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PR00930

Identifier
HIGHMOBLTYIY  [View Relations]  [View Alignment]  
Accession
PR00930
No. of Motifs
5
Creation Date
18-AUG-1998  (UPDATE 28-JUL-1999)
Title
High mobility group protein (HMGY) signature
Database References
PRINTS; PR00929 ATHOOK
PROSITE; PS00354 HMGI_Y
BLOCKS; BL00354
INTERPRO; IPR000116
PDB; 2EZD; 2EZE; 2EZF; 2EZG
SCOP; 2EZD
CATH; 2EZD
Literature References
1. REEVES, R. AND NISSEN, M.S.
The A.T-DNA-binding domain of mammalian high mobility group-I chromosomal
proteins - a novel peptide motif for recognizing DNA-structure.
J.BIOL.CHEM. 265 8573-8582 (1990).
 
2. FRIEDMANN, M., HOLTH, L.T., ZOGHBI H.Y. AND REEVES, R. 
Organization, inducible-expression and chromosome localization of the human
HMG-I(Y) nonhistone protein gene. 
NUCLEIC ACIDS RES. 21 4259-4267 (1993). 

Documentation
Members of the high mobility group HMG-I(Y) family of mammalian non-histone
proteins have been shown to bind specifically to the minor groove of 
A.T-rich sequences and to function as gene transcriptional regulatory 
proteins in vivo [1,2]. The human HMG-I(Y) gene has several potential 
promoter/enhancer regions, a number of different transcription start sites
and numerous alternatively-spliced exons, making it one of the most complex
non-histone chromatin protein-encoding genes reported to date [2]. 
 
Sequence analysis has shown that alternative splicing of precursor mRNAs
gives rise to the major HMG-I and HMG-Y isoforms found in human cells. Each
of the three different DNA-binding domain peptides present in an individual
HMG-I(Y) protein is coded for by sequences present on separate exons, 
suggesting exon `shuffling' of these functional domains during evolution 
[2]. The gene has been localised to the short arm of chromosome 6 in a 
region known to be involved in rearrangements, translocations and other 
abnormalities associated with human cancers [2]. 
 
HMG-I and HMG-Y are relatively short alternatively spliced forms containing
~100 residues (HMG-Y differs from HMG-I by the internal deletion of 11 amino
acids). The proteins preferentially bind to double-stranded DNA via an
11-residue domain known as an A.T-hook [1]. The hook domain is repeated
three times in the sequence of HMG-I/Y.
 
HIGHMOBLTYIY is a 5-element fingerprint that provides a signature for the
HMG-I/HMG-Y family of high mobility group proteins. The fingerprint was
derived from an initial alignment of 7 sequences: the motifs were drawn
from short conserved regions spanning virtually the full alignment length -
motif 1 encodes the first hook domain; motifs 2 and 3 span the second hook
region; motif 4 spans the third hook domain and includes the region encoded
by PROSITE pattern HMGI_Y (PS00354); and motif 5 encodes a C-terminal
acidic region. A single iteration on OWL30.2 was required to reach 
convergence, no further sequences being identified beyond the starting set.
Several partial matches were also found, all of which are HMG homologues or
DNA-binding proteins that match the hook domains. 
 
An update on SPTR37_9f identified a true set of 7 sequences, and 9
partial matches.
Summary Information
   7 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
9 codes involving 2 elements
Composite Feature Index
577777
400000
300000
290090
12345
True Positives
HMGC_HUMAN    HMGC_MOUSE    HMGI_HUMAN    HMGY_HUMAN    
HMGY_MOUSE O73816 O88791
True Positive Partials
Codes involving 2 elements
HMGA_SOYBN P92954 PRH_PETCR Q40725
Q42461 Q42492 Q43386 Q43600
Q43877
Sequence Titles
HMGC_HUMAN  HIGH MOBILITY GROUP PROTEIN HMGI-C - HOMO SAPIENS (HUMAN). 
HMGC_MOUSE HIGH MOBILITY GROUP PROTEIN HMGI-C - MUS MUSCULUS (MOUSE).
HMGI_HUMAN HIGH MOBILITY GROUP PROTEIN HMG-I - HOMO SAPIENS (HUMAN).
HMGY_HUMAN HIGH MOBILITY GROUP PROTEIN HMG-Y - HOMO SAPIENS (HUMAN).
HMGY_MOUSE HIGH MOBILITY GROUP PROTEIN HMG-Y - MUS MUSCULUS (MOUSE).
O73816 HIGH MOBILITY GROUP PROTEIN I-C - GALLUS GALLUS (CHICKEN).
O88791 NON-HISTONE CHROMOSOMAL ARCHITECTURAL PROTEIN HMGI-C - RATTUS NORVEGICUS (RAT).

HMGA_SOYBN HMG-Y RELATED PROTEIN A (SB16A PROTEIN) - GLYCINE MAX (SOYBEAN).
P92954 HMG-I/Y GENE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
PRH_PETCR PATHOGENESIS-RELATED HOMEODOMAIN PROTEIN (PRHP) - PETROSELINUM CRISPUM (PARSLEY) (PETROSELINUM HORTENSE).
Q40725 AT HOOK-CONTAINING PROTEIN - ORYZA SATIVA (RICE).
Q42461 HIGH MOBILITY GROUP PROTEIN - CANAVALIA GLADIATA (SWORD BEAN) (JAPANESE JACK BEAN).
Q42492 HIGH MOBILITY PROTEIN - CANAVALIA GLADIATA (SWORD BEAN) (JAPANESE JACK BEAN).
Q43386 HMG-I/Y PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Q43600 POSITIVE ELEMENT FACTOR 1 (PF1) - ORYZA SATIVA (RICE).
Q43877 HMGI/Y - PISUM SATIVUM (GARDEN PEA).
Scan History
OWL30_2    1  25   NSINGLE    
SPTR37_9f 3 40 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
TEKRGRGRPRKQP HMGY_HUMAN 20 20 -
PQKRGRGRPRKQQ HMGC_HUMAN 24 24 -
PQKRGRGRPRKQQ HMGC_MOUSE 24 24 -
PQKRGRGRPRKQP AF058287 24 24 -
TEKRGRGRPRKQP HUMHMGYD 21 21 -
TEKRGRGRPRKQP HMGY_MOUSE 20 20 -
TEKRGRGRPRKQP HMGI_HUMAN 20 20 -

