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PR00699

Identifier
TMPROTEINSRB  [View Relations]  [View Alignment]  
Accession
PR00699
No. of Motifs
8
Creation Date
08-APR-1997  (UPDATE 10-JUN-1999)
Title
C.elegans integral membrane protein Srb signature
Database References

INTERPRO; IPR002184
Literature References
1. TROEMEL, E.R., CHOU, J.H., DWYER, N.D., COLBERT, H.A. AND BARGMANN, C.I.
Divergent seven transmembrane receptors are candidate chemosensory
receptors in C.elegans.
CELL 83 207-218 (1995).

Documentation
Animals recognise a wide variety of chemicals using their senses of taste
and smell. The nematode C.elegans has only 14 types of chemosensory neuron,
yet is able to respond to dozens of chemicals because each neuron detects
several stimuli. More than 40 highly divergent transmembrane proteins that
could contribute to this functional diversity have been described [1]. Most
of the candidate receptor genes are in clusters of similar genes; 11 of 
these appear to be expressed in small subsets of chemosensory neurons. A
single type of neuron can potentially express at least 4 different receptor
genes [1]. Some of these might encode receptors for water-soluble
attractants, repellents and pheromones, which may be divergent members
of the G protein-coupled receptor family [1].
 
Sequences of the srb family of C.elegans receptor-like proteins contain
6-8 hydrophobic, putative transmembrane, regions. These can be
distinguished from other 7TM proteins (especially those known to couple
G proteins) by their own characteristic TM signatures.
 
TMPROTEINSRB is an 8-element fingerprint that provides a signature for the
C.elegans srb family of integral membrane proteins. The fingerprint was
derived from an initial alignment of 3 sequences: the motifs were drawn
from the putative TM regions. A single iteration on OWL29.1 was required to
reach convergence, no further sequences being identified beyond the starting
set. Several partial matches were found, all of which are homologues that
show certain differences in their TM signatures.
 
An update on SPTR37_9f identified a true set of 3 sequences, and 9
partial matches.
Summary Information
   3 codes involving  8 elements
0 codes involving 7 elements
3 codes involving 6 elements
1 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
833333333
700000000
632332212
511110100
410100110
311200011
200000000
12345678
True Positives
Q20962        Q20963        SRB8_CAEEL    
True Positive Partials
Codes involving 6 elements
O16578 Q10031 SRB7_CAEEL
Codes involving 5 elements
O01509
Codes involving 4 elements
SRB6_CAEEL
Codes involving 3 elements
SB11_CAEEL YLX5_CAEEL
Sequence Titles
Q20962      RELATED TO C. ELEGANS SERPENTINE RECEPTOR FAMILY B - CAENORHABDITIS ELEGANS. 
Q20963 RELATED TO C. ELEGANS SERPENTINE RECEPTOR FAMILY B - CAENORHABDITIS ELEGANS.
SRB8_CAEEL SRB-8/9 PROTEIN - CAENORHABDITIS ELEGANS.

O16578 C33C12.6 PROTEIN - CAENORHABDITIS ELEGANS.
Q10031 PUTATIVE SERINE/THREONINE-PROTEIN KINASE C27D6.2 IN CHROMOSOME II (EC 2.7.1.-) - CAENORHABDITIS ELEGANS.
SRB7_CAEEL SRB-7 PROTEIN - CAENORHABDITIS ELEGANS.

O01509 COSMID C48B6 - CAENORHABDITIS ELEGANS.

SRB6_CAEEL SRB-6 PROTEIN - CAENORHABDITIS ELEGANS.

SB11_CAEEL SRB-11 PROTEIN - CAENORHABDITIS ELEGANS.
YLX5_CAEEL HYPOTHETICAL 84.8 KD PROTEIN F23F12.5 IN CHROMOSOME III - CAENORHABDITIS ELEGANS.
Scan History
OWL29_1    1  50   NSINGLE    
SPTR37_9f 2 72 NSINGLE
Initial Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
HPVYRVAQIYQFLVACFAFPPLFYFI SRB8_CAEEL 29 29 -
HPFYMIAQFWSFFVSLLAMPSLIFFM CELF58A65 18 18 -
NTVYRFSQFYTFSVSSFAVPGLIYFM CELF58A66 18 18 -

Motif 2 width=21
Element Seqn Id St Int Rpt
GNLKFLLVSYFIGTFLFASII CELF58A65 54 10 -
GNLKCVLIGYFVTVLAFTINF SRB8_CAEEL 65 10 -
GNLKTLLIAYFISILLYAVML CELF58A66 54 10 -

