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PR00974

Identifier
RIBOSOMALS18  [View Relations]  [View Alignment]  
Accession
PR00974
No. of Motifs
4
Creation Date
05-OCT-1998  (UPDATE 07-JUN-1999)
Title
Ribosomal protein S18 family signature
Database References

PROSITE; PS00057 RIBOSOMAL_S18
PFAM; PF01084 Ribosomal_S18
INTERPRO; IPR001648
Literature References
1. KURLAND, C.G., JORGENSEN, F., RICHTER, A., EHRENBERG, M., BILGIN, N. 
AND ROJAS, A.-M.
IN THE RIBOSOME: STRUCTURE, FUNCTION AND EVOLUTION (ED. W.E.HILL ET AL.)
PP.513-526 (AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON DC).
 
2. MUELLER, F. AND BRIMACOMBE, R.
A new model for the three-dimensional folding of Escherichia coli
16S ribosomal RNA. II. The RNA-protein interaction data.
J.MOL.BIOL. 271(4) 545-565 (1997).
 
3. MCDOUGALL, J., CHOLI, T., KRUFT, V., KAPP, U. AND WITTMANN-LIEBOLD, B.
The complete amino acid sequence of ribosomal protein S18 from
the moderate thermophile Bacillus stearothermophilus.
FEBS LETT. 245 253-260 (1989).
 
4. AGAFONOV, D.E., KOLB, V.A. AND SPIRIN, A.S.
Proteins on ribosome surface: measurements of protein exposure by
hot tritium bombardment technique.
PROC.NATL.ACAD.SCI.U.S.A. 94(24) 12892-7 (1997).
 
5. OTAKA, E., SUZUKI, K. AND HASHIMOTO, T.
Examination of protein sequence homologies. VII. The complementary molecular
coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and 
L10.
PROTEIN SEQ.DATA ANAL. 3 11-19 (1990).

Documentation
Ribosomes are ribonucleoprotein particles that are the site of protein
synthesis. The structure of the ribosome is well conserved across the
prokaryotic and eukaryotic lineages, reflecting the early origin of their
essential function. They comprise two subunits, which can dissociate on 
heating. In prokaryotes, the small subunit contains a single large RNA 
moeity denoted, according to its sedimentation coefficient, 16S rRNA, and 21 
different ribosomal proteins, designated S1-S21. Eukaryotic small ribosomal
subunits contain 33 proteins, many of which are similar to those found
in prokaryotes. 
 
There are two major tRNA binding sites on the ribosome, termed the A site, 
where incoming aminoacyl-tRNA is bound, and the P site (for peptidyl tRNA), 
where new peptide bonds are formed. The ribosomal proteins catalyse ribosome 
assembly and stabilise the rRNA, tuning the structure of the ribosome for 
optimal function [1]. Evidence suggests that, in prokaryotes, the peptidyl
transferase reaction is performed by the large subunit 23S rRNA, whereas
proteins probably have a greater role in eukaryotic ribosomes. Most of the
proteins lie close to, or on the surface of, the 30S subunit, arranged
peripherally around the rRNA [2]. The small subunit ribosomal proteins can
be categorised as primary binding proteins, which bind directly and
independently to 16S rRNA; secondary binding proteins, which display no
specific affinity for 16S rRNA, but its assembly is contingent upon the
presence of one or more primary binding proteins; and tertiary binding
proteins, which require the presence of one or more secondary binding
proteins and sometimes other tertiary binding proteins.
 
The small ribosomal subunit protein S18 is known to be involved in binding
the aminoacyl-tRNA complex in E.coli [3], and appears to be situated at the
tRNA A-site. Experimental evidence has revealed that S18 is well exposed
on the surface of the E.coli ribosome, and is a secondary rRNA binding
protein [4]. S18 belongs to a family of ribosomal proteins [5] that includes:
eubacterial S18; algal and plant chloroplast S18; and cyanelle S18.
 
RIBOSOMALS18 is a 4-element fingerprint that provides a signature for S18 
ribosomal proteins. The fingerprint was derived from an initial alignment
of 14 sequences: the motifs were drawn from short conserved regions spanning 
the full alignment length - motifs 2 and 3 span the region encoded by 
PROSITE pattern RIBOSOMAL_S18 (PS00057), which contains two basic residues
that may be involved in RNA-binding. Two iterations on OWL30.2 were required
to reach convergence, at which point a true set comprising 29 sequences was
identified. A single partial match was also found, AE0006723, a gene product
from the hyperthermophilic bacterium Aquifex aeolicus that fails to make a
significant match with motif 2.
 
