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PR00680

Identifier
PTREFOIL  [View Relations]  [View Alignment]  
Accession
PR00680
No. of Motifs
3
Creation Date
05-MAR-1997  (UPDATE 23-JUN-1999)
Title
P-type trefoil domain signature
Database References

PROSITE; PS00025 P_TREFOIL
BLOCKS; BL00025
PFAM; PF00088 trefoil
INTERPRO; IPR000519
Literature References
1. HOFFMANN, W. AND HAUSER, F.
The P-domain or trefoil motif - a role in renewal and pathology of
mucous epithelia.
TRENDS BIOCHEM.SCI. 18 239-243 (1993).
 
2. OTTO, B. AND WRIGHT, N.
Trefoil peptides - coming up clover.
CURR.BIOL. 4 835-838 (1994).
 
3. BORK P.
A trefoil domain in the major rabbit zona-pellucida protein.
PROTEIN SCI. 2 669-670 (1993).

Documentation
The P-type trefoil or P-domain is a 45-residue cysteine-rich region, 
6 cysteines of which link together through 3 disulphide bonds with
connectivity 1-5, 2-4, 3-6, thus:
 
             +-------------------------+
             |         +--------------+|
             |         |              ||
           xxCxxxxxxxxxCxxxxxxxxxCxxxxCCxxxxxxxxxxCxxxxxxxxx
                                 |                |
                                 |                |
                                 +----------------+
 
The domain has been found in a variety of extracellular eukaryotic
proteins [1-3].
 
PTREFOIL is a 3-element fingerprint that provides a signature for P-type
trefoil domains. The fingerprint was derived from an initial alignment of
10 sequences: the motifs were drawn from short conserved regions in the
central portion of the alignment and span the full domain length - motifs 
1 and 2 include the region encoded by PROSITE pattern P_TREFOIL (PS00025),
which encodes the central 4 cysteine residues. Two iterations on OWL29.1
were required to reach convergence, at which point a true set comprising
20 sequences was identified.
 
An update on SPTR37_9f identified a true set of 14 sequences, and 8
partial matches.
Summary Information
  14 codes involving  3 elements
6 codes involving 2 elements
Composite Feature Index
3141414
2354
123
True Positives
ITF_HUMAN     ITF_MOUSE     ITF_RAT       MUA1_XENLA    
PS2_HUMAN PS2_MOUSE Q29183 Q63467
SP_HUMAN SP_MOUSE SP_RAT XP1_XENLA
XP2_XENLA XP4_XENLA
True Positive Partials
Codes involving 2 elements
LYAG_MOUSE O15999 O42464 O73626
Q91236 SUIS_HUMAN
Sequence Titles
ITF_HUMAN   INTESTINAL TREFOIL FACTOR PRECURSOR (HP1.B) - HOMO SAPIENS (HUMAN). 
ITF_MOUSE INTESTINAL TREFOIL FACTOR PRECURSOR - MUS MUSCULUS (MOUSE).
ITF_RAT INTESTINAL TREFOIL FACTOR PRECURSOR (POLYPEPTIDE P1.B) - RATTUS NORVEGICUS (RAT).
MUA1_XENLA INTEGUMENTARY MUCIN A.1 PRECURSOR (FIM-A.1) (PREPROSPASMOLYSIN) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
PS2_HUMAN PS2 PROTEIN PRECURSOR (HP1.A) (BREAST CANCER ESTROGEN-INDUCIBLE PROTEIN) (PNR-2) - HOMO SAPIENS (HUMAN).
PS2_MOUSE PS2 PROTEIN PRECURSOR - MUS MUSCULUS (MOUSE).
Q29183 INTESTINAL TREFOIL FACTOR PRECURSOR - SUS SCROFA (PIG).
Q63467 PS2 PROTEIN PRECURSOR - RATTUS NORVEGICUS (RAT).
SP_HUMAN SPASMOLYTIC POLYPEPTIDE PRECURSOR (SP) - HOMO SAPIENS (HUMAN).
SP_MOUSE SPASMOLYTIC POLYPEPTIDE PRECURSOR (SP) - MUS MUSCULUS (MOUSE).
SP_RAT SPASMOLYTIC POLYPEPTIDE PRECURSOR (SP) - RATTUS NORVEGICUS (RAT).
XP1_XENLA PUTATIVE GASTROINTESTINAL GROWTH FACTOR XP1 PRECURSOR - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
XP2_XENLA SKIN SECRETORY PROTEIN XP2 PRECURSOR (APEG PROTEIN) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
XP4_XENLA PUTATIVE GASTROINTESTINAL GROWTH FACTOR XP4 PRECURSOR - XENOPUS LAEVIS (AFRICAN CLAWED FROG).

