Friday, July 25, 2008

Biocyc: Database of Genome databases:

To illustrate the power of genome database netowrk, you need to have a look at biocyc page.
BioCyc is a collection of 371 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
http://biocyc.org/
BioCyc Pathway/Genome DatabasesThe BioCyc databases are divided into three tiers, based on their quality.
Tier 2 and Tier 3 databases contain computationally predicted metabolic pathways, predictions as to which genes code for missing enzymes in metabolic pathways, and predicted operons.

BioCyc Tier 1: Intensively Curated Databases




Database

Scope

Highlights


EcoCyc

Escherichia coli K-12 Model-Organism Database

Literature curation of complete genomeInformation from 17,000 publicationsTranscriptional regulatory networkProtein complexesEnzyme and transporter functionsGene Ontology assignments

MetaCyc

Multiorganism Metabolic Pathway and Enzyme Database

1,100 metabolic pathwaysPathways elucidated from 1,500 organismsExtensive commentary and references


The BioCyc Open Chemical Database is an open database of chemical compounds from other BioCyc databases. Because it contains chemical compounds only, it is not a Pathway/Genome Database.
The comparison of Urea cycle: pathway is possible between Homo Sapiens and E. coli O157:H7 EDL933 Pathway: urea cycle.


I did a cross species comparison between the two for a pathway, and I could choose any genome database


E. coli O157:H7 EDL933 Pathway: urea cycle



Homo Sapiens: Urea cycle pathway


The genes/enymes for Homosapiens
EC# 6.3.4.16
carbamoyl-phosphate synthase (ammonia), mitochondrial precursor: CPS1
EC# 2.1.3.3
ornithine carbamoyltransferase, mitochondrial precursor: OTC
EC# 6.3.4.5
argininosuccinate synthase: ENSG00000165232 argininosuccinate synthase: ENSG00000139130 argininosuccinate synthase: ENSG00000179595 argininosuccinate synthase: ASS argininosuccinate synthase: ENSG00000128605 argininosuccinate synthase: ENSG00000180191 argininosuccinate synthase: ENSG00000176192
EC# 4.3.2.1
argininosuccinate lyase: ENSG00000099934 argininosuccinate lyase: ASL
EC# 3.5.3.1
arginase II, mitochondrial precursor: ARG2 arginase 1: ARG1
The genes/enymes for Ecoli

EC# 6.3.4.16
None
EC# 2.1.3.3
ornithine carbamoyltransferase 1: argI
EC# 6.3.4.5
argininosuccinate synthetase: argG
EC# 4.3.2.1
argininosuccinate lyase: argH
EC# 3.5.3.1
None

There is a visible similarity between the two organisims and their functions for this pathway.

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