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PR00314

Identifier
CLATHRINADPT  [View Relations]  [View Alignment]  
Accession
PR00314
No. of Motifs
6
Creation Date
04-OCT-1994  (UPDATE 28-JUL-1999)
Title
Clathrin coat assembly protein signature
Database References

PROSITE; PS00990 CLAT_ADAPTOR_M_1; PS00991 CLAT_ADAPTOR_M_2
BLOCKS; BL00990
PFAM; PF00928 Adap_comp_sub
INTERPRO; IPR001392
Literature References
1. LEE, J., JONGEWARD, G.D. AND STERNBERG, P.W.
Unc-101, a gene required for many aspects of Caenorhabditis elegans
development and behaviour, encodes a clathrin-associated protein.
GENES DEV. 8 60-73 (1994).
 
2. NAKAYAMA, Y., GOEBL, M., GRECO, B.O., LEMMON, S., CHOW, E.P.C.
AND  KIRCHHAUSEN, T.
The medium chains of the mammalian clathrin-associated proteins have a
homolog in yeast.
EUR.J.BIOCHEMISTRY 202 569-574 (1991).

Documentation
Clathrin-coated pits and vesicles originate from the plasma membrane and 
the trans-Golgi, and mediate the trafficking of proteins to and from the
membranes [1]. The different vesicle types transport different proteins:
plasma membrane vesicles are involved in the endocytosis of membrane
proteins, such as LDL and EGF receptors; and trans-Golgi vesicles are
involved in protein sorting and regulated secretion. The main components
of the pits are clathrin, and the clathrin-associated protein complex, AP,
(also known as assembly or adaptor proteins) [1,2]. Both trans-Golgi
adaptor proteins, AP-1, and plasma membrane adaptor proteins, AP-2, are
heterotetramers that consist of 2 large chains (beta' and gamma in AP-1,
and alpha and beta in AP-2); a medium chain (AP47 in AP-1, and AP50 in
AP-2); and a small chain (AP19 in AP-1, and AP17 in AP-2).
 
The adaptor complexes are believed to couple clathrin lattices with 
particular membrane proteins by interacting with their cytoplasmic tails,
leading to their selection and concentration: the medium chains regulate
this process by self-phosphorylation via a mechanism that is still unclear
[2]. The medium chains possess a highly conserved N-terminal domain of
around 230 amino acids, which may be the region of interaction with other
AP proteins; a linker region of between 10 and 42 amino acids; and a less
well-conserved C-terminal domain of around 190 amino acids, which may be
the site of specific interaction with the protein being transported
in the vesicle [2].
 
CLATHRINADPT is a 6-element fingerprint that provides a signature for the 
medium chain of the clathrin-associated protein complex. The fingerprint
was derived from an initial alignment of 5 sequences: motifs 1-3 were drawn
from conserved regions in the N-terminal half of the protein, and motifs
4-6 from the C-terminal portion - motifs 2 and 4 include the regions
encoded by PROSITE patterns CLAT_ADAPTOR_M_1 (PS00990) and CLAT_ADAPTOR_M_2
(PS00991). Two iterations on OWL24.0 were required to reach convergence, at
which point a true set comprising 6 sequences was identified. Four partial
matches were also found, all of which fail to make significant matches with
motifs 1, 5 and 6.
 
