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PR01249

Identifier
RIBOSOMALL31  [View Relations]  [View Alignment]  
Accession
PR01249
No. of Motifs
3
Creation Date
19-SEP-1999
Title
Ribosomal protein L31 signature
Database References

PROSITE; PS01143 RIBOSOMAL_L31
BLOCKS; BL01143
PFAM; PF01197 Ribosomal_L31
INTERPRO; IPR002150
Literature References
1. GOLDEN, B.L., RAMAKRISHNAN, V. AND WHITE, S.W.
Ribosomal protein L: structural evidence of gene duplication from a 
primitive RNA binding protein.
EMBO J. 12 4901-4908 (1993).
 
2. BROSIUS, J.
Primary structure of Escherichia coli ribosomal protein L31.
BIOCHEMISTRY 17 501-508 (1978). 

Documentation
Protein synthesis is co-ordinated in all cells by ribosomes, ribonucleo-
protein particles containing more than 50 different proteins and several
large RNAs [1]. Low resolution models show the protein arrangement in both
the large and small ribosomal subunits, but higher resolution structures are
required to reveal the detailed mechanistic functioning of the complex [2].
 
Ribosomal protein L31 is one of the proteins from the large ribosomal
subunit. The protein contains 66-97 amino acid residues with a calculated
molecular weight of 6967. The sequence contains four cysteine residues,
which are believed to form two disulphide bridges [2]. To date, the
protein has only been found in eubacteria and in some algal chloroplasts. 
 
RIBOSOMALL31 is a 3-element fingerprint that provides a signature for 
ribosomal protein L31. The fingerprint was derived from an initial alignment
of 12 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_L31 (PS01143). Three iterations on SPTR37_10f 
were required to reach convergence, at which point a true set comprising 20 
sequences was identified. Two partial matches were also found, both of which
are RL31 proteins that fail to make a significant match with motif 1.
Summary Information
  20 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3202020
2022
123
True Positives
O84025        Q9Z969        Q9ZH28        RK31_GUITH    
RK31_ODOSI RK31_PORPU RL31_BACSU RL31_BORBU
RL31_ECOLI RL31_HAEDU RL31_HAEIN RL31_HELPY
RL31_MYCGE RL31_MYCLE RL31_MYCPN RL31_MYCTU
RL31_SYNY3 RL31_TREPA YKGM_ECOLI YTIA_BACSU
True Positive Partials
Codes involving 2 elements
Q9Z387 RL31_THEMA
Sequence Titles
O84025      50S RIBOSOMAL PROTEIN L31 - CHLAMYDIA TRACHOMATIS. 
Q9Z969 50S RIBOSOMAL PROTEIN L31 - CHLAMYDIA PNEUMONIAE.
Q9ZH28 RIBOSOMAL PROTEIN L31 - LISTERIA MONOCYTOGENES.
RK31_GUITH CHLOROPLAST 50S RIBOSOMAL PROTEIN L31 - GUILLARDIA THETA (CRYPTOMONAS PHI).
RK31_ODOSI CHLOROPLAST 50S RIBOSOMAL PROTEIN L31 - ODONTELLA SINENSIS.
RK31_PORPU CHLOROPLAST 50S RIBOSOMAL PROTEIN L31 - PORPHYRA PURPUREA.
RL31_BACSU 50S RIBOSOMAL PROTEIN L31 - BACILLUS SUBTILIS.
RL31_BORBU 50S RIBOSOMAL PROTEIN L31 - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RL31_ECOLI 50S RIBOSOMAL PROTEIN L31 - ESCHERICHIA COLI.
RL31_HAEDU 50S RIBOSOMAL PROTEIN L31 - HAEMOPHILUS DUCREYI.
RL31_HAEIN 50S RIBOSOMAL PROTEIN L31 - HAEMOPHILUS INFLUENZAE.
RL31_HELPY 50S RIBOSOMAL PROTEIN L31 - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
RL31_MYCGE 50S RIBOSOMAL PROTEIN L31 - MYCOPLASMA GENITALIUM.
RL31_MYCLE 50S RIBOSOMAL PROTEIN L31 - MYCOBACTERIUM LEPRAE.
RL31_MYCPN 50S RIBOSOMAL PROTEIN L31 - MYCOPLASMA PNEUMONIAE.
RL31_MYCTU 50S RIBOSOMAL PROTEIN L31 - MYCOBACTERIUM TUBERCULOSIS.
RL31_SYNY3 50S RIBOSOMAL PROTEIN L31 - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
RL31_TREPA 50S RIBOSOMAL PROTEIN L31 - TREPONEMA PALLIDUM.
YKGM_ECOLI HYPOTHETICAL 9.9 KD PROTEIN IN INTF-EAEH INTERGENIC REGION - ESCHERICHIA COLI.
YTIA_BACSU HYPOTHETICAL RIBOSOMAL PROTEIN IN DPS-MENE INTERGENIC REGION - BACILLUS SUBTILIS

