ABSTRACT
The Signal Recognition Particle Database (SRPDB) provides aligned SRP RNA and
SRP protein sequences, annotated and phylogenetically ordered. The current
release includes 93 RNAs and 29 proteins representing SRP9, SRP14, SRP19,
SRP21, SRP54, SRP68 and SRP72. The SRPDB can be downloaded and is accessible
via the World Wide Web.
The signal recognition particle database (SRPDB), located at The University of
Texas Health Science Center at Tyler, currently offers 93 aligned and annotated
sequences of SRP associated RNAs. The sequences are ordered according to the
phylogeny derived by the Ribosomal Database Project (
1
) from the corresponding small subunit ribosomal RNAs (SSU RNAs). Included are
also a total of 29 SRP related proteins. Representative SRP RNA secondary
structure diagrams are provided, one from
Bacillus subtilis
(Bacteria),
Halobacterium halobium
(Archaea) and
Canis sp.
(Eucaryotes).
In order to update SRPDB we screened the EMBL Data Library (
2
), current as of September 22, 1995, for sequences annotated as SRP-related using the Sequence Retrieval System (SRS;
3
). In addition, we used a local copy of the program PatScan (
4
) to search all sequences in EMBL for matches against a motif characteristic for
the SRP sequences that were part of the previous release of SRPDB (
5
). PatScan searches may be performed at the World Wide Web address
http://www.mcs.anl.gov/home/papka/ROSS/patscan.html. The search motifs can be
downloaded from our ftp server (see below), so that others may search new data
or modify the motifs. The new SRP RNAs were aligned using the rules previously
described (
6
).
Only six new SRP RNAs were identified. Two were from
Caenorhabditis elegans
genomic sequences (Cosmid B0285: approximate position 38 785-39 085; Cosmid CER144: approximate position 33 863-33 563 on the non-coding strand) submitted to EMBL, but without annotation of
SRP RNAs. Four SRP RNAs have so far been identified in the genomic sequences of
C.elegans
. They all differ at between one and six positions. Two new cultivars of
Humulus
are included. In the newly released complete genomic sequence of
Haemophilus influenzae
(
7
) we identified an SRP RNA analog (4.5S RNA) from approximate position 1 223 294-1 223 407, not previously annotated. This sequence seems most similar to
those of
Escherichia
and
Pseudomonas
(in agreement with the SSU RNA phylogeny) and it also lacks helices 1, 2, 3, 4
and 5. The SRP RNA from
Listeria monocytogenes
(
8
) includes helix 5, but does not align well with helices 1, 2 or 3 (which are
supported by compensating changes among
Bacillus
species and all nine Archaea representatives. Comparative evidence is needed to
determine the folding pattern for
Listeria
SRP RNA near the 5' end. While these new sequences exhibit a few supportive compensatory
changes, none of them provide comparative disproof for any of the known
pairings.
There are nine new SRP proteins in SPRDB (a total of 29) since its previous
announcement: Mouse SRP9,
Drosophila
and rice SRP19, yeast SRP21, an
Arabidopsis
chloroplast SRP54 homolog and a partial SRP54 sequence from
Hippoglossus
.
The SRP RNA alignment is available as concatenated GenBank (
9
) and EMBL (
2
) entries (but with gaps inserted in the sequences), in a human readable textual
format and as printable PostScript where helices are numbered and highlighted.
The corresponding sequences are available as separate GenBank and EMBL entries.
RNA secondary structure figure templates are in PostScript. The SRP protein
alignments (except for SRP21 and SRP68) are available in textual (ASCII) format
and as PostScript, the corresponding sequences as separate SwissProt (
10
) formatted entries.
SRPDB can be downloaded as one `tar-file' or as individual files by anonymous ftp: Connect to diana.uthct.edu
(currently 192.88.11.4) type `anonymous' (without the quotes) in response to
the prompt for a user name and give as password your local user name followed
by the @ character or your full electronic mail address. A help files named
00README explains where to find the data.
SRPDB is also freely available through the World Wide Web: connect your browser
to the address http://pegasus.uthct.edu/SRPDB/SRPDB.html. Sequences are linked
to their origin in EMBL or GenBank. Some data are shown as HTML tables and are
best viewed with a browser that supports these. Hard copies of the SRPDB are
available through written contact or e-mail (see address above), but we prefer electronic transfer. Submission of
SRP related data will be accepted in any form. We will align submitted
sequences and return the alignment to the submitter in the requested format.
The submitter may request that the data are not be released until after a given
date or upon notification.
N.L. can be contacted via: niels{at}truth.mph.msu.edu and C.Z. can be contacted
via: zwieb{at}jason.uthct.edu
We thank the Free Software Foundation and Larry Wall for their excellent
software. This work was assisted by NIH grant GM-49034 to C.Z.
REFERENCES
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