An update on SPTR37_9f identified a true set of 11 sequences, and 12
partial matches.
Summary Information
  11 codes involving  6 elements
2 codes involving 5 elements
1 codes involving 4 elements
7 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
6111111111111
5222112
4111100
3077700
2012100
123456
True Positives
AP47_CAEEL    AP47_MOUSE    AP50_CAEEL    AP50_DICDI    
AP50_HUMAN AP54_YEAST O01755 O22715
O23140 O62530 O62531
True Positive Partials
Codes involving 5 elements
AP50_SCHPO O02282
Codes involving 4 elements
O12969
Codes involving 3 elements
A471_RAT A472_HUMAN A472_RAT A47H_DISOM
O00189 O76928 Q20736
Codes involving 2 elements
APM2_YEAST APM4_YEAST
Sequence Titles
AP47_CAEEL  CLATHRIN COAT ASSEMBLY PROTEIN AP47 (CLATHRIN COAT ASSOCIATED PROTEIN AP47) (GOLGI ADAPTOR AP-1 47 KD PROTEIN) (HA1 47 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN) - CAENORHABDITIS ELEGANS. 
AP47_MOUSE CLATHRIN COAT ASSEMBLY PROTEIN AP47 (CLATHRIN COAT ASSOCIATED PROTEIN AP47) (GOLGI ADAPTOR AP-1 47 KD PROTEIN) (HA1 47 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN) - MUS MUSCULUS (MOUSE).
AP50_CAEEL CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KD PROTEIN) (HA2 50 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) - CAENORHABDITIS ELEGANS.
AP50_DICDI CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KD PROTEIN) (HA2 50 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) - DICTYOSTELIUM DISCOIDEUM (SLIME MOLD).
AP50_HUMAN CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KD PROTEIN) (HA2 50 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) (KIAA0109) - HOMO SAPIENS (HUMAN), MUS MUSCULUS (MOUSE), AND RATTUS NORVEGICUS (RAT).
AP54_YEAST CLATHRIN COAT ASSEMBLY PROTEIN AP54 (CLATHRIN COAT ASSOCIATED PROTEIN AP54) (GOLGI ADAPTOR AP-1 54 KD PROTEIN) (HA1 54 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
O01755 COSMID F55A12 - CAENORHABDITIS ELEGANS.
O22715 PUTATIVE CLATHRIN COAT ASSEMBLY PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O23140 AP47/50P - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O62530 CLATHRIN-ASSOCIATED PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
O62531 CLATHRIN-ASSOCIATED PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).

AP50_SCHPO PUTATIVE CLATHRIN COAT ASSEMBLY PROTEIN AP50 (CLATHRIN COAT ASSOCIATED PROTEIN AP50) (PLASMA MEMBRANE ADAPTOR AP-2 50 KD PROTEIN) (HA2 50 KD SUBUNIT) (CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O02282 UNC-101 PROTEIN - CAENORHABDITIS ELEGANS.

O12969 MU-ADAPTIN-RELATED PROTEIN 1 - GALLUS GALLUS (CHICKEN).

A471_RAT CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 1 (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 1) (GOLGI ADAPTOR AP-1 47 KD PROTEIN HOMOLOG 1) (HA1 47 KD SUBUNIT HOMOLOG 1) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN HOMOLOG 1) (P47A) - RATTUS NORVEGICUS (RAT).
A472_HUMAN CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2 (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KD PROTEIN HOMOLOG 2) (HA1 47 KD SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN HOMOLOG 2) (P47B) - HOMO SAPIENS (HUMAN).
A472_RAT CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2 (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KD PROTEIN HOMOLOG 2) (HA1 47 KD SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN HOMOLOG 2) (P47B) - RATTUS NORVEGICUS (RAT).
A47H_DISOM CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG) (GOLGI ADAPTOR AP-1 47 KD PROTEIN HOMOLOG) (HA1 47 KD SUBUNIT HOMOLOG) (CLATHRIN ASSEMBLY PROTEIN ASSEMBLY PROTEIN COMPLEX 1 MEDIUM CHAIN HOMOLOG) - DISCOPYGE OMMATA (ELECTRIC RAY).
O00189 MU-ADAPTIN-RELATED PROTEIN 2 - HOMO SAPIENS (HUMAN).
O76928 MU3 SUBUNIT OF CLATHRIN-ASSOCIATED PROTEIN COMPLEX AP-3 - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q20736 F53H8.1 PROTEIN - CAENORHABDITIS ELEGANS.

APM2_YEAST ADAPTIN MEDIUM CHAIN HOMOLOG APM2 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
APM4_YEAST ADAPTIN MEDIUM CHAIN HOMOLOG APM4 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL24_0    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 3 50 NSINGLE
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GEVLISRVYRDDIGRNAVDAF AP50_RAT 12 12 -
GKVLICRNYRGDVDMSEVEHF AP47_MOUSE 13 13 -
GKTIISRNYRGDIDMTAIDKF AP47_CAEEL 13 13 -
GEVLISRIYRDDVTRNAVDAF AP50_CAEEL 12 12 -
GKPLLSRRYRDDIPLSAIDKF AP54_YEAST 12 12 -

