SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR00709

Identifier
AVIDIN  [View Relations]  [View Alignment]  
Accession
PR00709
No. of Motifs
6
Creation Date
09-JUN-1997  (UPDATE 26-AUG-1999)
Title
Avidin signature
Database References
PRINTS; PR00179 LIPOCALIN
PROSITE; PS00577 AVIDIN
BLOCKS; BL00577
PFAM; PF01382 Avidin
INTERPRO; IPR000088
PDB; 2AVI; 1AVD; 1AVE
SCOP; 2AVI
CATH; 2AVI; 1AVD; 1AVE
Literature References
1. GREEN, N.M.
Avidin and Streptavidin.
METHODS ENZYMOL. 184 51-67 (1990).
 
2. FLOWER, D.R.
Structural relationship of streptavidin to the calycin protein superfamily.
FEBS LETT. 333 99-102 (1993).
 
3. FLOWER, D.R.
The lipocalin protein family: structure and function.
BIOCHEM.J. 318 1-14 (1996).

Documentation
Avidin is a minor egg white component in several groups of oviparous
vertebrates [1]; streptavidin is its bacterial homologue. The protein 
is characterised by its very tight (avid) binding to biotin, from where it 
derives its key role in biotechnology. Avidin has also been found as a
domain in sea-urchin cell surface proteins. 
 
Structurally and functionally the protein is closely related to the 
lipocalins, which are members of the calycin superfamily [2]; these are 
characterised by their high specificity for small hydrophobic molecules [3].
 
The crystal structures of avidin and avidin-biotin complexes have been 
solved, and reveal the characteristic lipocalin-like 8-stranded anti-
parallel beta-barrel. The protein forms a homotetrameric assembly of
non-covalently associated chains, each of which forms a strong and
specific non-covalent complex with one molecule of biotin.  
 
AVIDIN is a 6-element fingerprint that provides a signature for avidins.
The fingerprint was derived from an initial alignment of 4 sequences: the
motifs were drawn from conserved regions spanning virtually the full
alignment length - motif 1 spans beta-strands 1 and 2; motif 2 encodes 
strand 3; motif 3 includes strand 5; motif 4 encodes strand 6; motif 5 spans
the C-terminal half of strand 7; and motif 6 spans helix 1 and strand 8. Two
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 6 sequences was identified.
Summary Information
6 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
6666666
5000000
4000000
3000000
2000000
123456
True Positives
AVID_CHICK    FBP1_STRPU    FBP3_STRPU    SAV1_STRVL    
SAV2_STRVL SAV_STRAV
Sequence Titles
AVID_CHICK  AVIDIN PRECURSOR - GALLUS GALLUS (CHICKEN).   
FBP1_STRPU FIBROPELLIN I PRECURSOR (EPIDERMAL GROWTH FACTOR-RELATED PROTEIN 1) (UEGF-1) - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
FBP3_STRPU FIBROPELLIN C PRECURSOR (EPIDERMAL GROWTH FACTOR-RELATED PROTEIN 3) (EGF III) (FIBROPELLIN III) - STRONGYLOCENTROTUS PURPURATUS (PURPLE SEA URCHIN).
SAV1_STRVL STREPTAVIDIN V1 PRECURSOR (SA V1) - STREPTOMYCES VIOLACEUS (STREPTOMYCES VENEZUE
SAV2_STRVL STREPTAVIDIN V2 PRECURSOR (SA V2) - STREPTOMYCES VIOLACEUS (STREPTOMYCES VENEZUE
SAV_STRAV STREPTAVIDIN PRECURSOR - STREPTOMYCES AVIDINII.
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
ITGTWYNQLGSTFIV SAV1_STRVL 41 41 -
LEGMWYNECNDQVTI FBP1_STRPU 941 941 -
LTGKWTNDLGSNMTI AVID_CHICK 30 30 -
LEGVWFNECNDQITI FBP3_STRPU 447 447 -

Motif 2 width=9
Element Seqn Id St Int Rpt
GALTGTYES SAV1_STRVL 61 5 -
GMMLGDYMT FBP1_STRPU 961 5 -
GEFTGTYIT AVID_CHICK 51 6 -
GMMLGDHMT FBP3_STRPU 467 5 -

