Description of the genome query for

Sorted lists of ORF characteristics

A genome's ORFs can be sorted according to any of the following characteristics:

ORF product gi number, a unique identifier for the protein sequence.
ORF locus number, in order of annotation.
ORF locus start coordinate, as annotated.
ORF locus stop coordinate, as annotated.
ORF length, in amino acid residues.
ORF product molecular weight, in Daltons.
ORF mol% G+C.
ORF mol% G+C, first codon position.
ORF mol% G+C, second codon position.
ORF mol% G+C, third codon position.
ORF mol% A+G.
ORF product isoelectric point (pI), predicted from the sequence.
ORF product proportion of hydrophobic amino acids, these being Ala, Ile, Leu, Met, Phe, Pro, Trp, Val.
ORF product percent net charge, computed as %(Arg+Lys)-(Asp+Glu)
number of archaeal genomes reciprocally best matched.
number of bacterial genomes reciprocally best matched.
number of eukaryal genomes reciprocally best matched.
how well the ORF product matches outside of NCBI level 1 (e.g., Eubacteria).
how well the ORF product matches outside of NCBI level 2 (e.g., Proteobacteria).
how well the ORF product matches outside of NCBI level 3 (e.g., gamma subdivision).
how well the ORF product matches outside of NCBI level 4 (e.g., Enterobacteriaceae).
evolutionary scope.
PDS analysis at BLASTP cutoff e-value of 1.0e-5.

A few of these characteristics require further explanation:

(xviii - xxi): How well the ORF product matches outside of the genome's lineage, at the specified depth.: For instance, choosing taxonomic level 3 for Escherichia coli K12 would find the ORF's best match outside of the gamma subdivision of the Proteobacteria.
(xxii): Evolutionary scope.: Using the genomic distance matrix computed at a BLASTP cutoff e-value of 1.0e-5, we compute the evolutionary scope of an ORF's matches. For example, if an ORF from Mycoplasma genitalium matches one or more ORFs from Mycoplasma pneumoniae, Mycoplasma penetrans and Ureaplasma urealyticum, then that ORF's evolutionary scope is the mean distance between M. genitalium and these other three species.
(xxiii): PDS analysis.: What we have done is to determine how well correlated a gene's relationships to its orthologs in other species is to the genome's overall relationships to orthologous genes from other species. A low value indicates a "phylogenetically discordant sequence", or "PDS". A high value indicates that the gene's relationships track the genome's relationships well. Details of this analysis are available in:
Clarke et al. (2002) J. Bacteriol. 184, 2072-2080.

Example:

Choosing Deinococcus radiodurans from the genomic pop-up menu, selecting "ORF product isoelectric point" from the character pop-up menu, and clicking on 'ascending order', 'top n%', 'n = 5%', yields the 155 most acidic proteins from the D. radiodurans proteome. One could then feed this list into another query, in order to study this subset of the genome.