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PR00058

Identifier
RIBOSOMALL5  [View Relations]  [View Alignment]  
Accession
PR00058
No. of Motifs
6
Creation Date
09-MAR-1995  (UPDATE 07-JUN-1999)
Title
Ribosomal protein L5 signature
Database References

PFAM; PF00861 Ribosomal_L18p
INTERPRO; IPR001149
Literature References
1. DESHMUKH, M., TSAY, Y.-F., PAULOVICH, A.G. AND WOODFORD, J.L.
Yeast ribosomal protein L1 is required for the stability of newly
synthesized 5S rRNA and the assembly of 60S ribosomal subunits.
MOL.CELL.BIOL. 13 2835-2845 (1993).
 
2. KIM, J.K. AND WU, R. 
A rice (Oryza sativum L.) cDNA encodes a protein sequence homologous to
the eukaryotic ribosomal 5S rRNA binding protein gene.
PLANT MOL.BIOL. 23 409-413 (1993).
 
3. YEH, L-C.C. AND LEE, J.C.
Contributions on multiple basic amino acids in the C-terminal region of
yeast ribosomal protein L1 to 5S rRNA binding and 60S ribosome stability.
J.MOL.BIOL. 246(2) 295-307 (1995).

Documentation
The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal
protein before its assembly into the ribosomal subunits [1]. In eukaryotes,
the 5S rRNA molecule binds one protein species, while in bacteria it binds
2 or 3 different protein species [2]. The synthesis of the component RNA
and its binding protein appears to be closely linked; thus, disruption of
binding protein synthesis causes 5S rRNA instability and subsequent
failure of 60S ribosomal assembly [3].
 
In S.cerevisiae, the 5S rRNA binding protein is L1 (also known as L1a or
YL3): this contains 297 amino acid residues and shares more than 87%
sequence similarity with the other eukaryotic 5S rRNA binding proteins [2].
A conserved, C-terminal basic region of L1 is thought to be important for
its interaction with the 5S rRNA molecule - it is suggested that several
basic residues fall on the same face of an alpha-helix, making multiple
contacts with the 5S rRNA [3]. 
 
RIBOSOMALL5 is a 6-element fingerprint that provides a signature for L5
ribosomal proteins. The fingerprint was derived from an initial alignment
of 5 sequences: the motifs were drawn from conserved regions spanning
virtually the full alignment length (the C-terminal basic region was not
included as it is less well conserved than other motifs). Two iterations
on OWL25.2 were required to reach convergence, at which point a true set
comprising 8 sequences was identified. Two partial matches were also found,
RL18_METVA and RL18_HALMA, both 50S ribosomal proteins, which are known to
share a high degree of similarity with the L5 family.
 
An update on SPTR37_9f identified a true set of 16 sequences, and 8
partial matches.
Summary Information
  16 codes involving  6 elements
1 codes involving 5 elements
6 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6161616161616
5101111
4604644
3000000
2000000
123456
True Positives
RL5A_SCHPO    RL5A_XENLA    RL5B_SCHPO    RL5B_XENLA    
RL5_ANOGA RL5_BOMMO RL5_CAEEL RL5_CHICK
RL5_DUNSA RL5_HELAN RL5_HUMAN RL5_NEUCR
RL5_ORYSA RL5_RAT RL5_STYCL RL5_YEAST
True Positive Partials
Codes involving 5 elements
RL18_METTH
Codes involving 4 elements
RL18_ARCFU RL18_HALMA RL18_METJA RL18_METVA
RL18_PYRHO RL18_SULAC
Sequence Titles
RL5A_SCHPO  60S RIBOSOMAL PROTEIN L5-A - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). 
RL5A_XENLA 60S RIBOSOMAL PROTEIN L5A - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
RL5B_SCHPO 60S RIBOSOMAL PROTEIN L5-B - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
RL5B_XENLA 60S RIBOSOMAL PROTEIN L5B - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
RL5_ANOGA 60S RIBOSOMAL PROTEIN L5 - ANOPHELES GAMBIAE (AFRICAN MALARIA MOSQUITO).
RL5_BOMMO 60S RIBOSOMAL PROTEIN L5 - BOMBYX MORI (SILK MOTH).
RL5_CAEEL PROBABLE 60S RIBOSOMAL PROTEIN L5 - CAENORHABDITIS ELEGANS.
RL5_CHICK 60S RIBOSOMAL PROTEIN L5 - GALLUS GALLUS (CHICKEN).
RL5_DUNSA 60S RIBOSOMAL PROTEIN L5 - DUNALIELLA SALINA.
RL5_HELAN 60S RIBOSOMAL PROTEIN L5 - HELIANTHUS ANNUUS (COMMON SUNFLOWER).
RL5_HUMAN 60S RIBOSOMAL PROTEIN L5 - HOMO SAPIENS (HUMAN).
RL5_NEUCR 60S RIBOSOMAL PROTEIN L5 - NEUROSPORA CRASSA.
RL5_ORYSA 60S RIBOSOMAL PROTEIN L5 - ORYZA SATIVA (RICE).
RL5_RAT 60S RIBOSOMAL PROTEIN L5 - RATTUS NORVEGICUS (RAT).
RL5_STYCL 60S RIBOSOMAL PROTEIN L5 - STYELA CLAVA (SEA SQUIRT).
RL5_YEAST 60S RIBOSOMAL PROTEIN L5 (L1) (YL3) (RIBOSOMAL 5S RNA-BINDING PROTEIN) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

