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PR01153

Identifier
PAFRECEPTOR  [View Relations]  [View Alignment]  
Accession
PR01153
No. of Motifs
11
Creation Date
14-MAR-1999
Title
Platelet activating factor receptor signature
Database References
PRINTS; PR90007 7TM; PR90006 GPCRCLAN; PR00237 GPCRRHODOPSN

INTERPRO; IPR002282
GCRDB; GCR_1618; GCR_0186; GCR_0260; GCR_0285; GCR_0414; GCR_0478

GCRDB; GCR_0034
Literature References
1. ATTWOOD, T.K. AND FINDLAY, J.B.C. 
Fingerprinting G protein-coupled receptors.
PROTEIN ENG. 7(2) 195-203 (1994).
 
2. ATTWOOD, T.K. AND FINDLAY, J.B.C. 
G protein-coupled receptor fingerprints.
7TM, VOLUME 2, EDS. G.VRIEND AND B.BYWATER (1993).
 
3. BIRNBAUMER, L.
G proteins in signal transduction.
ANNU.REV.PHARMACOL.TOXICOL. 30 675-705 (1990).
 
4. CASEY, P.J. AND GILMAN, A.G.
G protein involvement in receptor-effector coupling.
J.BIOL.CHEM. 263(6) 2577-2580 (1988).
 
5. ATTWOOD, T.K. AND FINDLAY, J.B.C. 
Design of a discriminating fingerprint for G protein-coupled receptors.
PROTEIN ENG. 6(2) 167-176 (1993).
 
6. HONDA, Z., NAKAMURA, M., MIKI, I., MINAMI, M., WATANABE, T., SEYAMA, Y.,
OKADO, H., TOH, H., ITO, K. AND MIYAMOTO, T.
Cloning by functional expression of platelet-activating factor receptor
from guinea-pig lung.
NATURE 349 342-346 (1991). 
 
7. SEYFRIED, C.E., SCHWEICKART, V.L., GODISKA, R. AND GRAY, P.W.
The human platelet-activating factor receptor gene (PTAFR) contains no
introns and maps to chromosome 1.
GENOMICS 13 832-834 (1992). 

Documentation
G protein-coupled receptors (GPCRs) constitute a vast protein family that 
encompasses a wide range of functions (including various autocrine, para-
crine and endocrine processes). They show considerable diversity at the 
sequence level, on the basis of which they can be separated into distinct 
groups. We use the term clan to describe the GPCRs, as they embrace a group
of families for which there are indications of evolutionary relationship, 
but between which there is no statistically significant similarity in 
sequence [1]. The currently known clan members include the rhodopsin-like 
GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating
pheromone receptors, and the metabotropic glutamate receptor family.
 
The rhodopsin-like GPCRs themselves represent a widespread protein family 
that includes hormone, neurotransmitter and light receptors, all of
which transduce extracellular signals through interaction with guanine
nucleotide-binding (G) proteins. Although their activating ligands vary 
widely in structure and character, the amino acid sequences of the 
receptors are very similar and are believed to adopt a common structural 
framework comprising 7 transmembrane (TM) helices [3-5]. 
 
Platelet-activating factor (PAF), a unique phospholipid mediator, possesses
potent proinflammatory, smooth-muscle contractile and hypotensive activities,
and appears to be crucial in the pathogenesis of bronchial asthma and in the
lethality of endotoxin and anaphylactic shock [6,7]. However, little is 
known of the molecular properties of the PAF receptor and related signal
transduction systems [6]. The gene for the human PAF receptor (PAFR) has
been isolated, and encodes a protein that is highly similar to the guinea
pig PAF receptor. Analysis of somatic cell hybrids suggests that PAFR is
encoded by a single gene on human chromosome 1 [6].
 
PAFRECEPTOR is an 11-element fingerprint that provides a signature for the
platelet activating factor receptors. The fingerprint was derived from an
initial alignment of 4 sequences: the motifs were drawn from conserved
regions spanning the full alignment length, focusing on those sections 
that characterise the PAF receptors but distinguish them from the rest of
the rhodopsin-like superfamily - motif 1 resides at the N-terminus; motifs 2
and 3 span the first cytoplasmic and external loops respectively; motif 4
spans the C-terminus of TM domain 3 and the second cytoplasmic loop; motif
5 spans the C-terminus of TM domain 4, leading into the second external 
loop; motif 6 lies in the second external loop; motif 7 encodes the third
cytoplasmic loop; motif 8 lies at the C-terminus of TM domain 6; motif 9
lies at the N-terminus of TM domain 7; and motifs 10 and 11 reside at the
C-terminus. A single iteration on SPTR37_9f was required to reach convergence,
no further sequences being identified beyond the starting set.
Summary Information
4 codes involving 11 elements
0 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
1144444444444
1000000000000
900000000000
800000000000
700000000000
600000000000
500000000000
400000000000
300000000000
200000000000
1234567891011
True Positives
PAFR_CAVPO    PAFR_HUMAN    PAFR_MOUSE    PAFR_RAT      
Sequence Titles
PAFR_CAVPO  PLATELET ACTIVATING FACTOR RECEPTOR (PAF-R) - CAVIA PORCELLUS (GUINEA PIG). 
PAFR_HUMAN PLATELET ACTIVATING FACTOR RECEPTOR (PAF-R) - HOMO SAPIENS (HUMAN).
PAFR_MOUSE PLATELET ACTIVATING FACTOR RECEPTOR (PAF-R) - MUS MUSCULUS (MOUSE).
PAFR_RAT PLATELET ACTIVATING FACTOR RECEPTOR (PAF-R) - RATTUS NORVEGICUS (RAT).
Scan History
SPTR37_9f  1  5    NSINGLE    
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
EHNGSFRVDSEFRYTLFPI PAFR_MOUSE 2 2 -
EQNGSFRVDSEFRYTLFPI PAFR_RAT 2 2 -
ELNSSSRVDSEFRYTLFPI PAFR_CAVPO 2 2 -
EPHDSSHMDSEFRYTLFPI PAFR_HUMAN 2 2 -