An update on SPTR37_9f identified a true set of 33 sequences, and 1
partial match.
Summary Information
  33 codes involving  4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
433333333
30000
20011
1234
True Positives
O20032        O51140        O53125        O68127        
O69301 O84808 O86354 RR18_CHLVU
RR18_CYAPA RR18_EPIVI RR18_EUGGR RR18_GUITH
RR18_MAIZE RR18_MARPO RR18_ODOSI RR18_ORYSA
RR18_PEA RR18_PINTH RR18_PORPU RR18_SECCE
RR18_TOBAC RS18_BACST RS18_BACSU RS18_CHLTR
RS18_ECOLI RS18_HAEIN RS18_HELPY RS18_MYCGE
RS18_MYCPN RS18_MYCTU RS18_NEIGO RS18_SYNY3
RS18_TREPA
True Positive Partials
Codes involving 2 elements
O66476
Sequence Titles
O20032      30S RIBOSOMAL PROTEIN S18 (RPS18 PROTEIN) - CHLAMYDOMONAS REINHARDTII. 
O51140 RIBOSOMAL PROTEIN S18 (RPSR) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O53125 30S RIBOSOMAL PROTEIN S18 - MYCOBACTERIUM LEPRAE.
O68127 30S RIBOSOMAL PROTEIN S18 - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O69301 RIBOSOMAL PROTEIN S18 - CAMPYLOBACTER JEJUNI.
O84808 S18 RIBOSOMAL PROTEIN - CHLAMYDIA TRACHOMATIS.
O86354 RPSR2 - MYCOBACTERIUM TUBERCULOSIS.
RR18_CHLVU CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - CHLORELLA VULGARIS.
RR18_CYAPA CYANELLE 30S RIBOSOMAL PROTEIN S18 - CYANOPHORA PARADOXA.
RR18_EPIVI CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - EPIFAGUS VIRGINIANA (BEECHDROPS).
RR18_EUGGR CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - EUGLENA GRACILIS.
RR18_GUITH CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - GUILLARDIA THETA (CRYPTOMONAS PHI).
RR18_MAIZE CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - ZEA MAYS (MAIZE).
RR18_MARPO CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - MARCHANTIA POLYMORPHA (LIVERWORT).
RR18_ODOSI CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - ODONTELLA SINENSIS.
RR18_ORYSA CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - ORYZA SATIVA (RICE).
RR18_PEA CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - PISUM SATIVUM (GARDEN PEA).
RR18_PINTH CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - PINUS THUNBERGII (GREEN PINE) (JAPANESE BLACK PINE).
RR18_PORPU CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - PORPHYRA PURPUREA.
RR18_SECCE CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - SECALE CEREALE (RYE).
RR18_TOBAC CHLOROPLAST 30S RIBOSOMAL PROTEIN S18 - NICOTIANA TABACUM (COMMON TOBACCO).
RS18_BACST 30S RIBOSOMAL PROTEIN S18 (BS21) - BACILLUS STEAROTHERMOPHILUS.
RS18_BACSU 30S RIBOSOMAL PROTEIN S18 (BS21) - BACILLUS SUBTILIS.
RS18_CHLTR 30S RIBOSOMAL PROTEIN S18 - CHLAMYDIA TRACHOMATIS.
RS18_ECOLI 30S RIBOSOMAL PROTEIN S18 - ESCHERICHIA COLI.
RS18_HAEIN 30S RIBOSOMAL PROTEIN S18 - HAEMOPHILUS INFLUENZAE.
RS18_HELPY 30S RIBOSOMAL PROTEIN S18 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RS18_MYCGE 30S RIBOSOMAL PROTEIN S18 - MYCOPLASMA GENITALIUM.
RS18_MYCPN 30S RIBOSOMAL PROTEIN S18 - MYCOPLASMA PNEUMONIAE.
RS18_MYCTU 30S RIBOSOMAL PROTEIN S18 - MYCOBACTERIUM TUBERCULOSIS.
RS18_NEIGO 30S RIBOSOMAL PROTEIN S18 - NEISSERIA GONORRHOEAE.
RS18_SYNY3 30S RIBOSOMAL PROTEIN S18 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RS18_TREPA 30S RIBOSOMAL PROTEIN S18 - TREPONEMA PALLIDUM.

