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PR01721

Identifier
FRACTALKINE  [View Relations]  [View Alignment]  
Accession
PR01721
No. of Motifs
11
Creation Date
28-JUN-2002
Title
Fractalkine/neurotactin precursor signature
Database References

PDB; 1B2T; 1F2L
SCOP; 1B2T; 1F2L
CATH; 1B2T; 1F2L
Literature References
1. WATSON, S. AND ARKINSTALL, S.
Chemokines.
IN THE G PROTEIN-LINKED RECEPTOR FACTSBOOK, ACADEMIC PRESS, 1994, PP.83-88.
 
2. BAZAN, J.F., BACON, K.B., HARDIMAN, G., WANG, W., SOO, K., ROSSI, D.,
GREAVES, D.R., ZLOTNIK, A. AND SCHALL, T.J.
A new class of membrane-bound chemokine with a CX3X motif.
NATURE 385 640-644 (1997).

Documentation
Chemokines are proteins that have important physiological and patho-
physiological roles in a wide range of acute and chronic inflammatory
processes [1]. Their sequences are similar and are characterised by a
4-cysteine motif: the family can be divided according to whether the first 2
Cys residues are adjacent (the C-C family), or separated by an intervening
residue (the C-x-C family). 
 
Two additional chemokine families have also been identified, each containing
only one member. C chemokines have only one of the first two Cys residues,
while C-x3-C chemokines contain both cysteines, separated by three
intervening residues [2]. The only C-x3-C chemokine identified to date is
fractalkine, a transmembrane (TM) molecule containing a chemokine domain on
an extended mucin-like stalk [2]. The membrane-bound form of fractalkine can
be induced on endothelial cells in response to inflammation, and promotes
adhesion of monocytes and T lymphocytes. The chemokine can also be released
in a soluble form, which causes chemotaxis of monocytes and T cells [2].
 
FRACTALKINE is an 11-element fingerprint that provides a signature for the
fractalkine/neurotactin precursors. The fingerprint was derived from an
initial alignment of 4 sequences: the motifs were drawn from conserved
sections spanning virtually the full alignment length, focusing on those
areas that best characterise the fractalkine precursors - motifs 1-4 span
the N-terminal chemokine domain; motif 5 is located in the central portion
of the mucin stalk; motifs 6-8 span the C-terminal portion of the mucin
stalk; motifs 9 and 10 span the TM domain, leading into the cytoplasmic
domain; and motif 11 resides in the cytoplasmic domain. A single iteration
on SPTR40_20f 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
Q91V44        SYD1_HUMAN    SYD1_MOUSE    SYD1_RAT      
Sequence Titles
Q91V44      SMALL INDUCIBLE CYTOKINE SUBFAMILY D, 1 (FRACTALKINE/NEUROTACTIN) - Mus musculus (Mouse). 
SYD1_HUMAN Fractalkine precursor (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cytokine D1) - Homo sapiens (Human).
SYD1_MOUSE Fractalkine precursor (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cytokine D1) - Mus musculus (Mouse).
SYD1_RAT Fractalkine precursor (Neurotactin) (CX3C membrane-anchored chemokine) (Small inducible cytokine D1) - Rattus norvegicus (Rat).
Scan History
SPTR40_20f 1  100  NSINGLE    
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
LLPGQHLGMTKC Q91V44 21 21 -
LLPGQHLGMTKC SYD1_MOUSE 21 21 -
LLAGQHLGMTKC SYD1_RAT 21 21 -
LLAGQHHGVTKC SYD1_HUMAN 21 21 -

Motif 2 width=15
Element Seqn Id St Int Rpt
IRYQLNQESCGKRAI Q91V44 49 16 -
IRYQLNQESCGKRAI SYD1_MOUSE 49 16 -
IHYQLNQESCGKRAI SYD1_RAT 49 16 -
IHYQQNQASCGKRAI SYD1_HUMAN 49 16 -

Motif 3 width=18
Element Seqn Id St Int Rpt
LETTQHRRFCADPKEKWV Q91V44 65 1 -
LETTQHRRFCADPKEKWV SYD1_MOUSE 65 1 -
LETRQHRHFCADPKEKWV SYD1_RAT 65 1 -
LETRQHRLFCADPKEQWV SYD1_HUMAN 65 1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
DAMKHLDHQAAALTKNGG Q91V44 84 1 -
DAMKHLDHQAAALTKNGG SYD1_MOUSE 84 1 -
DAMKHLDHQTAALTRNGG SYD1_RAT 84 1 -
DAMQHLDRQAAALTRNGG SYD1_HUMAN 84 1 -

Motif 5 width=12
Element Seqn Id St Int Rpt
SSWAEEKATESP Q91V44 208 106 -
SSWAEEKATESP SYD1_MOUSE 208 106 -
SLWAEEKATESP SYD1_RAT 208 106 -
SLWAEAKTSEAP SYD1_HUMAN 208 106 -

Motif 6 width=20
Element Seqn Id St Int Rpt
HTDNFQERGPGNTVHPSVAP Q91V44 269 49 -
HTDNFQERGPGNTVHPSVAP SYD1_MOUSE 269 49 -
HTDIFQDRGPGSTVHPSVAP SYD1_RAT 267 47 -
HTDAFQDWGPGSMAHVSVVP SYD1_HUMAN 271 51 -

Motif 7 width=23
Element Seqn Id St Int Rpt
SSEETPSPELVASGSQAPKIEEP Q91V44 290 1 -
SSEETPSPELVASGSQAPKIEEP SYD1_MOUSE 290 1 -
SSEKTPSPELVASGSQAPKVEEP SYD1_RAT 288 1 -
SSEGTPSREPVASGSWTPKAEEP SYD1_HUMAN 292 1 -

