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PR00881

Identifier
L7ARS6FAMILY  [View Relations]  [View Alignment]  
Accession
PR00881
No. of Motifs
4
Creation Date
08-JUN-1998  (UPDATE 07-JUN-1999)
Title
Ribosomal protein L7A/RS6 family signature
Database References
PRINTS; PR00883 NUCLEARHMG; PR00884 RIBOSOMALHS6; PR00882 RIBOSOMALL7A

PROSITE; PS01082 RIBOSOMAL_L7AE
BLOCKS; BL01082
INTERPRO; IPR000955
Literature References
1. 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). 
 
2. 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). 
 
3. YON, J., GIALLONGO, A. AND FRIED, M.
The organization and expression of the Saccharomyces cerevisiae L4 ribosomal
protein genes and their identification as the homologues of the mammalian
ribosomal protein gene L7a. 
MOL.GEN.GENET. 227 72-80 (1991). 
 
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 genomic structure and sequence of the human ribosomal protein L7a has
been determined and shown to resemble other mammalian ribosomal protein 
genes [1]. The sequence of a gene for ribosomal protein L4 of S.cerevisiae
has also been determined; its single open reading frame is highly similar
to mammalian ribosomal protein L7a [2,3]. 
 
Several other ribosomal proteins have been found to share sequence 
similarity with L7a, including yeast NHP2 [4], B.subtilis hypothetical 
protein ylxQ, Halobacterium marismortui Hs6, and M.jannaschii MJ1203.
 
L7ARS6FAMILY is a 4-element fingerprint that provides a signature for the
L7a/Rs6 family of ribosomal proteins. The fingerprint was derived from an
initial alignment of 11 sequences: the motifs were drawn from short
conserved sections within the central portion of the alignment, motifs 3 and
4 spanning the region encoded by PROSITE pattern RIBOSOMAL_L7AE (PS01082).
Two iterations on OWL30.2 were required to reach convergence, at which point
a true set comprising 26 sequences was identified. A single partial match
was also found, ZETED6330, a Z.elegans HMG-like protein that matches motifs
3 and 4. 
 
An update on SPTR37_9f identified a true set of 22 sequences.
Summary Information
22 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
422222222
30000
20000
1234
True Positives
NHP2_YEAST    NHPX_CAEEL    NHPX_HUMAN    NHPX_YEAST    
O74690 RL7A_ANOGA RL7A_ARATH RL7A_CHICK
RL7A_DROME RL7A_FUGRU RL7A_HUMAN RL7A_MOUSE
RL7A_ORYSA RL8A_YEAST RL8B_YEAST RL8_SCHPO
RS6X_ARCFU RS6X_HALMA RS6X_METJA RS6X_METTH
RS6X_PYRHO RS6X_SULSO
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).
RL7A_ANOGA 60S RIBOSOMAL PROTEIN L7A - ANOPHELES GAMBIAE (AFRICAN MALARIA MOSQUITO).
RL7A_ARATH 60S RIBOSOMAL PROTEIN L7A - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
RL7A_CHICK 60S RIBOSOMAL PROTEIN L7A - GALLUS GALLUS (CHICKEN).
RL7A_DROME 60S RIBOSOMAL PROTEIN L7A - DROSOPHILA MELANOGASTER (FRUIT FLY).
RL7A_FUGRU 60S RIBOSOMAL PROTEIN L7A - FUGU RUBRIPES (JAPANESE PUFFERFISH) (TAKIFUGU RUBRIPES).
RL7A_HUMAN 60S RIBOSOMAL PROTEIN L7A (PLA-X POLYPEPTIDE) (SURF-3) - HOMO SAPIENS (HUMAN), AND RATTUS NORVEGICUS (RAT).
RL7A_MOUSE 60S RIBOSOMAL PROTEIN L7A (SURFEIT LOCUS PROTEIN 3) - MUS MUSCULUS (MOUSE).
RL7A_ORYSA 60S RIBOSOMAL PROTEIN L7A - ORYZA SATIVA (RICE).
RL8A_YEAST 60S RIBOSOMAL PROTEIN L8-A (L7A-2) (L4-2) (YL5) (RP6) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
RL8B_YEAST 60S RIBOSOMAL PROTEIN L8-B (L7A-1) (L4-1) (YL5) (RP6) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
RL8_SCHPO 60S RIBOSOMAL PROTEIN L8 (L7A) (L4) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
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    2  150  NSINGLE    
SPTR37_9f 2 23 NSINGLE
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
IKKGANEVTKAVERG RS6X_METJA 30 30 -
LRAGVNTVTTLVENK RL7A_MOUSE 135 135 -
VSAGTNTVTKLIEQK RL7A_DROME 141 141 -
VKYGLNHVVALIENK P10664 131 131 -
VKYGLNHVVSLIENK P49626 131 131 -
LRKGANEATKTLNRG NHPX_RAT 35 35 -
VKRGVKEVVKALRKG NHP2_YEAST 73 73 -
LKKGANEATKTLNRG NHPX_YEAST 33 33 -
LRKGANEATKTLNRG NHPX_HUMAN 35 35 -
LKKGANEATKTLNRG NHPX_CAEEL 35 35 -
IKKGTNETTKAVERG RS6X_SULSO 35 35 -

