SeedViewer Annotation

SEED Viewer Annotation Page

Overview

This page offers access to the data relating to a feature. By default the Overview version of the page

is initially displayed providing the feature's function assignment, source organism, the role it performs

in a subsystem, and a graphic displaying it's genomic context. If this feature's function is associated with one

or more functional roles, each functional role's name will be displayed and linked to a SEED Viewer Functional Role page.

A part of a feature's function that is not also a functional role is NOT linked.

If this feature is included in a subsystem detailed information about this feature's role or roles in one or more subsystems is provided in a shaded box

at the top of the page on the right. The functional role names and subsystem names are linked to the

SEED Viewer Functional Role page and the SEED Viewer Subsystem page.

In the graphic each line represents a different genome. The genome of the feature that is the subject of this page

is on the first line with the subject feature in red and centered in a 16kb window. Features on the same line that have

a gray shadow are functionally coupled to the subject feature. Features in different genome that share the same color or

number are similar. Clicking 'Diverse Genomes' will change the genomes in the graphic to a set that is more phylogentically

distant to the subject feature's genome.

If there are no close genomes only a single line for the subject feature's genome will be present.

If no data for diverse genomes has been computed a message saying so will be be displayed.

Sequence Data

From the green bar at the top of page, selecting the 'This Protein' menu will give the user the choice of viewing the

this feature's DNA sequence, DNA with flanking sequence or amino acid sequence.

Tools

From the green bar at the top of the page, selecting the 'Tools' menu will give the user the choice of the following tools

to analyze this feature:

TMpred

TMHMM

Gram negative PSORT

Gram negative SignalP

Gram positive PSORT

Gram positive SignalP

LipoP

InterProScan

Radar

PPSearch

Gram negative CELLO

Gram positive CELLO

ProDom

Literature

This menu list links to sources of literature discussing this specific feature. Currently PubMed is the only source.