Motif 3 width=13
Element Seqn Id St Int Rpt
TDGSGTALGWTVA SAV1_STRVL 90 20 -
NNYDFPSFGFTVV FBP1_STRPU 989 19 -
NKRTQPTFGFTVN AVID_CHICK 81 21 -
NNYDFPSFGITVV FBP3_STRPU 495 19 -

Motif 4 width=11
Element Seqn Id St Int Rpt
SATTWSGQYVG SAV1_STRVL 112 9 -
STTSWTGQCHL FBP1_STRPU 1007 5 -
STTVFTGQCFI AVID_CHICK 99 5 -
TTTSWTGQCHL FBP3_STRPU 513 5 -

Motif 5 width=12
Element Seqn Id St Int Rpt
INTQWLLTSGTT SAV1_STRVL 128 5 -
LYTTWINTNMVS FBP1_STRPU 1024 6 -
LKTMWLLRSSVN AVID_CHICK 117 7 -
LYTTWIESSMVS FBP3_STRPU 530 6 -

Motif 6 width=17
Element Seqn Id St Int Rpt
WKSTLVGHDTFTKVKPS SAV1_STRVL 144 4 -
KKSNMVGQDKWTRYEQS FBP1_STRPU 1041 5 -
WKATRVGINIFTRLRTQ AVID_CHICK 134 5 -
KRANKVGQDKWTRYEQS FBP3_STRPU 547 5 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
ITGTWYNQLGSTFIV SAV1_STRVL 41 41 -
ITGTWYNQLGSTFIV SAV_STRAV 41 41 -
ITGTWYNQLGSTFIV SAV2_STRVL 41 41 -
LEGMWYNECNDQVTI FBP1_STRPU 941 941 -
LTGKWTNDLGSNMTI AVID_CHICK 30 30 -
LEGVWFNECNDQITI FBP3_STRPU 447 447 -

Motif 2 width=9
Element Seqn Id St Int Rpt
GALTGTYES SAV1_STRVL 61 5 -
GALTGTYES SAV_STRAV 61 5 -
GSLTGTYES SAV2_STRVL 61 5 -
GMMLGDYMT FBP1_STRPU 961 5 -
GEFTGTYIT AVID_CHICK 51 6 -
GMMLGDHMT FBP3_STRPU 467 5 -

Motif 3 width=13
Element Seqn Id St Int Rpt
TDGSGTALGWTVA SAV1_STRVL 90 20 -
TDGSGTALGWTVA SAV_STRAV 90 20 -
TDGSGTALGWTVA SAV2_STRVL 90 20 -
NNYDFPSFGFTVV FBP1_STRPU 989 19 -
NKRTQPTFGFTVN AVID_CHICK 81 21 -
NNYDFPSFGITVV FBP3_STRPU 495 19 -

Motif 4 width=11
Element Seqn Id St Int Rpt
SATTWSGQYVG SAV1_STRVL 112 9 -
SATTWSGQYVG SAV_STRAV 112 9 -
SATTWSGQYVA SAV2_STRVL 112 9 -
STTSWTGQCHL FBP1_STRPU 1007 5 -
STTVFTGQCFI AVID_CHICK 99 5 -
TTTSWTGQCHL FBP3_STRPU 513 5 -

Motif 5 width=12
Element Seqn Id St Int Rpt
INTQWLLTSGTT SAV1_STRVL 128 5 -
INTQWLLTSGTT SAV_STRAV 128 5 -
INTQWLLTSGTT SAV2_STRVL 128 5 -
LYTTWINTNMVS FBP1_STRPU 1024 6 -
LKTMWLLRSSVN AVID_CHICK 117 7 -
LYTTWIESSMVS FBP3_STRPU 530 6 -

Motif 6 width=17
Element Seqn Id St Int Rpt
WKSTLVGHDTFTKVKPS SAV1_STRVL 144 4 -
WKSTLVGHDTFTKVKPS SAV_STRAV 144 4 -
WKSTLVGHDTFTKVKPS SAV2_STRVL 144 4 -
KKSNMVGQDKWTRYEQS FBP1_STRPU 1041 5 -
WKATRVGINIFTRLRTQ AVID_CHICK 134 5 -
KRANKVGQDKWTRYEQS FBP3_STRPU 547 5 -