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PR00220

Identifier
SYNAPTOPHYSN  [View Relations]  [View Alignment]  
Accession
PR00220
No. of Motifs
5
Creation Date
04-JUL-1994  (UPDATE 07-JUN-1999)
Title
Synaptophysin/synaptoporin family signature
Database References

PROSITE; PS00604 SYNAPTOP
BLOCKS; BL00604
PFAM; PF01284 Synaptophysin
INTERPRO; IPR001285
Literature References
1. JOHNSTON, P.A., JAHN, R. AND SUDHOF, T.C.
Transmembrane topography and evolutionary conservation of synaptophysin.
J.BIOL.CHEM. 264 1268-1273 (1989).
 
2. LEUBE, R.E., KAISER, P., SEITER, A., ZIMBELMANN, R., FRANKE, W.W., 
REHM, H., KNAUS, P., PRIOR, H., BETZ, H., REINKE, H., BEYREUTHER, K. AND
WIEDENMANN, B.
Synaptophysin: nolecular organization and mRNA expression as determined 
from cloned cDNA.
EMBO J. 6 3261-3268 (1987).

Documentation
Synaptophysin and synaptoporin are related glycoproteins: they are the major
integral membrane proteins of a certain class of small neurosecretory
vesicles [1,2], although they may also be found in vesicles of various
non-endocrine cells [2]. The polypeptide chain spans the membrane 4 times,
and possibly acts as an ion or solute channel.  
 
SYNAPTOPHYSN is a 5-element fingerprint that provides a signature for the 
synaptophysin/synaptoporin family. The fingerprint was derived from an 
initial alignment of 4 sequences: motifs 1 and 3-5 encode the 4 trans-
membrane regions; motif 2, which spans a conserved region in the first
intravesicular loop, includes the region encoded by PROSITE pattern
SYNAPTOP (PS00604), the cysteine of which may be in involved in disulphide
bond formation. Two iterations on OWL23.2 were required to reach
convergence, at which point a true set comprising 6 sequences was
identified. A single partial match was also found, S20316, a synaptophysin
fragment.
 
An update on SPTR37_9f identified a true set of 12 sequences.
Summary Information
12 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
51212121212
400000
300000
200000
12345
True Positives
O09117        O57343        O57344        O62646        
O89104 Q16563 Q90661 SYNP_RAT
SYPH_BOVIN SYPH_HUMAN SYPH_MOUSE SYPH_RAT
Sequence Titles
O09117      PANTOPHYSIN - MUS MUSCULUS (MOUSE).           
O57343 SYNAPTOPHYSIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O57344 SYNAPTOPHYSIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
O62646 MITSUGUMIN29 - ORYCTOLAGUS CUNICULUS (RABBIT).
O89104 MITSUGUMIN29 - MUS MUSCULUS (MOUSE).
Q16563 PANTOPHYSIN - HOMO SAPIENS (HUMAN).
Q90661 SYNAPTOPHYSIN IIA - GALLUS GALLUS (CHICKEN).
SYNP_RAT SYNAPTOPORIN - RATTUS NORVEGICUS (RAT).
SYPH_BOVIN SYNAPTOPHYSIN (MAJOR SYNAPTIC VESICLE PROTEIN P38) - BOS TAURUS (BOVINE).
SYPH_HUMAN SYNAPTOPHYSIN (MAJOR SYNAPTIC VESICLE PROTEIN P38) - HOMO SAPIENS (HUMAN).
SYPH_MOUSE SYNAPTOPHYSIN (MAJOR SYNAPTIC VESICLE PROTEIN P38) (BM89 ANTIGEN) - MUS MUSCULUS (MOUSE).
SYPH_RAT SYNAPTOPHYSIN (MAJOR SYNAPTIC VESICLE PROTEIN P38) - RATTUS NORVEGICUS (RAT).
Scan History
OWL23_2    2  100  NSINGLE    
OWL26_0 1 100 NSINGLE
SPTR37_9f 2 13 NSINGLE
Initial Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
VKVLQWVFAIFAFATCGSYSGEL SYPH_HUMAN 29 29 -
VKVLQWVFAIFAFATCGSYSGEL SYPH_BOVIN 23 23 -
VKVLQWVFAIFAFATCGSYTGEL SYPH_RAT 23 23 -
MVIFAPLFAIFAFATCGGYSGGL SYNP_RAT 3 3 -

