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PR00681

Identifier
RIBOSOMALS1  [View Relations]  [View Alignment]  
Accession
PR00681
No. of Motifs
9
Creation Date
06-APR-1997  (UPDATE 04-JUL-1999)
Title
Ribosomal protein S1 signature
Database References

PFAM; PF00575 S1
INTERPRO; IPR000110
Literature References
1. SCHNIER, J., KIMURA, M., FOULAKI, K., SUBRAMANIAN, A.R., ISONO, K.,
AND WITTMANN-LIEBOLD, B.
Primary structure of Escherichia coli ribosomal protein S1 and of
its gene rpsA.
PROC.NATL.ACAD.SCI.U.S.A. 79(4) 1008-1011 (1982).

Documentation
The S1 protein binds mRNA, facilitating recognition of the initiation point.
It is required to translate mRNA with short Shine-Dalgarno purine-rich
sequences, and is a member of the S1P family of ribosomal proteins.
 
Protein S1 is the largest component of the E.coli ribosome [1]. It has a
domain structure in which the ribosome-binding region is located towards
the N-terminus; the nucleic acid-binding domain, which is characterised
by several internal repeats (the so-called S1 motifs), lies in the central
portion of the sequence [1].
 
RIBOSOMALS1 is a 9-element fingerprint that provides a signature for 30S
ribosomal protein S1. The fingerprint was derived from an initial alignment
of 3 sequences: the motifs were drawn from conserved regions spanning the
N-terminal two-thirds of the alignment - motifs 1-6 span the ribosome-
binding domain; motif 7 lies in the first S1 motif of the nucleic acid-
binding domain; and motifs 8 and 9 lie in the second S1 motif. Two
iterations on OWL29.2 were required to reach convergence, at which point
a true set comprising 7 sequences was identified. Several partial matches
were also found, all of which are either fragments or S1 protein homologues.
 
An update on SPTR37_9f identified a true set of 7 sequences, and 22
partial matches.
Summary Information
   7 codes involving  9 elements
0 codes involving 8 elements
2 codes involving 7 elements
0 codes involving 6 elements
3 codes involving 5 elements
2 codes involving 4 elements
5 codes involving 3 elements
10 codes involving 2 elements
Composite Feature Index
9777777777
8000000000
7211022222
6000000000
5320111322
4000021212
3220100325
2211210157
123456789
True Positives
O06147        O84100        RS1_BUCAP     RS1_ECOLI     
RS1_HAEIN RS1_MYCLE RS1_RHIME
True Positive Partials
Codes involving 7 elements
RS1H_BACCE RS1H_BACSU
Codes involving 5 elements
O67462 O83303 RS1A_SYNY3
Codes involving 4 elements
P71450 RS1_SYNP6
Codes involving 3 elements
O51153 Q45141 RR1_SPIOL RS1B_SYNY3
RS1_HELPY
Codes involving 2 elements
GS13_BACSU O21261 O74835 O83894
Q45140 RRP5_YEAST RT01_MARPO YHGF_ECOLI
YHGF_HAEIN YHGF_NEIME
Sequence Titles
O06147      RPSA - MYCOBACTERIUM TUBERCULOSIS.            
O84100 S1 RIBOSOMAL PROTEIN - CHLAMYDIA TRACHOMATIS.
RS1_BUCAP 30S RIBOSOMAL PROTEIN S1 - BUCHNERA APHIDICOLA.
RS1_ECOLI 30S RIBOSOMAL PROTEIN S1 - ESCHERICHIA COLI.
RS1_HAEIN 30S RIBOSOMAL PROTEIN S1 - HAEMOPHILUS INFLUENZAE.
RS1_MYCLE 30S RIBOSOMAL PROTEIN S1 - MYCOBACTERIUM LEPRAE.
RS1_RHIME 30S RIBOSOMAL PROTEIN S1 - RHIZOBIUM MELILOTI.

RS1H_BACCE 30S RIBOSOMAL PROTEIN S1 HOMOLOG - BACILLUS CEREUS.
RS1H_BACSU 30S RIBOSOMAL PROTEIN S1 HOMOLOG - BACILLUS SUBTILIS.

O67462 RIBOSOMAL PROTEIN S01 - AQUIFEX AEOLICUS.
O83303 RIBOSOMAL PROTEIN S1 (RPSA) - TREPONEMA PALLIDUM.
RS1A_SYNY3 30S RIBOSOMAL PROTEIN S1 HOMOLOG A - SYNECHOCYSTIS SP. (STRAIN PCC 6803).

P71450 40S RIBOSOMAL PROTEIN S1 - LEUCONOSTOC LACTIS.
RS1_SYNP6 30S RIBOSOMAL PROTEIN S1 - SYNECHOCOCCUS SP. (STRAIN PCC 6301).