Motif 2 width=12
Element Seqn Id St Int Rpt
KEPSEVPTPKRP HMGY_HUMAN 34 1 -
PEPSEVPTPKRP HUMHMGYD 34 0 -
QEPTGEPSPKRP AF058287 37 0 -
QEPTCEPSPKRP HMGC_MOUSE 37 0 -
QEPTGEPSPKRP HMGC_HUMAN 37 0 -
KEPSEVPTPKRP HMGI_HUMAN 45 12 -
KEPSEVPTPKRP HMGY_MOUSE 34 1 -

Motif 3 width=12
Element Seqn Id St Int Rpt
PRGRPKGSKNKS AF058287 48 -1 -
PRGRPKGSKNKG HUMHMGYD 45 -1 -
PRGRPKGSKNKS HMGC_MOUSE 48 -1 -
PRGRPKGSKNKS HMGC_HUMAN 48 -1 -
PRGRPKGSKNKG HMGY_HUMAN 45 -1 -
PRGRPKGSKNKG HMGI_HUMAN 56 -1 -
PRGRPKGSKNKG HMGY_MOUSE 45 -1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
AKTRKTTTTPGRKPRGRPKK HMGI_HUMAN 69 1 -
AAQKKAEATGEKRPRGRPRK AF058287 63 3 -
AKTRKTTTTPGRKPRGRPKK HUMHMGYD 58 1 -
AKTRKVTTAPGRKPRGRPKK HMGY_MOUSE 58 1 -
AAQKKAETIGEKRPRGRPRK HMGC_MOUSE 63 3 -
AAQKKAEATGEKRPRGRPRK HMGC_HUMAN 63 3 -
AKTRKTTTTPGRKPRGRPKK HMGY_HUMAN 58 1 -

Motif 5 width=13
Element Seqn Id St Int Rpt
ETEETSSQESAEE HMGC_MOUSE 95 12 -
EEEEGISQESSEE HUMHMGYD 81 3 -
ETEETSSQESAEE HMGC_HUMAN 96 13 -
EEEEGISQESSEE HMGY_HUMAN 81 3 -
EEEEGISQESSEE HMGI_HUMAN 92 3 -
EEEEGISQESSEE HMGY_MOUSE 81 3 -
ETEETSSQESAEE AF058287 96 13 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
PQKRGRGRPRKQP O88791 24 24 -
PQKRGRGRPRKQP O73816 24 24 -
PQKRGRGRPRKQQ HMGC_MOUSE 24 24 -
PQKRGRGRPRKQQ HMGC_HUMAN 24 24 -
TEKRGRGRPRKQP HMGY_HUMAN 20 20 -
TEKRGRGRPRKQP HMGI_HUMAN 20 20 -
TEKRGRGRPRKQP HMGY_MOUSE 20 20 -

Motif 2 width=12
Element Seqn Id St Int Rpt
QEPTCEPSPKRP O88791 37 0 -
QEPTGEPSPKRP O73816 37 0 -
QEPTCEPSPKRP HMGC_MOUSE 37 0 -
QEPTGEPSPKRP HMGC_HUMAN 37 0 -
KEPSEVPTPKRP HMGY_HUMAN 34 1 -
KEPSEVPTPKRP HMGI_HUMAN 45 12 -
KEPSEVPTPKRP HMGY_MOUSE 34 1 -

Motif 3 width=12
Element Seqn Id St Int Rpt
PRGRPKGSKNKS O88791 48 -1 -
PRGRPKGSKNKS O73816 48 -1 -
PRGRPKGSKNKS HMGC_MOUSE 48 -1 -
PRGRPKGSKNKS HMGC_HUMAN 48 -1 -
PRGRPKGSKNKG HMGY_HUMAN 45 -1 -
PRGRPKGSKNKG HMGI_HUMAN 56 -1 -
PRGRPKGSKNKG HMGY_MOUSE 45 -1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
AAQKKAETIGEKRPRGRPRK O88791 63 3 -
AAQKKAEATGEKRPRGRPRK O73816 63 3 -
AAQKKAETIGEKRPRGRPRK HMGC_MOUSE 63 3 -
AAQKKAEATGEKRPRGRPRK HMGC_HUMAN 63 3 -
AKTRKTTTTPGRKPRGRPKK HMGY_HUMAN 58 1 -
AKTRKTTTTPGRKPRGRPKK HMGI_HUMAN 69 1 -
AKTRKVTTAPGRKPRGRPKK HMGY_MOUSE 58 1 -

Motif 5 width=13
Element Seqn Id St Int Rpt
ETEETSSQESAEE O88791 94 11 -
ETEETSSQESAEE O73816 96 13 -
ETEETSSQESAEE HMGC_MOUSE 95 12 -
ETEETSSQESAEE HMGC_HUMAN 96 13 -
EEEEGISQESSEE HMGY_HUMAN 81 3 -
EEEEGISQESSEE HMGI_HUMAN 92 3 -
EEEEGISQESSEE HMGY_MOUSE 81 3 -