Motif 2 width=26
Element Seqn Id St Int Rpt
LSVDCANKTESDLSIEVEFEYPFRLH SYPH_HUMAN 53 1 -
LSVDCANKTKSDLNIEVEFEYPFRLH SYPH_BOVIN 47 1 -
LSVECANKTESALNIEVEFEYPFRLH SYPH_RAT 47 1 -
LSVDCVNKTESNLSIDIAFAYPFRLH SYNP_RAT 27 1 -

Motif 3 width=25
Element Seqn Id St Int Rpt
FFVTVAVFAFLYSMGALATYIFLQN SYPH_HUMAN 106 27 -
FFVTVAVFAFLYSMGALATYIFLQN SYPH_BOVIN 100 27 -
FFVTVAVFAFLYSMGALATYIFLQN SYPH_RAT 101 28 -
FFVTVAVFAFLYSLAATVVYIFFQN SYNP_RAT 81 28 -

Motif 4 width=24
Element Seqn Id St Int Rpt
GPMLDFLATAVFAFMWLVSSSAWA SYPH_HUMAN 138 7 -
GPMLDFLATAVFAFMWLVSSSAWA SYPH_BOVIN 132 7 -
GPMMDFLATAVFAFMWLVSSSAWA SYPH_RAT 133 7 -
GPLIDFIVTVVFSFLWLVGSSAWA SYNP_RAT 113 7 -

Motif 5 width=19
Element Seqn Id St Int Rpt
VVFGFLNLVLWVGNLWFVF SYPH_HUMAN 205 43 -
VVFGFLNLVLWVGNLWFVF SYPH_BOVIN 199 43 -
VVFGFLNLVLWVGNLWFVF SYPH_RAT 200 43 -
VVFGFLNFILWAGNIWFVF SYNP_RAT 180 43 -
Final Motifs
Motif 1  width=23
Element Seqn Id St Int Rpt
VKVLQWVFAIFAFATCGSYSGEL SYPH_HUMAN 29 29 -
VKVLQWVFAIFAFATCGSYSGEL SYPH_BOVIN 23 23 -
VKVLQWVFAIFAFATCGSYTGEL SYPH_MOUSE 23 23 -
VKVLQWVFAIFAFATCGSYTGEL SYPH_RAT 23 23 -
IKVLEWLFSIFAFATCGGYSGQF O57344 23 23 -
IKVLQWLFSIFAFATCGGYSGQF O57343 23 23 -
MVIFAPLFAIFAFATCGGYSGGL Q90661 3 3 -
MVIFAPLFAIFAFATCGGYSGGL SYNP_RAT 3 3 -
IKVLQWLFAIFAFGSCGSYSGET O62646 38 38 -
IKVLQWLFAIFAFGSCGSYSGET O89104 38 38 -
IKVLEWIASIFAFATCGGFKGQT Q16563 36 36 -
IKILEWFASIFAFATCGGFKGKT O09117 36 36 -