O66476 RIBOSOMAL PROTEIN S18 - AQUIFEX AEOLICUS.
Scan History
OWL30_2    2  300  NSINGLE    
SPTR37_9f 2 112 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
LLRKFITEQGK RR18_PORPU 24 24 -
TLKNYITESGK RS18_ECOLI 27 27 -
LLRTYISERGK RS18_MYCTU 37 37 -
LLQRYIGLGGK CHCRRPS93 86 86 -
LLQRYIGLGGK CHCRRPS18 74 74 -
MLKHTLSERYK RS18_HELPY 28 28 -
ILRRFINFQGK RR18_EUGGR 14 14 -
AIKRFLSPYAK RS18_MYCGE 60 60 -
LLKKFISERGK RS18_BACST 31 31 -
LLRTFITDQGK RR18_CYAPA 24 24 -
LLKLFITEQGK RR18_ODOSI 24 24 -
LLRKFITERGK RS18_SYNY3 24 24 -
LLRRFVSEQGK RR18_MARPO 28 28 -
LISRFISEQGK RR18_EPIVI 28 28 -

Motif 2 width=8
Element Seqn Id St Int Rpt
KILPRRVT RR18_CYAPA 34 -1 -
KILPRRQT CHCRRPS18 84 -1 -
KILPRRQT CHCRRPS93 96 -1 -
KILPRRVT RS18_BACST 41 -1 -
KILPRRAT RR18_ODOSI 34 -1 -
KILPRRIT RS18_SYNY3 34 -1 -
KILSRRMN RR18_MARPO 38 -1 -
KILSRRVN RR18_EPIVI 38 -1 -
KILPKRST RR18_PORPU 34 -1 -
KIVPSRIT RS18_ECOLI 37 -1 -
KIRARRVT RS18_MYCTU 47 -1 -
KINPRRIT RS18_MYCGE 70 -1 -
KIIPKRLN RR18_EUGGR 24 -1 -
KIMPRRLT RS18_HELPY 38 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
KLTYKQHRLLRKSVK RR18_EUGGR 34 2 -
GNSKKWQERVEVAIK RS18_HELPY 46 0 -
GTSAKYQRKLTVAIK RS18_BACST 49 0 -
GLTAKQQRAVTKAIK RR18_CYAPA 42 0 -
GVTVQQQRQIAKAIK RR18_ODOSI 42 0 -
RLTAKQQRFVAKTIK CHCRRPS93 104 0 -
GLTAKQQRDLTTAVK RS18_SYNY3 42 0 -
RLTAKQQRFVAKTIK CHCRRPS18 92 0 -
RLTSKQQRLLTIAIK RR18_MARPO 46 0 -
RLTLKQQRLITIAIK RR18_EPIVI 46 0 -
GLTSKQQKKLTKAIK RR18_PORPU 42 0 -
GTRAKYQRQLARAIK RS18_ECOLI 45 0 -
GNCVQHQRDIALAVK RS18_MYCTU 55 0 -
GNCNMHQRHVANALK RS18_MYCGE 78 0 -