Motif 2 width=28
Element Seqn Id St Int Rpt
EENVKNNFVLIYELLDEILDFGYPQNTD AP50_CAEEL 98 65 -
EESVRDNFVVIYELLDEMMDFGFPQTTE AP47_CAEEL 100 66 -
EENIKNNFVLIYELLDEILDFGYPQNSE AP50_RAT 98 65 -
EESIRDNFVIIYELLDEVMDYGIPQITE AP54_YEAST 101 68 -
EESIRDNFVIIYELLDELMDFGYPQTTD AP47_MOUSE 100 66 -

Motif 3 width=29
Element Seqn Id St Int Rpt
WRSEGIKYRKNEVFLDVIESVNMLASANG AP47_CAEEL 158 30 -
WRREGIKYRRNELFLDVLESVNLLMSPQG AP50_RAT 161 35 -
WRSEGIKYRKNEVFLDVIEAVNLLVSANG AP47_MOUSE 159 31 -
WRREGIKYRRNELFLDVIEYVNLLMNQQG AP50_CAEEL 165 39 -
WRPEGITHKKNEAFLDIVESINMLMTQKG AP54_YEAST 166 37 -

Motif 4 width=28
Element Seqn Id St Int Rpt
IDDCQFHQCVKLTKFETEHAISFIPPDG AP50_CAEEL 247 53 -
IDDCTFHQCVRLSKFDSERSISFIPPDG AP50_RAT 243 53 -
LEDLKFHQCVRLSKFENEKIITFIPPDG AP54_YEAST 272 77 -
LEDVKFHQCVRLSRFENDRTISFIPPDG AP47_MOUSE 233 45 -
LEDVKFHQCVRLSRFDTDRTISFIPPDG AP47_CAEEL 232 45 -

Motif 5 width=16
Element Seqn Id St Int Rpt
KRRSTANNVEIHIPVP AP47_MOUSE 302 41 -
KRRSTANNVEIIIPVP AP47_CAEEL 301 41 -
KPSLLAQKLEVRIPTP AP50_CAEEL 316 41 -
KRKSTATNVEILIPVP AP54_YEAST 341 41 -
KPSLLAQKIEVRIPTP AP50_RAT 312 41 -

Motif 6 width=12
Element Seqn Id St Int Rpt
VWTIKNFPGGKE AP47_CAEEL 341 24 -
LWKIRSFPGGKE AP54_YEAST 381 24 -
VWKIKRMAGMKE AP50_CAEEL 356 24 -
VWSVKSFPGGKE AP47_MOUSE 342 24 -
VWKIKRMAGMKE AP50_RAT 352 24 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GKVLICRNYRGDVDMSEVEHF AP47_MOUSE 13 13 -
GKVLISRNYRGDNIDMAVIDK O62531 13 13 -
GKTIISRNYRGDIDMTAIDKF AP47_CAEEL 13 13 -
GEVLISRVYRDDIGRNAVDAF AP50_HUMAN 12 12 -
GEVLISRIYRDDVTRNAVDAF AP50_CAEEL 12 12 -
GEVLISRVYRDDIGRNAVDAF O62530 12 12 -
GNVVISRNYRGDVDMSCIEKF O01755 13 13 -
GRVLVWRDYRGDVSAAQAERF O22715 15 15 -
GKPLLSRRYRDDIPLSAIDKF AP54_YEAST 12 12 -
GDVLINRTYRDDVGGNMVDAF O23140 15 15 -
GEVLISRIYRDDISRGVGNAF AP50_DICDI 12 12 -

Motif 2 width=28
Element Seqn Id St Int Rpt
EESIRDNFVIIYELLDELMDFGYPQTTD AP47_MOUSE 100 66 -
EESIRDNFVIIYELLDELLDFGYPQTTD O62531 103 69 -
EESVRDNFVVIYELLDEMMDFGFPQTTE AP47_CAEEL 100 66 -
EENIKNNFVLIYELLDEILDFGYPQNSE AP50_HUMAN 98 65 -
EENVKNNFVLIYELLDEILDFGYPQNTD AP50_CAEEL 98 65 -
EENIKNNFVLIYELLDEILDFGYPQNTD O62530 98 65 -
EEAVRDNFVIIYELFDEMLDFGYPQTTE O01755 100 66 -
EESLRDNFVVVYELLDEMMDFGYPQYTE O22715 103 67 -
EESIRDNFVIIYELLDEVMDYGIPQITE AP54_YEAST 101 68 -
EDAIRNNFVLIYELLDEIMDFGYPQNLS O23140 102 66 -
EDSIRNNFVLVYELLDEILDFGYPQNCS AP50_DICDI 97 64 -