Motif 8 width=19
Element Seqn Id St Int Rpt
IHATADPQKLSVLITPVPD Q91V44 313 0 -
IHATADPQKLSVLITPVPD SYD1_MOUSE 313 0 -
IHATADPQKLSVFITPVPD SYD1_RAT 311 0 -
IHATMDPQRLGVLITPVPD SYD1_HUMAN 315 0 -

Motif 9 width=17
Element Seqn Id St Int Rpt
QAATRRQAVGLLAFLGL Q91V44 333 1 -
QAATRRQAVGLLAFLGL SYD1_MOUSE 333 1 -
QAATRRQAVGLLAFLGL SYD1_RAT 331 1 -
QAATRRQAVGLLAFLGL SYD1_HUMAN 335 1 -

Motif 10 width=19
Element Seqn Id St Int Rpt
FCLGVAMFAYQSLQGCPRK Q91V44 351 1 -
FCLGVAMFAYQSLQGCPRK SYD1_MOUSE 351 1 -
FCLGVAMFAYQSLQGCPRK SYD1_RAT 349 1 -
FCLGVAMFTYQSLQGCPRK SYD1_HUMAN 353 1 -

Motif 11 width=25
Element Seqn Id St Int Rpt
MAGEMVEGLRYVPRSCGSNSYVLVP Q91V44 370 0 -
MAGEMVEGLRYVPRSCGSNSYVLVP SYD1_MOUSE 370 0 -
MAGEMVEGLRYVPRSCGSNSYVLVP SYD1_RAT 368 0 -
MAGEMAEGLRYIPRSCGSNSYVLVP SYD1_HUMAN 372 0 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
LLPGQHLGMTKC Q91V44 21 21 -
LLPGQHLGMTKC SYD1_MOUSE 21 21 -
LLAGQHLGMTKC SYD1_RAT 21 21 -
LLAGQHHGVTKC SYD1_HUMAN 21 21 -

Motif 2 width=15
Element Seqn Id St Int Rpt
IRYQLNQESCGKRAI Q91V44 49 16 -
IRYQLNQESCGKRAI SYD1_MOUSE 49 16 -
IHYQLNQESCGKRAI SYD1_RAT 49 16 -
IHYQQNQASCGKRAI SYD1_HUMAN 49 16 -

Motif 3 width=18
Element Seqn Id St Int Rpt
LETTQHRRFCADPKEKWV Q91V44 65 1 -
LETTQHRRFCADPKEKWV SYD1_MOUSE 65 1 -
LETRQHRHFCADPKEKWV SYD1_RAT 65 1 -
LETRQHRLFCADPKEQWV SYD1_HUMAN 65 1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
DAMKHLDHQAAALTKNGG Q91V44 84 1 -
DAMKHLDHQAAALTKNGG SYD1_MOUSE 84 1 -
DAMKHLDHQTAALTRNGG SYD1_RAT 84 1 -
DAMQHLDRQAAALTRNGG SYD1_HUMAN 84 1 -

Motif 5 width=12
Element Seqn Id St Int Rpt
SSWAEEKATESP Q91V44 208 106 -
SSWAEEKATESP SYD1_MOUSE 208 106 -
SLWAEEKATESP SYD1_RAT 208 106 -
SLWAEAKTSEAP SYD1_HUMAN 208 106 -

Motif 6 width=20
Element Seqn Id St Int Rpt
HTDNFQERGPGNTVHPSVAP Q91V44 269 49 -
HTDNFQERGPGNTVHPSVAP SYD1_MOUSE 269 49 -
HTDIFQDRGPGSTVHPSVAP SYD1_RAT 267 47 -
HTDAFQDWGPGSMAHVSVVP SYD1_HUMAN 271 51 -

Motif 7 width=23
Element Seqn Id St Int Rpt
SSEETPSPELVASGSQAPKIEEP Q91V44 290 1 -
SSEETPSPELVASGSQAPKIEEP SYD1_MOUSE 290 1 -
SSEKTPSPELVASGSQAPKVEEP SYD1_RAT 288 1 -
SSEGTPSREPVASGSWTPKAEEP SYD1_HUMAN 292 1 -

Motif 8 width=19
Element Seqn Id St Int Rpt
IHATADPQKLSVLITPVPD Q91V44 313 0 -
IHATADPQKLSVLITPVPD SYD1_MOUSE 313 0 -
IHATADPQKLSVFITPVPD SYD1_RAT 311 0 -
IHATMDPQRLGVLITPVPD SYD1_HUMAN 315 0 -

Motif 9 width=17
Element Seqn Id St Int Rpt
QAATRRQAVGLLAFLGL Q91V44 333 1 -
QAATRRQAVGLLAFLGL SYD1_MOUSE 333 1 -
QAATRRQAVGLLAFLGL SYD1_RAT 331 1 -
QAATRRQAVGLLAFLGL SYD1_HUMAN 335 1 -

Motif 10 width=19
Element Seqn Id St Int Rpt
FCLGVAMFAYQSLQGCPRK Q91V44 351 1 -
FCLGVAMFAYQSLQGCPRK SYD1_MOUSE 351 1 -
FCLGVAMFAYQSLQGCPRK SYD1_RAT 349 1 -
FCLGVAMFTYQSLQGCPRK SYD1_HUMAN 353 1 -

Motif 11 width=25
Element Seqn Id St Int Rpt
MAGEMVEGLRYVPRSCGSNSYVLVP Q91V44 370 0 -
MAGEMVEGLRYVPRSCGSNSYVLVP SYD1_MOUSE 370 0 -
MAGEMVEGLRYVPRSCGSNSYVLVP SYD1_RAT 368 0 -
MAGEMAEGLRYIPRSCGSNSYVLVP SYD1_HUMAN 372 0 -