Database Overview

See also List of Databases

Content & Features at different databases

Genomes

DNA sequences for complete and partial genomes are mostly at Genbank.

E. coli

Strain	Genbank Accession	Other Sources	Notes
MG1655	Refseq: NC_000913 GenBank: U00096
W3110	Refseq: AC_000091 GenBank: AP009048

Genes

Gene models

A gene model defines where a gene is on the genomic DNA. Different annotators may disagree about where a gene starts and stops.

Query types

Query by gene name

Query inputs and outputs

Input	Output	How this is handled in different databases
gene name (e.g. lacY)	sequence	ASAP (participant of the NAR 06 paper) GenoBase (participant of the NAR 06 paper) EcoCyc (participant of the NAR 06 paper) EcoGene (participant of the NAR 06 paper) RegulonDB (?) KEGG: AA and nucleotide sequences (imported from Genbank)
	description	ASAP GenoBase: Yes EcoCyc EcoGene: Yes RegulonDB KEGG: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
	function	ASAP GenoBase: Indirectly (linked to COG) EcoCyc EcoGene: Included in Description RegulonDB KEGG: (no result)
	localization	ASAP GenoBase: Included in Experimental Data EcoCyc EcoGene: No RegulonDB KEGG: (no result)
	process (GO definitions )	ASAP GenoBase: No EcoCyc EcoGene: Indirectly (linked to AmiGO) RegulonDB KEGG: (no result)
gene name (namespace1)	gene name (namespace2) Some namespaces:
	genbank ID	ASAP GenoBase: No EcoCyc EcoGene: Indirectly (Linked to GenBank) RegulonDB KEGG: yes + link to GenBank
	pdb ID	ASAP GenoBase: No EcoCyc EcoGene: Indirectly (Linked to PDB) RegulonDB KEGG: id not explicitly shown, but link to PDB
	ecogene ID	ASAP GenoBase: Indirectly (Linked to EcoGene) EcoCyc EcoGene: Yes RegulonDB KEGG: no
gene name	pathway	ASAP GenoBase: No EcoCyc EcoGene: Indirectly (Linked to AmiGO) RegulonDB KEGG: links to relevant KEGG Pathway entries from retrieved GENES entry
gene name	experimental data
	gene expression	ASAP GenoBase: Included in Experimental Data EcoCyc EcoGene: No RegulonDB KEGG: (no result)
	protein interaction	ASAP GenoBase: Included in Experimental Data EcoCyc EcoGene: No RegulonDB KEGG: (no result)
gene name (species 1)	gene name( species 2)	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes
gene name	mutations	ASAP GenoBase: Included in Experimental Data EcoCyc EcoGene: Indirectly (Linked to CGSC) RegulonDB KEGG: (no result)
	sequence difference	ASAP GenoBase: Yes EcoCyc EcoGene: No RegulonDB KEGG: (no result)
	phenotype	ASAP GenoBase: Yes EcoCyc EcoGene: No RegulonDB KEGG: (no result)

Query by pathway

Query inputs and outputs

Input	Output	How this is handled in different databases
pathway	gene name	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: retrieves links to KEGG Pathway and KEGG GENES entries
metabolic process	regulatory circuits	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB
	transcription factors/sites	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: (no result)

Query by DNA location or sequence

Query inputs and outputs

Input	Output	How this is handled in different databases
DNA location	Gene name	ASAP GenoBase: Yes EcoCyc EcoGene: Yes RegulonDB KEGG: (no result)
sequence	related sequence (BLAST)	ASAP GenoBase: Yes EcoCyc EcoGene: No RegulonDB KEGG: (no result)

Query by Function

Query inputs and outputs

Input	Output	How this is handled in different databases
gene function (GO term) same for process and other GO branches	gene name	ASAP GenoBase: No EcoCyc EcoGene: Yes RegulonDB KEGG: (no result)

Query by strain

Query inputs and outputs

Input	Output	How this is handled in different databases
strain ID	gene name	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: (no result)
	mutation	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: (no result)
	source	ASAP GenoBase: No EcoCyc EcoGene: No RegulonDB KEGG: (no result)