Motif 2 width=26
Element Seqn Id St Int Rpt
LSVDCANKTESDLSIEVEFEYPFRLH SYPH_HUMAN 53 1 -
LSVDCANKTKSDLNIEVEFEYPFRLH SYPH_BOVIN 47 1 -
LSVECANKTESALNIEVEFEYPFRLH SYPH_MOUSE 47 1 -
LSVECANKTESALNIEVEFEYPFRLH SYPH_RAT 47 1 -
LSIDCKNKNESKPNIKVDFEYPFRLH O57344 47 1 -
LSIECKNKNESKPNIKVDFEYPFRLH O57343 47 1 -
LSVDCANKSESDLNIDIAFAYPFRLH Q90661 27 1 -
LSVDCVNKTESNLSIDIAFAYPFRLH SYNP_RAT 27 1 -
AMVRCNNEAKDVSSIIVLFGYPFRLH O62646 62 1 -
ALVLCNNEAKDVSSIIVLFGYPFRLY O89104 62 1 -
IQVNCPPAVTENKTVTATFGYPFRLN Q16563 60 1 -
QVNCPKVGVNKNQTVTATFGYPFRLN O09117 61 2 -

Motif 3 width=25
Element Seqn Id St Int Rpt
FFVTVAVFAFLYSMGALATYIFLQN SYPH_HUMAN 106 27 -
FFVTVAVFAFLYSMGALATYIFLQN SYPH_BOVIN 100 27 -
FFVTVAVFAFLYSMGALATYIFLQN SYPH_MOUSE 101 28 -
FFVTVAVFAFLYSMGALATYIFLQN SYPH_RAT 101 28 -
FFVTIAVFAFLYSLAAMVVYIFMQN O57344 100 27 -
FFVTIAVFSFLYSLAAMAVYMFLQN O57343 100 27 -
FFVTIAVFAFLYSLAATVVYIFFQN Q90661 81 28 -
FFVTVAVFAFLYSLAATVVYIFFQN SYNP_RAT 81 28 -
FFVTLGIFSFFYTMAALVVYLRFHK O62646 117 29 -
FFVTLGIFSFFYTMAALVIYLRFHK O89104 117 29 -
FYVTFAVFVFLYCIAALLLYVGYTS Q16563 117 31 -
FYVTFAVFVFLYCIAALLLYVGYTN O09117 118 31 -

Motif 4 width=24
Element Seqn Id St Int Rpt
GPMLDFLATAVFAFMWLVSSSAWA SYPH_HUMAN 138 7 -
GPMLDFLATAVFAFMWLVSSSAWA SYPH_BOVIN 132 7 -
GPMMDFLATAVFAFMWLVSSSAWA SYPH_MOUSE 133 7 -
GPMMDFLATAVFAFMWLVSSSAWA SYPH_RAT 133 7 -
GPMIDCIATAIFTFIWLVSSSAWA O57344 132 7 -
GPMIDCIATAIFTFLWLVSSSAWA O57343 132 7 -
GPLIDFIVTVVFSFLWLVGSSAWA Q90661 113 7 -
GPLIDFIVTVVFSFLWLVGSSAWA SYNP_RAT 113 7 -
FPLVDFCVTVSFTFFWLVAAAAWG O62646 149 7 -
FPLVDFCVTVSFTFFWLVAAAAWG O89104 149 7 -
LPMIDFVVTLVATFLWLVSTSAWA Q16563 149 7 -
LPMIDFIVTLVATFLWLVSSSAWA O09117 150 7 -

Motif 5 width=19
Element Seqn Id St Int Rpt
VVFGFLNLVLWVGNLWFVF SYPH_HUMAN 205 43 -
VVFGFLNLVLWVGNLWFVF SYPH_BOVIN 199 43 -
VVFGFLNLVLWVGNLWFVF SYPH_MOUSE 200 43 -
VVFGFLNLVLWVGNLWFVF SYPH_RAT 200 43 -
VAFGFLNCILWLGNLWFVF O57344 202 46 -
VAFGFLNCILWLGNVWFVF O57343 202 46 -
VVFGFLNFILWAGNIWFVF Q90661 180 43 -
VVFGFLNFILWAGNIWFVF SYNP_RAT 180 43 -
VLFGFINFFLWAGNCWFVF O62646 216 43 -
VLFGFINFFLWAGNCWFVF O89104 216 43 -
VIFGFLNMILWGGNAWFVY Q16563 215 42 -
VIFGFLNMILWGGNAWFVY O09117 217 43 -