Motif 2 width=17
Element Seqn Id St Int Rpt
VFANLYPSKKLNEIKIF PAFR_MOUSE 39 18 -
VFATLYPSKKLNEIKIF PAFR_RAT 39 18 -
VFARLYPSKKLNEIKIF PAFR_CAVPO 39 18 -
VFARLYPCKKFNEIKIF PAFR_HUMAN 39 18 -

Motif 3 width=17
Element Seqn Id St Int Rpt
WIVYYYNEGDWILPNFL PAFR_MOUSE 73 17 -
WIVYYSNEGDWIVHKFL PAFR_RAT 73 17 -
WIVYYSNQGNWFLPKFL PAFR_CAVPO 73 17 -
WIVYYQNQGNWILPKFL PAFR_HUMAN 73 17 -

Motif 4 width=26
Element Seqn Id St Int Rpt
GVITYNRYQAVAYPIKTAQATTRKRG PAFR_MOUSE 109 19 -
GVITYNRYQAVAYPIKTAQATTRKRG PAFR_RAT 109 19 -
GVITYNRFQAVKYPIKTAQATTRKRG PAFR_CAVPO 109 19 -
GVITYNRFQAVTRPIKTAQANTRKRG PAFR_HUMAN 109 19 -

Motif 5 width=23
Element Seqn Id St Int Rpt
ASYFLATDSTNLVPNKDGSGNIT PAFR_MOUSE 149 14 -
ASYFLATDSTNVVPKKDGSGNIT PAFR_RAT 149 14 -
ASYFLVMDSTNVVSNKAGSGNIT PAFR_CAVPO 149 14 -
ASYFLILDSTNTVPDSAGSGNVT PAFR_HUMAN 149 14 -

Motif 6 width=18
Element Seqn Id St Int Rpt
TRCFEHYEPYSVPILVVH PAFR_MOUSE 171 -1 -
TRCFEHYEPYSVPILVVH PAFR_RAT 171 -1 -
TRCFEHYEKGSKPVLIIH PAFR_CAVPO 171 -1 -
TRCFEHYEKGSVPVLIIH PAFR_HUMAN 171 -1 -

Motif 7 width=22
Element Seqn Id St Int Rpt
HTLLTQPMRQQRKAGVKRRALW PAFR_MOUSE 211 22 -
HTLLTRPVRQQRKPEVKRRALW PAFR_RAT 211 22 -
HTLLRQPVKQQRNAEVRRRALW PAFR_CAVPO 211 22 -
RTLLMQPVQQQRNAEVKRRALW PAFR_HUMAN 211 22 -

Motif 8 width=15
Element Seqn Id St Int Rpt
PHHVVQLPWTLAELG PAFR_MOUSE 247 14 -
PHHVVQLPWTLAELG PAFR_RAT 247 14 -
PHHMVQLPWTLAELG PAFR_CAVPO 247 14 -
PHHVVQLPWTLAELG PAFR_HUMAN 247 14 -

Motif 9 width=13
Element Seqn Id St Int Rpt
HQAINDAHQITLC PAFR_MOUSE 267 5 -
HQAINDAHQITLC PAFR_RAT 267 5 -
HQAINDAHQVTLC PAFR_CAVPO 268 6 -
HQAINDAHQVTLC PAFR_HUMAN 268 6 -

Motif 10 width=23
Element Seqn Id St Int Rpt
CFLTKKFRKHLSEKFYSMRSSRK PAFR_MOUSE 293 13 -
CFLTKKFRKHLSEKFYSMRSSRK PAFR_RAT 293 13 -
CFLTKKFRKHLSEKLNIMRSSQK PAFR_CAVPO 294 13 -
CFLTKKFRKHLTEKFYSMRSSRK PAFR_HUMAN 294 13 -