RL18_METTH 50S RIBOSOMAL PROTEIN L18P - METHANOBACTERIUM THERMOAUTOTROPHICUM.

RL18_ARCFU 50S RIBOSOMAL PROTEIN L18P - ARCHAEOGLOBUS FULGIDUS.
RL18_HALMA 50S RIBOSOMAL PROTEIN L18 (HMAL18) (HL12) - HALOARCULA MARISMORTUI (HALOBACTERIUM MARISMORTUI).
RL18_METJA 50S RIBOSOMAL PROTEIN L18P - METHANOCOCCUS JANNASCHII.
RL18_METVA 50S RIBOSOMAL PROTEIN L18P - METHANOCOCCUS VANNIELII.
RL18_PYRHO 50S RIBOSOMAL PROTEIN L18P - PYROCOCCUS HORIKOSHII.
RL18_SULAC 50S RIBOSOMAL PROTEIN L18P - SULFOLOBUS ACIDOCALDARIUS.
Scan History
OWL25_2    2  100  NSINGLE    
SPTR37_9f 2 61 NSINGLE
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
FRRRREGKTDYYQRKRLVTQ RL1_YEAST 20 20 -
FRRRREGKTDYYARKRLVIQ RL5_CHICK 19 19 -
FRRRREGKTDYYARKRLVIQ RL5_RAT 19 19 -
FRRRREGKTDYYARKRLVIQ RL5B_XENLA 19 19 -
FRRRREGKTDYYARKRLVIQ RL5A_XENLA 19 19 -

Motif 2 width=20
Element Seqn Id St Int Rpt
KYNTPKYRMIVRVTNRDIIC RL5B_XENLA 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5_RAT 42 3 -
KYNTPKYRLVVRFTNKDIIC RL1_YEAST 43 3 -
KYNTPKYRMIVRVTNRDIIC RL5A_XENLA 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5_CHICK 42 3 -

Motif 3 width=21
Element Seqn Id St Int Rpt
PKYGVKVGLTNYAAAYCTGLL RL5_RAT 83 21 -
PRYGITHGLTNWAAAYATGLL RL1_YEAST 84 21 -
PKYGVKVGLTNYAAAYCTGLL RL5_CHICK 83 21 -
PKYGVKVGLTNYAAAYCTGLL RL5B_XENLA 83 21 -
PKYGIKVGLTNYAAAYCTGLL RL5A_XENLA 83 21 -

Motif 4 width=20
Element Seqn Id St Int Rpt
YLDAGLTRTTTGNKVFGALK RL5B_XENLA 144 40 -
FLDIGLQRTTTGARVFGALK RL1_YEAST 145 40 -
YLDAGLTRTTTGNKVFGALK RL5A_XENLA 144 40 -
YLDAGLARTTTGNKVFGALK RL5_CHICK 144 40 -
YLDAGLARTTTGNKVFGALK RL5_RAT 144 40 -