O51153 RIBOSOMAL PROTEIN S1 (RPSA) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
Q45141 HEME UPTAKE PROTEIN A - BACTEROIDES FRAGILIS.
RR1_SPIOL 30S RIBOSOMAL PROTEIN S1, CHLOROPLAST PRECURSOR (CS1) - SPINACIA OLERACEA (SPINACH).
RS1B_SYNY3 30S RIBOSOMAL PROTEIN S1 HOMOLOG B - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RS1_HELPY 30S RIBOSOMAL PROTEIN S1 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).

GS13_BACSU GENERAL STRESS PROTEIN 13 (GSP13) - BACILLUS SUBTILIS.
O21261 RIBOSOMAL PROTEIN S1 - RECLINOMONAS AMERICANA.
O74835 PUTATIVE RRNA BIOGENESIS PROTEIN, RRP5 HOMOLOG, MULTIPLE S1 RNA BINDING DOMAIN PROTEIN - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
O83894 TEX PROTEIN (TEX) - TREPONEMA PALLIDUM.
Q45140 HEME UPTAKE PROTEIN B - BACTEROIDES FRAGILIS.
RRP5_YEAST RRNA BIOGENESIS PROTEIN RRP5 - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
RT01_MARPO MITOCHONDRIAL RIBOSOMAL PROTEIN S1 - MARCHANTIA POLYMORPHA (LIVERWORT).
YHGF_ECOLI HYPOTHETICAL 85.1 KD PROTEIN IN GREB-FEOA INTERGENIC REGION - ESCHERICHIA COLI.
YHGF_HAEIN HYPOTHETICAL PROTEIN HI0568 - HAEMOPHILUS INFLUENZAE.
YHGF_NEIME HYPOTHETICAL 83.1 KD PROTEIN IN REGION E - NEISSERIA MENINGITIDIS.
Scan History
OWL29_2    2  100  NSINGLE    
SPTR37_9f 1 75 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
GSIVRGVVVAIDKDVVLVD RS1_ECOLI 21 21 -
GYVAKGIVTAIEKDVAIVD RS1_RHIME 27 27 -
GDIVEGTIVKVDRDEVLLD RS1_MYCLE 36 36 -

Motif 2 width=15
Element Seqn Id St Int Rpt
DAGLKSESAIPAEQF RS1_ECOLI 39 -1 -
DVGLKVEGRVPLKEF RS1_RHIME 45 -1 -
DIGYKTEGVIPAREL RS1_MYCLE 54 -1 -

Motif 3 width=20
Element Seqn Id St Int Rpt
LSREKAKRHEAWITLEKAYE RS1_ECOLI 84 30 -
LSREKARREESWQRLEVKFE RS1_RHIME 90 30 -
LSKKRAQYERAWGTIEALKE RS1_MYCLE 102 33 -

Motif 4 width=17
Element Seqn Id St Int Rpt
VTGVINGKVKGGFTVEL RS1_ECOLI 108 4 -
VEGIIFNQVKGGFTVDL RS1_RHIME 114 4 -
VKGIVIEVVKGGLILDI RS1_MYCLE 126 4 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GAVAFLPRSQVDIRPIRD RS1_RHIME 132 1 -
GIRAFLPGSLVDVRPVRD RS1_ECOLI 126 1 -
GLRGFLPASLVEMRRVRD RS1_MYCLE 143 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
KVIKLDQKRNNVVVSRRAVIE RS1_ECOLI 155 11 -
RNLKMDKRRGNIVVSRRTVLE RS1_RHIME 161 11 -
KIIELDKNRNNVVLSRRAWLE RS1_MYCLE 172 11 -

Motif 7 width=22
Element Seqn Id St Int Rpt
GGVDGLLHITDMAWKRVKHPSE RS1_ECOLI 212 36 -
GGIDGLLHVTDMAWRRVKHPSE RS1_RHIME 218 36 -
GGVDGLVHVSELSWKHIDHPSE RS1_MYCLE 229 36 -

Motif 8 width=20
Element Seqn Id St Int Rpt
YGCFVEIEEGVEGLVHVSEM RS1_ECOLI 290 56 -
YGAFVELEPGIEGLIHISEM RS1_RHIME 296 56 -
FGAFVRVEEGIEGLVHISEL RS1_MYCLE 307 56 -

Motif 9 width=19
Element Seqn Id St Int Rpt
VMVLDIDEERRRISLGLKQ RS1_ECOLI 330 20 -
VVVLEVDPTKRRISLGLKQ RS1_RHIME 336 20 -
VKVIDIDLERRRISLSLKA RS1_MYCLE 346 19 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
GSIIRGTIVSIEKDIVLVD RS1_BUCAP 21 21 -
GSIVSGTVVAIQKGFVLVD RS1_HAEIN 21 21 -
GSIVRGVVVAIDKDVVLVD RS1_ECOLI 21 21 -
GYVAKGIVTAIEKDVAIVD RS1_RHIME 27 27 -
GDIVEGTIVKVDRDEVLLD RS1_MYCLE 36 36 -
GDIVEGTIVKVDRDEVLLD O06147 36 36 -
GAILKGTVVDISKDFVVVD O84100 52 52 -