Motif 4 width=11
Element Seqn Id St Int Rpt
KRARYLSLLPY RS18_ECOLI 59 -1 -
KRARYLALVPF RS18_MYCGE 92 -1 -
KQARYLGLLPF RR18_EUGGR 48 -1 -
KRARHMALIPY RS18_HELPY 60 -1 -
KRARQMALLPY RS18_BACST 63 -1 -
KTARVMGLLPF CHCRRPS93 118 -1 -
KTARVMGLLPF CHCRRPS18 106 -1 -
KQARVLALLPF RR18_CYAPA 56 -1 -
KRARVLSLLPF RR18_ODOSI 56 -1 -
KRSRLVALLPF RS18_SYNY3 56 -1 -
KRARVLALLPF RR18_MARPO 60 -1 -
KQARILSLLPF RR18_EPIVI 60 -1 -
KQARILSLLPF RR18_PORPU 56 -1 -
KNAREVALLPF RS18_MYCTU 69 -1 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
LLKKFISERGK RS18_BACST 31 31 -
LLRTFITDQGK RR18_CYAPA 24 24 -
LLKLFITEQGK RR18_ODOSI 24 24 -
LLRKFITERGK RS18_SYNY3 24 24 -
LLSKFLTEQGK RR18_GUITH 24 24 -
LLRRFVSEQGK RR18_MARPO 28 28 -
LISRFISEQGK RR18_TOBAC 35 35 -
LISRFISEQGK RR18_EPIVI 28 28 -
LLKKFVSERGK RS18_BACSU 32 32 -
LLRKFITEQGK RR18_PORPU 24 24 -
LINRFISEQGK RR18_MAIZE 69 69 -
LINRFISEQGK RR18_ORYSA 62 62 -
LINRFISEQGK RR18_SECCE 69 69 -
LLFKFISRQGK RR18_PEA 35 35 -
FLKKFITEQGK O51140 51 51 -
LISRFISEQGK RR18_PINTH 53 53 -
TLKRFITERGK O84808 35 35 -
TLRRFITERGK RS18_TREPA 53 53 -
LLVKFISPQGK RR18_CHLVU 52 52 -
LLQRYISERGK O68127 30 30 -
TLKNYISESGK RS18_HAEIN 27 27 -
LLKDFISENGK RS18_NEIGO 29 29 -
TLKNYITESGK RS18_ECOLI 27 27 -
TLKRFITERGK RS18_CHLTR 35 35 -
LLRTYISERGK RS18_MYCTU 37 37 -
LLRTYISERGK O53125 37 37 -
LLQRYIGLGGK O20032 86 86 -
TLRVFISDRGK O86354 33 33 -
ALKRFLSPYAK RS18_MYCPN 59 59 -
AIKRFLSPYAK RS18_MYCGE 60 60 -
ILRRFINFQGK RR18_EUGGR 14 14 -
MLKHALSERFK O69301 29 29 -
MLKHTLSERYK RS18_HELPY 28 28 -

Motif 2 width=8
Element Seqn Id St Int Rpt
KILPRRVT RS18_BACST 41 -1 -
KILPRRVT RR18_CYAPA 34 -1 -
KILPRRAT RR18_ODOSI 34 -1 -
KILPRRIT RS18_SYNY3 34 -1 -
KILPRRIT RR18_GUITH 34 -1 -
KILSRRMN RR18_MARPO 38 -1 -
KILSRRVN RR18_TOBAC 45 -1 -
KILSRRVN RR18_EPIVI 38 -1 -
KILPRRVT RS18_BACSU 42 -1 -
KILPKRST RR18_PORPU 34 -1 -
KILSRRIN RR18_MAIZE 79 -1 -
KILSRRIN RR18_ORYSA 72 -1 -
KILSRRIN RR18_SECCE 79 -1 -
KILSRRVN RR18_PEA 45 -1 -
KILPKRIT O51140 61 -1 -
KILSGRVN RR18_PINTH 63 -1 -
KILPRRIT O84808 45 -1 -
KILPRRIT RS18_TREPA 63 -1 -
KILSRRAT RR18_CHLVU 62 -1 -
KIVPARIT O68127 40 -1 -
KIVPSRIT RS18_HAEIN 37 -1 -
KIIPARIT RS18_NEIGO 39 -1 -
KIVPSRIT RS18_ECOLI 37 -1 -
KILPRRIT RS18_CHLTR 45 -1 -
KIRARRVT RS18_MYCTU 47 -1 -
KIRARRVT O53125 47 -1 -
KILPRRQT O20032 96 -1 -
KIRSRGVT O86354 43 -1 -
KINPRRIT RS18_MYCPN 69 -1 -
KINPRRIT RS18_MYCGE 70 -1 -
KIIPKRLN RR18_EUGGR 24 -1 -
KIMPRRLT O69301 39 -1 -
KIMPRRLT RS18_HELPY 38 -1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
GTSAKYQRKLTVAIK RS18_BACST 49 0 -
GLTAKQQRAVTKAIK RR18_CYAPA 42 0 -
GVTVQQQRQIAKAIK RR18_ODOSI 42 0 -
GLTAKQQRDLTTAVK RS18_SYNY3 42 0 -
GLTMKQQSRLTKAVK RR18_GUITH 42 0 -
RLTSKQQRLLTIAIK RR18_MARPO 46 0 -
RLTLKQQRLITLAIK RR18_TOBAC 53 0 -
RLTLKQQRLITIAIK RR18_EPIVI 46 0 -
GTNAKYQRKLTAAIK RS18_BACSU 50 0 -
GLTSKQQKKLTKAIK RR18_PORPU 42 0 -
RLTLKQQRLITLAIK RR18_MAIZE 87 0 -
RLTLKQQRLITLAIK RR18_ORYSA 80 0 -
RLTLKQQRLITLAIK RR18_SECCE 87 0 -
KLTLKQQRLITIAIK RR18_PEA 53 0 -
GTSAKHQRRLALEIK O51140 69 0 -
RLTSKQQRLMTNAIK RR18_PINTH 71 0 -
GVSSRFQALLAQAVK O84808 53 0 -
GTCAKHQRRVALEVK RS18_TREPA 71 0 -
GLTAKQQRIMANAIK RR18_CHLVU 70 0 -
AVSAKKQRELAQAIK O68127 48 0 -
GTRAKYQRQLARAIK RS18_HAEIN 45 0 -
GTKAFYQRQLAVAVK RS18_NEIGO 47 0 -
GTRAKYQRQLARAIK RS18_ECOLI 45 0 -
GVSSRFQALLAQAVK RS18_CHLTR 53 0 -
GNCVQHQRDIALAVK RS18_MYCTU 55 0 -
GNCVQHQRDIAIAVK O53125 55 0 -
RLTAKQQRFVAKTIK O20032 104 0 -
GLTVQQQRQVAQAIK O86354 51 0 -
GNCQMHQRHVAKALK RS18_MYCPN 77 0 -
GNCNMHQRHVANALK RS18_MYCGE 78 0 -
KLTYKQHRLLRKSVK RR18_EUGGR 34 2 -
GTSKKYQEMVEVAIK O69301 47 0 -
GNSKKWQERVEVAIK RS18_HELPY 46 0 -