LYAG_MOUSE LYSOSOMAL ALPHA-GLUCOSIDASE PRECURSOR (EC 3.2.1.20) (ACID MALTASE) - MUS MUSCULUS (MOUSE).
O15999 EPIDERMIS-SPACIFIC PROTEIN 1 - CIONA SAVIGNYI.
O42464 EGGSHELL PROTEIN - SALMO SALAR (ATLANTIC SALMON).
O73626 ACID ALPHA GLUCOSIDASE - COTURNIX COTURNIX JAPONICA (JAPANESE QUAIL).
Q91236 ZONA PELLUCIDA PROTEIN (ZP) - PSEUDOPLEURONECTA AMERICANUS (WINTER FLOUNDER).
SUIS_HUMAN SUCRASE-ISOMALTASE, INTESTINAL [INCLUDES: SUCRASE (EC 3.2.1.48); ISOMALTASE (EC 3.2.1.10)] - HOMO SAPIENS (HUMAN).
Scan History
OWL29_1    2  50   NSINGLE    
SPTR37_9f 2 300 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PKNRVNCGFPGIT SP_PIG 34 34 -
PKNRVNCGFPGIT NRL_1PCP 13 13 -
PRERINCGFPGVT RATPS2P 32 32 -
PHNRTNCGFPGIT SP_HUMAN 37 37 -
PFKRTDCGYPGIT XP2_XENLA 355 355 -
PRERINCGFPGVT PS2_MOUSE 38 38 -
PRERQNCGFPGVT PS2_HUMAN 35 35 -
PSVRTDCGYPGIT MUA1_XENLA 357 357 -
PKARVNCGYPGIT XP4_XENLA 80 80 -
RLARVNCGYSGIT XP1_XENLA 36 36 -

Motif 2 width=13
Element Seqn Id St Int Rpt
TDKECREKGCCYD MUA1_XENLA 369 -1 -
TMDQCYKKGCCYD XP4_XENLA 191 98 -
TPQECTKQGCCFD XP1_XENLA 48 -1 -
TSDQCFTSGCCFD SP_PIG 46 -1 -
TSDQCFTSGCCFD NRL_1PCP 25 -1 -
TAQQCKEKGCCFD RATPS2P 44 -1 -
TSDQCFDNGCCFD SP_HUMAN 49 -1 -
TEGQCKAKGCCFD XP2_XENLA 367 -1 -
TAQQCTERGCCFD PS2_MOUSE 50 -1 -
TPSQCANKGCCFD PS2_HUMAN 47 -1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
DSSVTGVPWCFHP SP_HUMAN 61 -1 -
DDSVRGFPWCFHP PS2_MOUSE 62 -1 -
DDTVRGVPWCFYP PS2_HUMAN 59 -1 -
DECIPDVIWCFEK MUA1_XENLA 381 -1 -
DSSESDSIWCFYP XP4_XENLA 203 -1 -
DSTIQDAPWCFYP XP1_XENLA 60 -1 -
DSQVPGVPWCFKP SP_PIG 58 -1 -
DSQVPGVPWCFKP NRL_1PCP 37 -1 -
DDSVRGFPWCFRP RATPS2P 56 -1 -
DSSIVGVKWCFFP XP2_XENLA 379 -1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PSNRKNCGFPGIT SP_RAT 36 36 -
PHNRKNCGFPGIT SP_MOUSE 36 36 -
AKDRVDCGYPQVT Q29183 36 36 -
PHNRTNCGFPGIT SP_HUMAN 37 37 -
ANVRVDCGYPTVT ITF_RAT 37 37 -
ANVRVDCGYPSVT ITF_MOUSE 37 37 -
PFKRTDCGYPGIT XP2_XENLA 355 355 -
PRERINCGFPGVT PS2_MOUSE 38 38 -
PRERQNCGFPGVT PS2_HUMAN 35 35 -
PRERINCGFPGVT Q63467 32 32 -
AKDRVDCGYPHVT ITF_HUMAN 36 36 -
PSVRTDCGYPGIT MUA1_XENLA 357 357 -
PKARVNCGYPGIT XP4_XENLA 80 80 -
RLARVNCGYSGIT XP1_XENLA 36 36 -

Motif 2 width=13
Element Seqn Id St Int Rpt
TSDQCFNLGCCFD SP_RAT 48 -1 -
TSEQCFDLGCCFD SP_MOUSE 48 -1 -
TPEQCNNRGCCFD Q29183 48 -1 -
TSDQCFDNGCCFD SP_HUMAN 49 -1 -
TSEQCNNRGCCFD ITF_RAT 49 -1 -
TSEQCNNRGCCFD ITF_MOUSE 49 -1 -
TEGQCKAKGCCFD XP2_XENLA 367 -1 -
TAQQCTERGCCFD PS2_MOUSE 50 -1 -
TPSQCANKGCCFD PS2_HUMAN 47 -1 -
TAQQCKEKGCCFD Q63467 44 -1 -
TPKECNNRGCCFD ITF_HUMAN 48 -1 -
TDKECREKGCCYD MUA1_XENLA 369 -1 -
TMDQCYKKGCCYD XP4_XENLA 191 98 -
TPQECTKQGCCFD XP1_XENLA 48 -1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
DSSVAGVPWCFHP SP_RAT 60 -1 -
DSSVAGVPWCFHP SP_MOUSE 60 -1 -
DSSIXGVPWCFKP Q29183 60 -1 -
DSSVTGVPWCFHP SP_HUMAN 61 -1 -
DSSIPNVPWCFKP ITF_RAT 61 -1 -
DSSIPNVPWCFKP ITF_MOUSE 61 -1 -
DSSIVGVKWCFFP XP2_XENLA 379 -1 -
DDSVRGFPWCFHP PS2_MOUSE 62 -1 -
DDTVRGVPWCFYP PS2_HUMAN 59 -1 -
DDSVRGFPWCFRP Q63467 56 -1 -
DSRIPGVPWCFKP ITF_HUMAN 60 -1 -
DECIPDVIWCFEK MUA1_XENLA 381 -1 -
DSSESDSIWCFYP XP4_XENLA 203 -1 -
DSTIQDAPWCFYP XP1_XENLA 60 -1 -