Drosophila melanogaster [GN:dme]
REFERENCE   3
  AUTHORS   Negelein, E. and Wulff, H.-J.
  TITLE     Diphosphopyridinproteid ackohol, acetaldehyd.
  JOURNAL   Biochem. Z. 293 (1937) 351-389.
REFERENCE   4
  AUTHORS   Sund, H. and Theorell, H.
  TITLE     Alcohol dehydrogenase.
  JOURNAL   In: Boyer, P.D., Lardy, H. and Myrback, K. (Eds.), The Enzymes, 2nd
            ed., vol. 7, Academic Press, New York, 1963, p. 25-83.
  ORGANISM  horse, Saccharomyces cerevisiae [GN:sce]
REFERENCE   5  [PMID:13605979]
  AUTHORS   THEORELL H.
  TITLE     Kinetics and equilibria in the liver alcohol dehydrogenase system.
  JOURNAL   Adv. Enzymol. Relat. Subj. Biochem. 20 (1958) 31-49.
PATHWAY     PATH: ec00010  Glycolysis / Gluconeogenesis
            PATH: ec00071  Fatty acid metabolism
            PATH: ec00120  Bile acid biosynthesis
            PATH: ec00260  Glycine, serine and threonine metabolism
            PATH: ec00350  Tyrosine metabolism
            PATH: ec00624  1- and 2-Methylnaphthalene degradation
            PATH: ec00641  3-Chloroacrylic acid degradation
            PATH: ec00830  Retinol metabolism
            PATH: ec00980  Metabolism of xenobiotics by cytochrome P450
            PATH: ec00982  Drug metabolism - cytochrome P450
ORTHOLOGY   KO: K00001  alcohol dehydrogenase
            KO: K11440  choline dehydrogenase
GENES       HSA: 124(ADH1A) 125(ADH1B) 126(ADH1C) 127(ADH4) 128(ADH5) 130(ADH6)
                 131(ADH7)
            PTR: 461394(ADH4) 461395(ADH6) 461396(ADH1B) 462908(RTN4IP1)
                 471257(ADH7) 743928(ADH5) 744064(ADH1A) 744176(ADH1C)
            MCC: 697703(ADH5) 707258(ADH5) 707367 707682(ADH1A) 708520
                 711061(ADH1C)
            MMU: 11522(Adh1) 11529(Adh7) 11532(Adh5) 26876(Adh4)
<snip>
            TPE: Tpen_1006 Tpen_1516
STRUCTURES  PDB: 1A4U  1A71  1A72  1ADB  1ADC  1ADF  1ADG  1AGN  1AXE  1AXG
                 1B14  1B15  1B16  1B2L  1BTO  1CDO  1D1S  1D1T  1DEH  1E3E
                 1E3I  1E3L  1EE2  1H2B  1HDX  1HDY  1HDZ  1HET  1HEU  1HF3
                 1HLD  1HSO  1HSZ  1HT0  1HTB  1JU9  1JVB  1LDE  1LDY  1LLU
                 1M6H  1M6W  1MA0  1MC5  1MG0  1MG5  1MGO  1MP0  1N8K  1N92
                 1NTO  1NVG  1O2D  1P1R  1QLH  1QLJ  1QV6  1QV7  1R37  1RJW
                 1SBY  1TEH  1U3T  1U3U  1U3V  1U3W  1VJ0  1YE3  2EER  2FZE
                 2FZW  2HCY  2JHF  2JHG  2OHX  2OXI  3BTO  3COS  3HUD  5ADH
                 6ADH  7ADH
DBLINKS     IUBMB Enzyme Nomenclature: 1.1.1.1
            ExPASy - ENZYME nomenclature database: 1.1.1.1
            ExplorEnz - The Enzyme Database: 1.1.1.1
            ERGO genome analysis and discovery system: 1.1.1.1
            UM-BBD (Biocatalysis/Biodegradation Database): 1.1.1.1
            BRENDA, the Enzyme Database: 1.1.1.1
            CAS: 9031-72-5
///
---------

You can find this download here: (23 MB)
http://heybryan.org/~bbishop/docs/dopamine/enzyme

Skeleton "enzyme" file parser:
http://heybryan.org/~bbishop/docs/dopamine/parseenzyme.pl

- Bryan
http://heybryan.org/
1 512 203 0507