Motif 4 width=11
Element Seqn Id St Int Rpt
KRARQMALLPY RS18_BACST 63 -1 -
KQARVLALLPF RR18_CYAPA 56 -1 -
KRARVLSLLPF RR18_ODOSI 56 -1 -
KRSRLVALLPF RS18_SYNY3 56 -1 -
KRARILSLLPF RR18_GUITH 56 -1 -
KRARVLALLPF RR18_MARPO 60 -1 -
KQARILSLLPF RR18_TOBAC 67 -1 -
KQARILSLLPF RR18_EPIVI 60 -1 -
KRARQMALLPY RS18_BACSU 64 -1 -
KQARILSLLPF RR18_PORPU 56 -1 -
KQARILSFLPF RR18_MAIZE 101 -1 -
KQARILSFLPF RR18_ORYSA 94 -1 -
KQARILSFLPF RR18_SECCE 101 -1 -
KQARILSLLPF RR18_PEA 67 -1 -
KRARYMALLPF O51140 83 -1 -
KRARILSLLPF RR18_PINTH 85 -1 -
KRARHVGLLPF O84808 67 -1 -
KRSRAVALLPF RS18_TREPA 85 -1 -
KRARMGGLVPF RR18_CHLVU 84 -1 -
KRARFLALLPY O68127 62 -1 -
KRARYLALLPY RS18_HAEIN 59 -1 -
KRARFLALLPY RS18_NEIGO 61 -1 -
KRARYLSLLPY RS18_ECOLI 59 -1 -
KRARHVGLLLS RS18_CHLTR 67 -1 -
KNAREVALLPF RS18_MYCTU 69 -1 -
KNAREVALLPF O53125 69 -1 -
KTARVMGLLPF O20032 118 -1 -
KNAREMALLPY O86354 65 -1 -
KRARYLALVPF RS18_MYCPN 91 -1 -
KRARYLALVPF RS18_MYCGE 92 -1 -
KQARYLGLLPF RR18_EUGGR 48 -1 -
KRARHVALIPY O69301 61 -1 -
KRARHMALIPY RS18_HELPY 60 -1 -