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PR00883

Identifier
NUCLEARHMG  [View Relations]  [View Alignment]  
Accession
PR00883
No. of Motifs
4
Creation Date
08-JUN-1998  (UPDATE 07-JUN-1999)
Title
High mobility group-like nuclear protein signature
Database References
PRINTS; PR00881 L7ARS6FAMILY
INTERPRO; IPR002415
Literature References
1. KOLODRUBETZ, D. AND BURGUM, A.
Sequence and genetic analysis of NHP2: a moderately abundant high
mobility group-like nuclear protein with an essential function in
Saccharomyces cerevisiae. 
YEAST 7 79-90 (1991). 
 
2. COLOMBO, P., YON J. AND FRIED, M.
The organization and expression of the human L7a ribosomal protein gene. 
BIOCHIM.BIOPHYS.ACTA 1129 93-95 (1991). 

Documentation
The gene for high mobility group (HMG)-like nuclear protein NHP2 from 
S.cerevisiae has been cloned and characterised [1]. NHP2 has been termed
`HMG-like' in that it shares certain physical/chemical properties with
HMG proteins from higher eukaryotes. Nevertheless, it shows no significant
sequence similarity to such proteins, and thus constitutes a distinct HMG
protein class. NHP2 does, however, share sequence similarity with two
ribosomal proteins: the acidic ribosomal protein S6 from H.marismorium
and mammalian L7a ribosomal protein [2]. 
 
The biological implications of the observed similarities to S6 and L7a are
unclear, as biochemical studies have indicated that NHP2 is not a ribosomal
protein. Nevertheless, deletion experiments have indicated NHP2 to have an
essential physiological function [1].
 
NUCLEARHMG is a 4-element fingerprint that provides a signature for high-
mobility group-like proteins. The fingerprint was derived from an initial
alignment of 5 sequences: the motifs were drawn from short conserved
N- and C-terminal sections, focusing on those regions that characterise the
nuclear HMG-like proteins but distinguish them from the L7A/RS6 family of
ribosomal proteins - motifs 1-3 span the N-terminus; and motif 4, which lies
towards the C-terminus, includes part of the region encoded by PROSITE
pattern RIBOSOMAL_L7AE (PS01082). A single iteration on OWL30.2 was required
to reach convergence, no further sequences being identified beyond the
starting set. A single partial match was found, RS6X_METJA, a related 30S
ribosomal HS6-like protein that matches motifs 3 and 4.
 
An update on SPTR37_9f identified a true set of 5 sequences.
Summary Information
5 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
45555
30000
20000
1234
True Positives
NHP2_YEAST    NHPX_CAEEL    NHPX_HUMAN    NHPX_YEAST    
O74690
Sequence Titles
NHP2_YEAST  HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). 
NHPX_CAEEL NHP2/RS6 FAMILY PROTEIN YEL026W HOMOLOG - CAENORHABDITIS ELEGANS.
NHPX_HUMAN NHP2/RS6 FAMILY PROTEIN YEL026W HOMOLOG (HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG) - HOMO SAPIENS (HUMAN).
NHPX_YEAST NHP2/RS6 FAMILY PROTEIN YEL026W - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
O74690 RS6/L7A RIBOSOMAL PROTEIN HOMOLOG - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
Scan History
OWL30_2    1  100  NSINGLE    
SPTR37_9f 2 6 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
PKAYPLADAHLTKK NHPX_HUMAN 8 8 -
PKAFPLADAALTQQ NHPX_YEAST 6 6 -
PKAYPLADAHLTKK NHPX_RAT 8 8 -
PFAKPLASKKLNKK NHP2_YEAST 46 46 -
PKAFPLADTNLSQK NHPX_CAEEL 8 8 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QILDVVQQAANLRQLK NHPX_YEAST 19 -1 -
KLLDLVQQSCNYKQLR NHPX_RAT 21 -1 -
KLMDLVQQAMNYKQLK NHPX_CAEEL 21 -1 -
KLLDLVQQSCNYKQLR NHPX_HUMAN 21 -1 -
KVLKTVKKASKAKNVK NHP2_YEAST 59 -1 -

Motif 3 width=11
Element Seqn Id St Int Rpt
GANEATKTLNR NHPX_RAT 38 1 -
GANEATKTLNR NHPX_CAEEL 38 1 -
GANEATKTLNR NHPX_HUMAN 38 1 -
GANEATKTLNR NHPX_YEAST 36 1 -
GVKEVVKALRK NHP2_YEAST 76 1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
FVPSRVALGRACG NHPX_YEAST 80 33 -
FIPSKQDLGAAGA NHP2_YEAST 120 33 -
FVRSKAALGRACG NHPX_CAEEL 82 33 -
FXRSKKALGRAXG NHPX_RAT 82 33 -
FVRSKQALGRACG NHPX_HUMAN 82 33 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
PKAFPLADSGLTQQ O74690 5 5 -
PKAFPLADTNLSQK NHPX_CAEEL 8 8 -
PKAYPLADAHLTKK NHPX_HUMAN 8 8 -
PKAFPLADAALTQQ NHPX_YEAST 6 6 -
PFAKPLASKKLNKK NHP2_YEAST 46 46 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QILDLVQQASHYKQLR O74690 18 -1 -
KLMDLVQQAMNYKQLK NHPX_CAEEL 21 -1 -
KLLDLVQQSCNYKQLR NHPX_HUMAN 21 -1 -
QILDVVQQAANLRQLK NHPX_YEAST 19 -1 -
KVLKTVKKASKAKNVK NHP2_YEAST 59 -1 -

Motif 3 width=11
Element Seqn Id St Int Rpt
GANEATKTLNR O74690 35 1 -
GANEATKTLNR NHPX_CAEEL 38 1 -
GANEATKTLNR NHPX_HUMAN 38 1 -
GANEATKTLNR NHPX_YEAST 36 1 -
GVKEVVKALRK NHP2_YEAST 76 1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
FVPSKAALGRACG O74690 79 33 -
FVRSKAALGRACG NHPX_CAEEL 82 33 -
FVRSKQALGRACG NHPX_HUMAN 82 33 -
FVPSRVALGRACG NHPX_YEAST 80 33 -
FIPSKQDLGAAGA NHP2_YEAST 120 33 -