Motif 2 width=14
Element Seqn Id St Int Rpt
VLIANDVDPIELVV P49626 150 4 -
IVMAADAEPLEIIL NHPX_RAT 54 4 -
VLIANDVDPIELVV P10664 150 4 -
VVIAHDVDPIELVV RL7A_MOUSE 154 4 -
VVIAHDVDPLELVL RL7A_DROME 160 4 -
VIIAEDVKPEEVVA RS6X_METJA 49 4 -
VIIAEDVQPEEIVA RS6X_SULSO 54 4 -
IVMAADAEPLEILL NHPX_CAEEL 54 4 -
IVMAADAEPLEIIL NHPX_HUMAN 54 4 -
IIMAADCEPIEILL NHPX_YEAST 52 4 -
VVIAGDISPADVIS NHP2_YEAST 92 4 -

Motif 3 width=11
Element Seqn Id St Int Rpt
PLLCEDKNVPY NHPX_HUMAN 70 2 -
PLLCEDKNVPY NHPX_YEAST 68 2 -
PVLCEDHSVPY NHP2_YEAST 108 2 -
PALCRKMGVPY RL7A_MOUSE 170 2 -
PALCRKMGVPY RL7A_DROME 176 2 -
PYLCEEKGIPY RS6X_METJA 65 2 -
PALCKKMGVPY P49626 166 2 -
PALCKKMGVPY P10664 166 2 -
PLLCEDKNVPY NHPX_RAT 70 2 -
PLLCDEKKIPY RS6X_SULSO 70 2 -
PLLCEDKNVPY NHPX_CAEEL 70 2 -

Motif 4 width=15
Element Seqn Id St Int Rpt
YCIVKGKARLGRLVR RL7A_DROME 186 -1 -
YVYVSSKKALGEACG RS6X_SULSO 80 -1 -
YVFVRSKAALGRACG NHPX_CAEEL 80 -1 -
YVFVRSKQALGRACG NHPX_HUMAN 80 -1 -
YVFVPSRVALGRACG NHPX_YEAST 78 -1 -
YIFIPSKQDLGAAGA NHP2_YEAST 118 -1 -
YAIIKGKARLGTLVN P49626 176 -1 -
YAIVKGKARLGTLVN P10664 176 -1 -
YVFXRSKKALGRAXG NHPX_RAT 80 -1 -
YCIIKGKARLGHLVH RL7A_MOUSE 180 -1 -
YAYVASKQDLGKAAG RS6X_METJA 75 -1 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
LRAGVNTVTTLVENK RL7A_CHICK 135 135 -
LRAGVNTVTTLVENK RL7A_HUMAN 135 135 -
LRAGVNTVTTLVENK RL7A_MOUSE 135 135 -
VSAGTNTVTKLIEQK RL7A_DROME 141 141 -
LRAGVNTITSLVENK RL7A_FUGRU 135 135 -
VKYGLNHVTYLIEQS RL7A_ORYSA 128 128 -
VKYGLNHVTYLIEQN RL7A_ARATH 127 127 -
VKKGTNETTKAVERG RS6X_ARCFU 28 28 -
VKYGLNHVVALIENK RL8A_YEAST 131 131 -
LRQGINSVVKMVEQK RL7A_ANOGA 142 142 -
VKYGLNHVVSLIENK RL8B_YEAST 131 131 -
VKYGLNHVVALIEAK RL8_SCHPO 131 131 -
IRKGTNETTKAVERG RS6X_PYRHO 33 33 -
IKKGANEVTKAVERG RS6X_METJA 30 30 -
IKKGTNETTKAVERG RS6X_SULSO 35 35 -
LRKGANEATKTLNRG O74690 32 32 -
LKKGANEATKTLNRG NHPX_CAEEL 35 35 -
VSKGTNEVTKAVERG RS6X_METTH 39 39 -
LRKGANEATKTLNRG NHPX_HUMAN 35 35 -
LKKGANEATKTLNRG NHPX_YEAST 33 33 -
VKKGTNETTKSIERG RS6X_HALMA 29 29 -
VKRGVKEVVKALRKG NHP2_YEAST 73 73 -

