[Bioperl-l] Is Bio::KEGG:Enzyme implemented?
Brian Osborne
bosborne11 at verizon.net
Wed Feb 25 14:45:56 UTC 2009
Bryan,
Right, more like a "reaction" file, which builds pathways. No parser
like this in the core Bioperl, no. In principle this would fit into
bioperl-network but that package only has parsers for PSI-MI and
simple pathway formats like DIP.
Brian O.
On Feb 25, 2009, at 9:36 AM, Bryan Bishop wrote:
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l
mailing list