Motif 3 width=29
Element Seqn Id St Int Rpt
WRSEGIKYRKNEVFLDVIEAVNLLVSANG AP47_MOUSE 159 31 -
WRSEGIKYRKNEVFLDVIESVNLLANANG O62531 161 30 -
WRSEGIKYRKNEVFLDVIESVNMLASANG AP47_CAEEL 158 30 -
WRREGIKYRRNELFLDVLESVNLLMSPQG AP50_HUMAN 161 35 -
WRREGIKYRRNELFLDVIEYVNLLMNQQG AP50_CAEEL 165 39 -
WRREGIKYRRNELFLDVLEYVNLLMSPQG O62530 159 33 -
WRSEGIKYRKNEVFLDVIESVNMLANAQG O01755 157 29 -
WRSEGIQYKKNEVFLDVIENVNILVNSNG O22715 161 30 -
WRPEGITHKKNEAFLDIVESINMLMTQKG AP54_YEAST 166 37 -
WRREGLAYKKNEVFLDIVESVNLLMSSKG O23140 168 38 -
WRTPDIKYKRNELYIDVVESVNLLMSAEG AP50_DICDI 163 38 -

Motif 4 width=28
Element Seqn Id St Int Rpt
LEDVKFHQCVRLSRFENDRTISFIPPDG AP47_MOUSE 233 45 -
LEDVKFHQCVRLSRFENDRTISFIPPDG O62531 235 45 -
LEDVKFHQCVRLSRFDTDRTISFIPPDG AP47_CAEEL 232 45 -
IDDCTFHQCVRLSKFDSERSISFIPPDG AP50_HUMAN 243 53 -
IDDCQFHQCVKLTKFETEHAISFIPPDG AP50_CAEEL 247 53 -
IDDCQFHQCVKLSKFETEHSISFIPPDG O62530 245 57 -
LEDIKFHQCVRLSRFDSERTISFIPPDG O01755 236 50 -
LEDIKFHQCVRLARFENDRTISFIPPDG O22715 236 46 -
LEDLKFHQCVRLSKFENEKIITFIPPDG AP54_YEAST 272 77 -
LDDVTFHQCVNLTRFNSEKTVSFVPPDG O23140 248 51 -
IDDITFHQCVRLGKFDSDRTVSFIPPDG AP50_DICDI 248 56 -

Motif 5 width=16
Element Seqn Id St Int Rpt
KRRSTANNVEIHIPVP AP47_MOUSE 302 41 -
KRRSTANNVEIVIPVP O62531 304 41 -
KRRSTANNVEIIIPVP AP47_CAEEL 301 41 -
KPSLLAQKIEVRIPTP AP50_HUMAN 312 41 -
KPSLLAQKLEVRIPTP AP50_CAEEL 316 41 -
KPSLLGQKIEVKIPTP O62530 314 41 -
KRQSVANHVEVIIPVP O01755 305 41 -
KERSTATNVEIELPVP O22715 305 41 -
KRKSTATNVEILIPVP AP54_YEAST 341 41 -
GAKMFALGVVVKIPVP O23140 317 41 -
SSKMFGANVKVIIPTP AP50_DICDI 317 41 -

Motif 6 width=12
Element Seqn Id St Int Rpt
VWSVKSFPGGKE AP47_MOUSE 342 24 -
IWTIKSFPGGKE O62531 344 24 -
VWTIKNFPGGKE AP47_CAEEL 341 24 -
VWKIKRMAGMKE AP50_HUMAN 352 24 -
VWKIKRMAGMKE AP50_CAEEL 356 24 -
VWKIKRMAGMKE O62530 354 24 -
VWSIRSFPGEHQ O01755 345 24 -
VWKIKSFPGNKE O22715 345 24 -
LWKIRSFPGGKE AP54_YEAST 381 24 -
VWKIRKFPGQTE O23140 357 24 -
IWRIRRFPGDTE AP50_DICDI 357 24 -