Motif 2 width=14
Element Seqn Id St Int Rpt
VVIAHDVDPIELVV RL7A_CHICK 154 4 -
VVIAHDVDPIELVV RL7A_HUMAN 154 4 -
VVIAHDVDPIELVV RL7A_MOUSE 154 4 -
VVIAHDVDPLELVL RL7A_DROME 160 4 -
VVIAHDVDPIELVI RL7A_FUGRU 154 4 -
VVIAHDVDPIELVV RL7A_ORYSA 147 4 -
VVIAHDVDPIELVV RL7A_ARATH 146 4 -
VYIAEDVDPPEIVA RS6X_ARCFU 47 4 -
VLIANDVDPIELVV RL8A_YEAST 150 4 -
VIIAHDVDPIELVV RL7A_ANOGA 161 4 -
VLIANDVDPIELVV RL8B_YEAST 150 4 -
VLIASDVDPIELVV RL8_SCHPO 150 4 -
VIIAEDVDPEEIVA RS6X_PYRHO 52 4 -
VIIAEDVKPEEVVA RS6X_METJA 49 4 -
VIIAEDVQPEEIVA RS6X_SULSO 54 4 -
IVMAADTEPIEILL O74690 51 4 -
IVMAADAEPLEILL NHPX_CAEEL 54 4 -
VLIAEDVEPAEIVA RS6X_METTH 58 4 -
IVMAADAEPLEIIL NHPX_HUMAN 54 4 -
IIMAADCEPIEILL NHPX_YEAST 52 4 -
VFVAEDVQPEEIVM RS6X_HALMA 48 4 -
VVIAGDISPADVIS NHP2_YEAST 92 4 -

Motif 3 width=11
Element Seqn Id St Int Rpt
PALCRKMGVPY RL7A_CHICK 170 2 -
PALCRKMGVPY RL7A_HUMAN 170 2 -
PALCRKMGVPY RL7A_MOUSE 170 2 -
PALCRKMGVPY RL7A_DROME 176 2 -
PALCRKMGVPY RL7A_FUGRU 170 2 -
PALCRKMEVPY RL7A_ORYSA 163 2 -
PALCRKMEVPY RL7A_ARATH 162 2 -
PLLCEEKNVPY RS6X_ARCFU 63 2 -
PALCKKMGVPY RL8A_YEAST 166 2 -
PALCRKMGVPY RL7A_ANOGA 177 2 -
PALCKKMGVPY RL8B_YEAST 166 2 -
PALCKKMGVPY RL8_SCHPO 166 2 -
PPLCEEKEIPY RS6X_PYRHO 68 2 -
PYLCEEKGIPY RS6X_METJA 65 2 -
PLLCDEKKIPY RS6X_SULSO 70 2 -
PLLCEDKNVPY O74690 67 2 -
PLLCEDKNVPY NHPX_CAEEL 70 2 -
PLLAEEKEIPY RS6X_METTH 74 2 -
PLLCEDKNVPY NHPX_HUMAN 70 2 -
PLLCEDKNVPY NHPX_YEAST 68 2 -
PELADEKGVPF RS6X_HALMA 64 2 -
PVLCEDHSVPY NHP2_YEAST 108 2 -

Motif 4 width=15
Element Seqn Id St Int Rpt
YCIIKSKARLGRLVH RL7A_CHICK 180 -1 -
YCIIKGKARLGRLVH RL7A_HUMAN 180 -1 -
YCIIKGKARLGHLVH RL7A_MOUSE 180 -1 -
YCIVKGKARLGRLVR RL7A_DROME 186 -1 -
YCIVKGKARLGRLVH RL7A_FUGRU 180 -1 -
YCIVKGKARLGSIVH RL7A_ORYSA 173 -1 -
YCIVKGKSRLGAVVH RL7A_ARATH 172 -1 -
YIYVKSKNDLGRAVG RS6X_ARCFU 73 -1 -
YAIVKGKARLGTLVN RL8A_YEAST 176 -1 -
YCIIKGKARLGTLVY RL7A_ANOGA 187 -1 -
YAIIKGKARLGTLVN RL8B_YEAST 176 -1 -
YAIVKNKARLGTVIH RL8_SCHPO 176 -1 -
YIYVPSKKELGAAAG RS6X_PYRHO 78 -1 -
YAYVASKQDLGKAAG RS6X_METJA 75 -1 -
YVYVSSKKALGEACG RS6X_SULSO 80 -1 -
YVFVPSKAALGRACG O74690 77 -1 -
YVFVRSKAALGRACG NHPX_CAEEL 80 -1 -
YIYIPTKDELGAAAG RS6X_METTH 84 -1 -
YVFVRSKQALGRACG NHPX_HUMAN 80 -1 -
YVFVPSRVALGRACG NHPX_YEAST 78 -1 -
FIFVEQQDDLGHAAG RS6X_HALMA 74 -1 -
YIFIPSKQDLGAAGA NHP2_YEAST 118 -1 -