Motif 5 width=20
Element Seqn Id St Int Rpt
GAVDGGLSIPHSTKRFPGYD RL5_CHICK 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5_RAT 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5B_XENLA 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5A_XENLA 164 0 -
GASDGGLYVPHSENRFPGWD RL1_YEAST 165 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
YMRYLMEEDEDAYKKQFSQYI RL5_RAT 206 22 -
YMRLLMEEDEDAYKKQFSQYI RL5A_XENLA 206 22 -
YMRLLMEEDEDAYKKQFSQYI RL5B_XENLA 206 22 -
YMRYLMEEDEDAYKKQFSQYI RL5_CHICK 206 22 -
YMEELADDDEERFSELFKGYL RL1_YEAST 207 22 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
FRRRREGKTDYYARKRLVIQ RL5_CHICK 19 19 -
FRRRREGKTDYYARKRLVIQ RL5_RAT 19 19 -
FRRRREGKTDYYARKRLVIQ RL5_HUMAN 19 19 -
FRRRREGKTDYYARKRLVIQ RL5B_XENLA 19 19 -
FRRRREGKTDYYARKRLVIQ RL5A_XENLA 19 19 -
FRRRREGKTDYYARKRLIFQ RL5_ANOGA 20 20 -
YKRRRQGKTDYFARKRLVVQ RL5_STYCL 19 19 -
FKRRREGKTDYFARKRLIAQ RL5_HELAN 20 20 -
FKRRREGKTDYYARKRLVVQ RL5_BOMMO 20 20 -
YRRRREGKTDYYARKRLIAQ RL5A_SCHPO 20 20 -
YRRRREGKTDYYARKRLIAQ RL5B_SCHPO 20 20 -
YKRRREGKTDYYARKRLITQ RL5_NEUCR 20 20 -
FRRRREGKTDYYQRKRLVTQ RL5_YEAST 20 20 -
LRRRREGKTDYYARKRLTVQ RL5_CAEEL 20 20 -
FKRRRQGKTDYRARIRLTNQ RL5_ORYSA 21 21 -
YRRRRQGKTDYRARLRLVRQ RL5_DUNSA 20 20 -

Motif 2 width=20
Element Seqn Id St Int Rpt
KYNTPKYRMIVRVTNRDIIC RL5_CHICK 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5_RAT 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5_HUMAN 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5B_XENLA 42 3 -
KYNTPKYRMIVRVTNRDIIC RL5A_XENLA 42 3 -
KYNTPKFRLIVRLSNRDITC RL5_ANOGA 43 3 -
KYNTPKYRMIVRFTNKDIVC RL5_STYCL 42 3 -
KYNTPKYRLVVRFSNRDITC RL5_HELAN 43 3 -
KYNTPKYRLIVRLSNKDVTC RL5_BOMMO 43 3 -
KYNAPKYRLVVRFSNRFVTC RL5A_SCHPO 43 3 -
KYNAPKYRLVVRFSNRFVTC RL5B_SCHPO 43 3 -
KYNAPKYRLVVRFTNRDIIL RL5_NEUCR 43 3 -
KYNTPKYRLVVRFTNKDIIC RL5_YEAST 43 3 -
KYNTPKYRLIVRITNKDVVA RL5_CAEEL 43 3 -
KYNTPKYRFVVRFTNKDITA RL5_ORYSA 44 3 -
KYNTHKYRLVVRFSNKNVTC RL5_DUNSA 43 3 -

Motif 3 width=21
Element Seqn Id St Int Rpt
PKYGVKVGLTNYAAAYCTGLL RL5_CHICK 83 21 -
PKYGVKVGLTNYAAAYCTGLL RL5_RAT 83 21 -
PKYGVKVGLTNYAAAYCTGLL RL5_HUMAN 83 21 -
PKYGVKVGLTNYAAAYCTGLL RL5B_XENLA 83 21 -
PKYGIKVGLTNYAAAYCTGLL RL5A_XENLA 83 21 -
PRYGVKVGLTNYAAAYCTGLL RL5_ANOGA 84 21 -
PRYGVKVGLTNYAAAYCTGLL RL5_STYCL 83 21 -
PQYGVKVGLTNYAAAYCTGLL RL5_HELAN 84 21 -
PRYGVKVGLTNYAAAYSTGLL RL5_BOMMO 84 21 -
PRYGIKWGLANWTAAYATGLL RL5A_SCHPO 84 21 -
PRYGIKWGLANWTAAYATGLL RL5B_SCHPO 84 21 -
KAYGIEHGLTNWAAAYATGLL RL5_NEUCR 84 21 -
PRYGITHGLTNWAAAYATGLL RL5_YEAST 84 21 -
PRYGLKVGLTNYAAAYATGLL RL5_CAEEL 84 21 -
PRYGLEVGLTNYAAAYCTGLL RL5_ORYSA 85 21 -
PNYGLKVGLTNYSAAYCVGLL RL5_DUNSA 84 21 -