Motif 3 width=28
Element Seqn Id St Int Rpt
KYGHPTGSFIMTLSTLLPICITIERFFA SRB8_CAEEL 113 27 -
KYIHTSVIFLLTTPMMFPLGFSIERFTA CELF58A66 102 27 -
KYGHMIALIFMTIPMILPTAFTVERFVA CELF58A65 102 27 -

Motif 4 width=26
Element Seqn Id St Int Rpt
YEKTPVKLGPIITFLLIIIDLTTVSM SRB8_CAEEL 147 6 -
YEHVRTLLGPVLVLVVIAIDSMFLYD CELF58A65 136 6 -
YENIRTLIGPVLVIFLIIPNCIIFYF CELF58A66 136 6 -

Motif 5 width=21
Element Seqn Id St Int Rpt
YLWFLLYLNIGNLALNVLLLL CELF58A66 189 27 -
FLWYMLYLKITNFICNLILLF CELF58A65 189 27 -
FFIIIVIFNVINFLFNIKLIR SRB8_CAEEL 201 28 -

Motif 6 width=27
Element Seqn Id St Int Rpt
FVITVVFYHVAFFCSYIILVLTFLVVG SRB8_CAEEL 248 26 -
FTLIITFTHLLFFGCNTICSILVRVLG CELF58A66 240 30 -
FTLIVTFTHLLFFGWYVSTILLIRTVG CELF58A65 240 30 -

Motif 7 width=23
Element Seqn Id St Int Rpt
HSVARGVNCAVPTYNLVIVVVGF CELF58A66 276 9 -
YTVMRGVYCATPTYNLVIVFIGF CELF58A65 276 9 -
WAGNGILMTIMATYNLVIGIVAV SRB8_CAEEL 284 9 -

Motif 8 width=21
Element Seqn Id St Int Rpt
TGKEGARNYDNITANQWATIT CELF58A66 321 22 -
TGNTGAQNYVNVTNRIWNSNS SRB8_CAEEL 329 22 -
TGQEGAENYDNAISNYWDSVY CELF58A65 321 22 -
Final Motifs
Motif 1  width=26
Element Seqn Id St Int Rpt
HPFYMIAQFWSFFVSLLAMPSLIFFM Q20962 18 18 -
NTVYRFSQFYTFSVSSFAVPGLIYFM Q20963 18 18 -
HPVYRVAQIYQFLVACFAFPPLFYFI SRB8_CAEEL 29 29 -

Motif 2 width=21
Element Seqn Id St Int Rpt
GNLKFLLVSYFIGTFLFASII Q20962 54 10 -
GNLKTLLIAYFISILLYAVML Q20963 54 10 -
GNLKCVLIGYFVTVLAFTINF SRB8_CAEEL 65 10 -

Motif 3 width=28
Element Seqn Id St Int Rpt
KYGHMIALIFMTIPMILPTAFTVERFVA Q20962 102 27 -
KYIHTSVIFLLTTPMMFPLGFSIERFTA Q20963 102 27 -
KYGHPTGSFIMTLSTLLPICITIERFFA SRB8_CAEEL 113 27 -

Motif 4 width=26
Element Seqn Id St Int Rpt
YEHVRTLLGPVLVLVVIAIDSMFLYD Q20962 136 6 -
YENIRTLIGPVLVIFLIIPNCIIFYF Q20963 136 6 -
YEKTPVKLGPIITFLLIIIDLTTVSM SRB8_CAEEL 147 6 -

Motif 5 width=21
Element Seqn Id St Int Rpt
FLWYMLYLKITNFICNLILLF Q20962 189 27 -
YLWFLLYLNIGNLALNVLLLL Q20963 189 27 -
FFIIIVIFNVINFLFNIKLIR SRB8_CAEEL 201 28 -

Motif 6 width=27
Element Seqn Id St Int Rpt
FTLIVTFTHLLFFGWYVSTILLIRTVG Q20962 240 30 -
FTLIITFTHLLFFGCNTICSILVRVLG Q20963 240 30 -
FVITVVFYHVAFFCSYIILVLTFLVVG SRB8_CAEEL 248 26 -

Motif 7 width=23
Element Seqn Id St Int Rpt
YTVMRGVYCATPTYNLVIVFIGF Q20962 276 9 -
HSVARGVNCAVPTYNLVIVVVGF Q20963 276 9 -
WAGNGILMTIMATYNLVIGIVAV SRB8_CAEEL 284 9 -

Motif 8 width=21
Element Seqn Id St Int Rpt
TGQEGAENYDNAISNYWDSVY Q20962 321 22 -
TGKEGARNYDNITANQWATIT Q20963 321 22 -
TGNTGAQNYVNVTNRIWNSNS SRB8_CAEEL 329 22 -