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Domains that have the same macromolecule name will be drawn on the same bar. In the
case of domains that span overlapping regions, the domains will be drawn such
that the color and range of each domain is visible.
Domains and motifs of different types will be drawn as different shapes. Here, domains or
motifs that are defined by their functional role are drawn as rounded rectangles;
domains or
motifs that are characterized by their structural role are drawn as rectangles;
domains or motifs that consist of a single residue or have an unknown range (but
a starting position) are
drawn as an asterisk.
The status of the validity of the domain is encoded by a colored border around
the domain/motif shape drawn on the macromolecule bar.
If no domain or motif is selected to align multiple macromolecule schematics to,
the macromolecule
bars will be left-aligned with their first residue. If a domain is chosen to
align macromolecule bars to, the last instance of that domain on a macromolecule bar is used
to align all schematics.
Web form-based input:
Listed here are some sample domains.
File-based input:
These are the domains as they would be entered in a file for input. An ampersand
(&) is
used a delimiter between the columns. White space before or after the delimiters
is ignored. [Download this file]
CAA46951 & Homeobox domain & 192:248 & F & #CDC1C5 & NULL & PFAM & Y & 433 &
CAA46951 & Homeodomain-like & 165:252 & S & #CD5B45 & NULL & SCOP & Y & 433 &
5330400P12 & WD domain, G-beta repeat & 131:168 & F & #FF8C69 & NULL & PFAM & Y & 296 &
5330400P12 & WD domain, G-beta repeat & 173:210 & F & #FF8C69 & NULL & PFAM & Y & 296 &
5330400P12 & WD40-repeat & 1:296 & S & #00FF7F & NULL & SCOP & Y & 296 &
AAH62206 & Cell division protein & 38:311 & S & #00CED1 & NULL & PFAM & Y & 425 &
AAH62206 & P-loop containing nucleoside triphosphate hydrolases & 36:279 & S & #00FFFF & NULL & SCOP & Y & 425 &
For uploaded input files, an additional feature is available: an imagemap file
that links domain shapes with a URL. The desired URL is listed at the end of
each domain entry in the input file. See the example below. [Download this file]
BAA88685 & Choline/Carnitine o-acyltransferase & 172:763 & F & #ADD8E6 & PF00755 & PFAM & Y & 772 & http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00755
BAA88685 & E set domains & 9:63 & S & #CD2626 & 81296 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=81296
BAA88685 & CoA-dependent acyltransferases & 168:542 & S & #CD6889 & 52777 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=52777
BAA88685 & CoA-dependent acyltransferases & 544:766 & S & #CD6889 & 52777 & SCOP & Y & 772 & http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=52777
Sometimes it is useful to display partial protein sequences or sections of DNA
with respect to a transcriptional start site. In these cases, the range
displayed at the start and end of the bar representing the molecule will not be
1 to N but rather -1000 to 10 or 200 to 500, for example. To support
these cases, a range for the bar can be included in place of the length of the
molecule and the format is the same as that used to describe the range of the
domain (e.g., -1000:10). See the example below which represents predicted
transcription factor binding sites in the upstream regulatory region of the IL-2
receptor alpha gene. [Download this file]
IL-2Ra & AML-1a & -548:-543 & S & #EFEFEF & NULL & & R & -600:1 &
IL-2Ra & CdxA & -500:-494 & S & #000000 & NULL & & R & -600:1 &
IL-2Ra & CdxA & -457:-451 & S & #000000 & NULL & & R & -600:1 &
IL-2Ra & CdxA & -235:-229 & S & #000000 & NULL & & R & -600:1 &
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