Motif 2 width=15
Element Seqn Id St Int Rpt
DVGLKSEGVIPMSEF O84100 70 -1 -
DAGLKSESAIPVEQF RS1_BUCAP 39 -1 -
DAGLKSESAIPAEQF RS1_ECOLI 39 -1 -
DAGLKSESAIPVAEF RS1_HAEIN 39 -1 -
DVGLKVEGRVPLKEF RS1_RHIME 45 -1 -
DIGYKTEGVIPAREL RS1_MYCLE 54 -1 -
DIGYKTEGVIPAREL O06147 54 -1 -

Motif 3 width=20
Element Seqn Id St Int Rpt
LSREKAKRHEAWITLEKAYE RS1_ECOLI 84 30 -
LSREKAKRHEAWLILEQAHE RS1_BUCAP 84 30 -
LSREKAVRHESWIELEKAYE RS1_HAEIN 84 30 -
LSREKARREESWQRLEVKFE RS1_RHIME 90 30 -
LSKKRAQYERAWGTIEALKE RS1_MYCLE 102 33 -
LSKKRAQYERAWGTIEALKE O06147 102 33 -
LSREKATRQRQWEYILAHCE O84100 113 28 -

Motif 4 width=17
Element Seqn Id St Int Rpt
VTGVINGKVKGGFTVEL RS1_ECOLI 108 4 -
VIGIINGKVKGGFTVEL RS1_BUCAP 108 4 -
VIGLIXGKVKGGFTVEL RS1_HAEIN 108 4 -
VEGIIFNQVKGGFTVDL RS1_RHIME 114 4 -
VKGIVIEVVKGGLILDI RS1_MYCLE 126 4 -
VKGTVIEVVKGGLILDI O06147 126 4 -
VKGQITRKVKGGLIVDI O84100 137 4 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GAVAFLPRSQVDIRPIRD RS1_RHIME 132 1 -
GIRAFLPGSLVDVRPVRD RS1_ECOLI 126 1 -
EIRAFLPGSLVDVRPVRD RS1_BUCAP 126 1 -
GVRAFLPGSLVDTRPARE RS1_HAEIN 126 1 -
GLRGFLPASLVEMRRVRD RS1_MYCLE 143 0 -
GLRGFLPASLVEMRRVRD O06147 143 0 -
GMEAFLPGSQIDNKKIKN O84100 154 0 -

Motif 6 width=21
Element Seqn Id St Int Rpt
KVIKLDQKRNNVVVSRRAVIE RS1_ECOLI 155 11 -
KVIKLDQKRNNVVVSRRAVIE RS1_BUCAP 155 11 -
KVIKLDQKRNNVVVSRRAVIE RS1_HAEIN 155 11 -
RNLKMDKRRGNIVVSRRTVLE RS1_RHIME 161 11 -
KIIELDKNRNNVVLSRRAWLE RS1_MYCLE 172 11 -
KIIELDKNRNNVVLSRRAWLE O06147 172 11 -
KILKINVDRRNVVVSRRELLE O84100 183 11 -

Motif 7 width=22
Element Seqn Id St Int Rpt
GGVDGLLHITDMAWKRVKHPSE RS1_ECOLI 212 36 -
GGVDGLLHITDMAWKRVKHPSE RS1_BUCAP 212 36 -
GGVDGLLHITDMAWKRVKHPSE RS1_HAEIN 212 36 -
GGIDGLLHVTDMAWRRVKHPSE RS1_RHIME 218 36 -
GGVDGLVHVSELSWKHIDHPSE RS1_MYCLE 229 36 -
GGVDGLVHVSELSWKHIDHPSE O06147 229 36 -
DGIDGLLHITDMTWKRIRHPSE O84100 240 36 -

Motif 8 width=20
Element Seqn Id St Int Rpt
YGCFVEIEEGVEGLVHVSEM RS1_ECOLI 290 56 -
YGCFVEIEEGVEGLVHVSEM RS1_BUCAP 290 56 -
YGCFVEILDGVEGLVHVSEM RS1_HAEIN 290 56 -
YGAFVELEPGIEGLIHISEM RS1_RHIME 296 56 -
FGAFVRVEEGIEGLVHISEL RS1_MYCLE 307 56 -
FGAFVRVEEGIEGLVHISEL O06147 307 56 -
YGAFIEIEEGIEGLIHVSEM O84100 318 56 -

Motif 9 width=19
Element Seqn Id St Int Rpt
VMVLDIDEERRRISLGLKQ RS1_ECOLI 330 20 -
VIVLDIDEERRRISLGLKQ RS1_BUCAP 330 20 -
VMVLEIDEERRRISLGLKQ RS1_HAEIN 330 20 -
VVVLEVDPTKRRISLGLKQ RS1_RHIME 336 20 -
VKVIDIDLERRRISLSLKA RS1_MYCLE 346 19 -
VKVIDIDLERRRISLSLKQ O06147 346 19 -
VVVLSIQKDEGKISLGLKQ O84100 358 20 -