Database Overview

See also List of Databases

Content & Features at different databases

These sections list information we want...add text to indicate where the information can be found.

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		Complete genome
W3110	Refseq: AC_000091 GenBank: AP009048		Complete genome

Genetics

Genes

Note that some customization will be needed for phage and plasmid genes vs. chromosomal genes.

Nomenclature

• Standard name: e.g. lacZ, or rpoD
• Synonyms: e.g. groP for dnaK, alt for rpoD
• Accessions
  • To genomic sequence (bnum, JW, ECK)
  • To external databases (GenBank, Swissprot, ASAP, EcoCyc, etc.)

History and references for the above, e.g. "lac for lactose metabolism (ref)"

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. Need to look at Sequence Ontology features

Map information

• Location in map units
• Cotransduction frequencies to nearby markers
• Presence or absence in different strains
  • Covered by deletions
  • Covered by F's
  • Hfr to transfer
  • Covered by AKSA clones
  • Covered by Kohara phage
  • Covered by Clark-Carbon clone

References and commentary

Gene Products

Proteins

Nomenclature

• Protein Name - just gene product notation e.g. DnaK. (this will be pagename in wiki)
  • Protein name synonyms
• Product description/name - e.g. Hsp70-family chaperone
  • Protein family (pfam, Interpro)
  • NCBI
  • From Uniprot
  • Other synonyms
• Accessions/IDs/Crossrefs
  • Protein genbank ID (gi)
  • Uniprot/Swissprot/TrEmbl
  • Systematic gene name (EcoliHub ID)
  • Genome ID# (bnum JW ECK)
• Source (organism, strain, substrain)

Sequence

• Protein seqence/length
• Annotation Version (Reference)
• Codon adaptation index
• Sequence features
  • Domains/Motifs (Interpro, Pfam, CDD)
  • Signal sequences
  • Other localization/post-translational modification motifs

References

Physical Properties

• Calculated molecular weight/PI
• Observed molecular weight/PI
• Calculated extinction coefficient

Protein Structure

• Structure (PDB)
• Predicted
  • structure
  • coiled coils
  • other motifs
  • transmembrane segments/topology
• Structure families (SCOP,CATH)

Protein Function

• Function (GO has refs)
• Enzyme activity EC number (add refs) - look at BRENDA
• Ligands
• Regulation (allosteric/feedback)
• Interactions

Experimental Data

• Proteomics study
• Protein-protein interaction
• Purification
• Antibody
• Localization

Evolutionary relationships

• BLAST/FASTA/Homolog listing
• Orthologous groups (COG)
• Taxonomic distribution
  • Origin (horizontal vs vertical)
• Ortholog lists (by whatever method)

Query types

Query by gene name

Query inputs and outputs

Input	Output	How this is handled in different databases
gene name (e.g. lacY) ASAP (participant of the NAR 06 paper) enter query as feature name from query page (link is to MG1655; other genomes available) returns page with link to features page. 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)	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)