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PR00884

Identifier
RIBOSOMALHS6  [View Relations]  [View Alignment]  
Accession
PR00884
No. of Motifs
5
Creation Date
08-JUN-1998  (UPDATE 07-JUN-1999)
Title
Ribosomal protein HS6 signature
Database References
PRINTS; PR00881 L7ARS6FAMILY
INTERPRO; IPR000948
Literature References
1. KIMURA, J., ARNDT, E. AND KIMURA, M.
Primary structures of three highly acidic ribosomal proteins S6, S12 and S15
from the archaebacterium Halobacterium marismortui. 
FEBS LETT. 224 65-70 (1987). 
 
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). 
 
3. AREVALO, S.G. AND WARNER, J.R.
Ribosomal protein L4 of Saccharomyces cerevisiae: the gene and its protein. 
NUCLEIC ACIDS RES. 18 1447-1449 (1990). 
 
4. 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(2) 79-90 (1991).

Documentation
The sequence of the acidic ribosomal protein S6 from Halobacterium
marismortui has been determined [1]. The protein consists of 116 amino acid
residues, and has a molecular mass of 12,251 Da. Sequence comparison with
ribosomal proteins of other organisms has revealed that halobacterial
protein S6 is similar to mammalian protein L7a [2], yeast L4 [3], yeast NHP2
[4], B.subtilis hypothetical protein ylxQ and M.jannaschii MJ1203.
 
RIBOSOMALHS6 is a 5-element fingerprint that provides a signature for
the HS6-like family of ribosomal proteins. The fingerprint was derived from
an initial alignment of 5 sequences: the motifs were drawn from short
conserved sections spanning virtually the full alignment length, focusing
on those regions that characterise the ribosomal HS6-like proteins but
distinguish them from the rest of the high mobility group-like family. 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, S11615, a Halobacterium HS14 ribosomal protein fragment that
matches motifs 1 and 2. 
 
An update on SPTR37_9f identified a true set of 6 sequences.
Summary Information
6 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
566666
400000
300000
200000
12345
True Positives
RS6X_ARCFU    RS6X_HALMA    RS6X_METJA    RS6X_METTH    
RS6X_PYRHO RS6X_SULSO
Sequence Titles
RS6X_ARCFU  30S RIBOSOMAL PROTEIN HS6-LIKE - ARCHAEOGLOBUS FULGIDUS. 
RS6X_HALMA 30S RIBOSOMAL PROTEIN HS6 - HALOARCULA MARISMORTUI (HALOBACTERIUM MARISMORTUI).
RS6X_METJA 30S RIBOSOMAL PROTEIN HS6-LIKE - METHANOCOCCUS JANNASCHII.
RS6X_METTH 30S RIBOSOMAL PROTEIN HS6-LIKE - METHANOBACTERIUM THERMOAUTOTROPHICUM.
RS6X_PYRHO 30S RIBOSOMAL PROTEIN HS6-LIKE - PYROCOCCUS HORIKOSHII.
RS6X_SULSO 30S RIBOSOMAL PROTEIN HS6-LIKE - SULFOLOBUS SOLFATARICUS.
Scan History
OWL30_2    1  100  NSINGLE    
SPTR37_9f 2 9 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
YVKFDVPKELAD A69132 13 13 -
YVRFEVPEDMQN D69345 2 2 -
YVKFEVPQDLAD RS6X_SULSO 9 9 -
YVKFKVPEEIQK RS6X_METJA 7 7 -
YVDFDVPADLED RS6X_HALMA 3 3 -

Motif 2 width=11
Element Seqn Id St Int Rpt
TKAVERGQAKL RS6X_SULSO 43 22 -
TKAVERGLAKL D69345 36 22 -
TKAVERGVAQL A69132 47 22 -
TKSIERGSAEL RS6X_HALMA 37 22 -
TKAVERGIAKL RS6X_METJA 38 19 -

Motif 3 width=12
Element Seqn Id St Int Rpt
LVLIAEDVEPAE A69132 57 -1 -
LVIIAEDVQPEE RS6X_SULSO 53 -1 -
LVIIAEDVKPEE RS6X_METJA 48 -1 -
LVFVAEDVQPEE RS6X_HALMA 47 -1 -
LVYIAEDVDPPE D69345 46 -1 -

Motif 4 width=11
Element Seqn Id St Int Rpt
YAYVASKQDLG RS6X_METJA 75 15 -
FIFVEQQDDLG RS6X_HALMA 74 15 -
YIYVKSKNDLG D69345 73 15 -
YIYIPTKDELG A69132 84 15 -
YVYVSSKKALG RS6X_SULSO 80 15 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GIEVPCASAAIINEGEL D69345 87 3 -
GLEVAASSVAIINEGDA RS6X_METJA 89 3 -
GLEVGSAAAAVTDAGAA RS6X_HALMA 88 3 -
GLQVATASAAILEPGEA RS6X_SULSO 94 3 -
GLNVGTASSAIVEAGDA A69132 98 3 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
YVKFEVPKELAE RS6X_PYRHO 7 7 -
YVKFEVPQDLAD RS6X_SULSO 9 9 -
YVKFKVPEEIQK RS6X_METJA 7 7 -
YVRFEVPEDMQN RS6X_ARCFU 2 2 -
YVKFDVPKELAD RS6X_METTH 13 13 -
YVDFDVPADLED RS6X_HALMA 3 3 -

Motif 2 width=11
Element Seqn Id St Int Rpt
TKAVERGQAKL RS6X_PYRHO 41 22 -
TKAVERGQAKL RS6X_SULSO 43 22 -
TKAVERGIAKL RS6X_METJA 38 19 -
TKAVERGLAKL RS6X_ARCFU 36 22 -
TKAVERGVAQL RS6X_METTH 47 22 -
TKSIERGSAEL RS6X_HALMA 37 22 -

Motif 3 width=12
Element Seqn Id St Int Rpt
LVIIAEDVDPEE RS6X_PYRHO 51 -1 -
LVIIAEDVQPEE RS6X_SULSO 53 -1 -
LVIIAEDVKPEE RS6X_METJA 48 -1 -
LVYIAEDVDPPE RS6X_ARCFU 46 -1 -
LVLIAEDVEPAE RS6X_METTH 57 -1 -
LVFVAEDVQPEE RS6X_HALMA 47 -1 -

Motif 4 width=11
Element Seqn Id St Int Rpt
YIYVPSKKELG RS6X_PYRHO 78 15 -
YVYVSSKKALG RS6X_SULSO 80 15 -
YAYVASKQDLG RS6X_METJA 75 15 -
YIYVKSKNDLG RS6X_ARCFU 73 15 -
YIYIPTKDELG RS6X_METTH 84 15 -
FIFVEQQDDLG RS6X_HALMA 74 15 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GIEVAAASVAIIEPGKA RS6X_PYRHO 92 3 -
GLQVATASAAILEPGEA RS6X_SULSO 94 3 -
GLEVAASSVAIINEGDA RS6X_METJA 89 3 -
GIEVPCASAAIINEGEL RS6X_ARCFU 87 3 -
GLNVGTASSAIVEAGDA RS6X_METTH 98 3 -
GLEVGSAAAAVTDAGAA RS6X_HALMA 88 3 -