Motif 4 width=20
Element Seqn Id St Int Rpt
YLDAGLARTTTGNKVFGALK RL5_CHICK 144 40 -
YLDAGLARTTTGNKVFGALK RL5_RAT 144 40 -
YLDAGLARTTTGNKVFGALK RL5_HUMAN 144 40 -
YLDAGLTRTTTGNKVFGALK RL5B_XENLA 144 40 -
YLDAGLTRTTTGNKVFGALK RL5A_XENLA 144 40 -
YLDVGLARTTTGSRVFGAMK RL5_ANOGA 145 40 -
FLDVGLARTTTGAKVFGAMK RL5_STYCL 144 40 -
YLDVGLMRTTTGARVFGAMK RL5_HELAN 145 40 -
YLDVGLARTTTGRRVFGAMK RL5_BOMMO 145 40 -
FLDVGLKRTSTGSRVFGAMK RL5A_SCHPO 145 40 -
FLDVGLKRTSTGSRVFGAMK RL5B_SCHPO 145 40 -
FLDVGLARTSTGARVFGAMK RL5_NEUCR 148 43 -
FLDIGLQRTTTGARVFGALK RL5_YEAST 145 40 -
VLDIGLARTTTGSKIFAVMK RL5_CAEEL 144 39 -
LLDVGLIRTTTGNRVFGALK RL5_ORYSA 145 39 -
LLDTGLKRTSTGSKVFAAMK RL5_DUNSA 145 40 -

Motif 5 width=20
Element Seqn Id St Int Rpt
GAVDGGLSIPHSTKRFPGYD RL5_CHICK 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5_RAT 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5_HUMAN 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5B_XENLA 164 0 -
GAVDGGLSIPHSTKRFPGYD RL5A_XENLA 164 0 -
GAVDGGLNIPHSVKRFPGYS RL5_ANOGA 165 0 -
GAADGGLDIPHSTKRFPGYD RL5_STYCL 164 0 -
GAVDGGLNILHSTKRFPGFD RL5_HELAN 165 0 -
GAVDGGLNVPHSIKRFPGYD RL5_BOMMO 165 0 -
GASDGGLFIPHSPNRFPGFD RL5A_SCHPO 165 0 -
GASDGGLFIPHSPNRFPGFD RL5B_SCHPO 165 0 -
GASDGGIFIPHSENRFPGYD RL5_NEUCR 168 0 -
GASDGGLYVPHSENRFPGWD RL5_YEAST 165 0 -
GVADGGINVPHSESRFFGFD RL5_CAEEL 164 0 -
GALDGGLDIPHSDKRFAGFK RL5_ORYSA 165 0 -
GALDGGLDIPHNEKRFVGYA RL5_DUNSA 165 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
YMRYLMEEDEDAYKKQFSQYI RL5_CHICK 206 22 -
YMRYLMEEDEDAYKKQFSQYI RL5_RAT 206 22 -
YMRYLMEEDEDAYKKQFSQYI RL5_HUMAN 206 22 -
YMRLLMEEDEDAYKKQFSQYI RL5B_XENLA 206 22 -
YMRLLMEEDEDAYKKQFSQYI RL5A_XENLA 206 22 -
YMRTLEEEDEEAFKRQFSKYI RL5_ANOGA 207 22 -
YMKELEEEDEEAFKRQFSQYI RL5_STYCL 206 22 -
YMRQLAEEDDEAYKRQFSQYI RL5_HELAN 207 22 -
YMRSLEQDDEDSFKRQFSKYI RL5_BOMMO 207 22 -
YMEMLIDDDEERYQKQFSGLI RL5A_SCHPO 207 22 -
YMEMLIDDDEERYQKQFSGLI RL5B_SCHPO 207 22 -
YMETLADDDEERYKSQFNRYI RL5_NEUCR 210 22 -
YMEELADDDEERFSELFKGYL RL5_YEAST 207 22 -
YMTYLKEEDEDRYKRQFSKFL RL5_CAEEL 206 22 -
YMRSMAEEEPEKFQAHFSEYL RL5_ORYSA 207 22 -
YQETMQEEEPEKYQAHFSSYV RL5_DUNSA 205 20 -