Motif 11 width=25
Element Seqn Id St Int Rpt
CSRATSDTCTEVIVPANQTPIVSLK PAFR_MOUSE 316 0 -
CSRATSDTCTEVMMPANQTPVLPLK PAFR_RAT 316 0 -
CSRVTTDTGTEMAIPINHTPVNPIK PAFR_CAVPO 317 0 -
CSRATTDTVTEVVVPFNQIPGNSLK PAFR_HUMAN 317 0 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
EHNGSFRVDSEFRYTLFPI PAFR_MOUSE 2 2 -
EQNGSFRVDSEFRYTLFPI PAFR_RAT 2 2 -
ELNSSSRVDSEFRYTLFPI PAFR_CAVPO 2 2 -
EPHDSSHMDSEFRYTLFPI PAFR_HUMAN 2 2 -

Motif 2 width=17
Element Seqn Id St Int Rpt
VFANLYPSKKLNEIKIF PAFR_MOUSE 39 18 -
VFATLYPSKKLNEIKIF PAFR_RAT 39 18 -
VFARLYPSKKLNEIKIF PAFR_CAVPO 39 18 -
VFARLYPCKKFNEIKIF PAFR_HUMAN 39 18 -

Motif 3 width=17
Element Seqn Id St Int Rpt
WIVYYYNEGDWILPNFL PAFR_MOUSE 73 17 -
WIVYYSNEGDWIVHKFL PAFR_RAT 73 17 -
WIVYYSNQGNWFLPKFL PAFR_CAVPO 73 17 -
WIVYYQNQGNWILPKFL PAFR_HUMAN 73 17 -

Motif 4 width=26
Element Seqn Id St Int Rpt
GVITYNRYQAVAYPIKTAQATTRKRG PAFR_MOUSE 109 19 -
GVITYNRYQAVAYPIKTAQATTRKRG PAFR_RAT 109 19 -
GVITYNRFQAVKYPIKTAQATTRKRG PAFR_CAVPO 109 19 -
GVITYNRFQAVTRPIKTAQANTRKRG PAFR_HUMAN 109 19 -

Motif 5 width=23
Element Seqn Id St Int Rpt
ASYFLATDSTNLVPNKDGSGNIT PAFR_MOUSE 149 14 -
ASYFLATDSTNVVPKKDGSGNIT PAFR_RAT 149 14 -
ASYFLVMDSTNVVSNKAGSGNIT PAFR_CAVPO 149 14 -
ASYFLILDSTNTVPDSAGSGNVT PAFR_HUMAN 149 14 -

Motif 6 width=18
Element Seqn Id St Int Rpt
TRCFEHYEPYSVPILVVH PAFR_MOUSE 171 -1 -
TRCFEHYEPYSVPILVVH PAFR_RAT 171 -1 -
TRCFEHYEKGSKPVLIIH PAFR_CAVPO 171 -1 -
TRCFEHYEKGSVPVLIIH PAFR_HUMAN 171 -1 -

Motif 7 width=22
Element Seqn Id St Int Rpt
HTLLTQPMRQQRKAGVKRRALW PAFR_MOUSE 211 22 -
HTLLTRPVRQQRKPEVKRRALW PAFR_RAT 211 22 -
HTLLRQPVKQQRNAEVRRRALW PAFR_CAVPO 211 22 -
RTLLMQPVQQQRNAEVKRRALW PAFR_HUMAN 211 22 -

Motif 8 width=15
Element Seqn Id St Int Rpt
PHHVVQLPWTLAELG PAFR_MOUSE 247 14 -
PHHVVQLPWTLAELG PAFR_RAT 247 14 -
PHHMVQLPWTLAELG PAFR_CAVPO 247 14 -
PHHVVQLPWTLAELG PAFR_HUMAN 247 14 -

Motif 9 width=13
Element Seqn Id St Int Rpt
HQAINDAHQITLC PAFR_MOUSE 267 5 -
HQAINDAHQITLC PAFR_RAT 267 5 -
HQAINDAHQVTLC PAFR_CAVPO 268 6 -
HQAINDAHQVTLC PAFR_HUMAN 268 6 -

Motif 10 width=23
Element Seqn Id St Int Rpt
CFLTKKFRKHLSEKFYSMRSSRK PAFR_MOUSE 293 13 -
CFLTKKFRKHLSEKFYSMRSSRK PAFR_RAT 293 13 -
CFLTKKFRKHLSEKLNIMRSSQK PAFR_CAVPO 294 13 -
CFLTKKFRKHLTEKFYSMRSSRK PAFR_HUMAN 294 13 -

Motif 11 width=25
Element Seqn Id St Int Rpt
CSRATSDTCTEVIVPANQTPIVSLK PAFR_MOUSE 316 0 -
CSRATSDTCTEVMMPANQTPVLPLK PAFR_RAT 316 0 -
CSRVTTDTGTEMAIPINHTPVNPIK PAFR_CAVPO 317 0 -
CSRATTDTVTEVVVPFNQIPGNSLK PAFR_HUMAN 317 0 -