Q9Z387 50S RIBOSOMAL PROTEIN L31 - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
RL31_THEMA 50S RIBOSOMAL PROTEIN L31 - THERMOTOGA MARITIMA.
Scan History
SPTR37_10f 3  100  NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
KANIHPAYAETTVVCGCG RL31_MYCLE 2 2 -
KSDIHPAYEETTVVCGCG RL31_MYCTU 2 2 -
KQGIHPEYKEITATCSCG RL31_HAEDU 2 2 -
KQGIHPEYKEITATCSCG RL31_HAEIN 2 2 -
KKDIHPKYEEITASCSCG RL31_ECOLI 2 2 -
KAGIHPNFKKATVKCACG RL31_BACSU 2 2 -
KVDIHPIWYPDAKVYCDG RK31_PORPU 3 3 -
KKGIHPEYIPCKVTCVTS RL31_HELPY 2 2 -
KPNIHPEYRTVVFHDTSV YKGM_ECOLI 2 2 -
KPEIHPTWFNETPIVCDG RK31_ODOSI 3 3 -
KKAIHFQSQPVVFNCASC RL31_MYCGE 2 2 -
KKDFHFPSQSVSFKCASC RL31_MYCPN 2 2 -

Motif 2 width=16
Element Seqn Id St Int Rpt
RIVVEVCSQCHPFYTG RL31_MYCLE 32 12 -
RIVVEVCSQCHPFYTG RL31_MYCTU 32 12 -
NLNLDVCGNCHPFYTG RL31_HAEDU 31 11 -
DINLDVCGNCHPFYTG RL31_HAEIN 31 11 -
DLNLDVCSKCHPFFTG RL31_ECOLI 31 11 -
EVRVEICSECHPFYTG RL31_BACSU 30 10 -
ELHVDIWSGNHPFFTG RK31_PORPU 32 11 -
EMRIDISSFCHPFYTG RL31_HELPY 31 11 -
YVTIDVSSKSHPFYTG YKGM_ECOLI 44 24 -
ELQVDIWLANHPFYTD RK31_ODOSI 32 11 -
DLAIDICGKCHPFYIG RL31_MYCGE 33 13 -
EITIDICGKCHPFYIG RL31_MYCPN 33 13 -

Motif 3 width=19
Element Seqn Id St Int Rpt
GKQKILDSGGRVARFEKRY RL31_MYCLE 47 -1 -
GKQKILDSGGRVARFEKRY RL31_MYCTU 47 -1 -
GKQRVVDTGGRVERFNKRF RL31_HAEDU 46 -1 -
GKQRVVDTGGRVERFNSRF RL31_HAEIN 46 -1 -
GKQRDVATGGRVDRFNKRF RL31_ECOLI 46 -1 -
GRQKFASADGRVDRFNKKY RL31_BACSU 45 -1 -
GSQRIIDTEGRVERFMRKY RK31_PORPU 47 -1 -
GSDKIADTAGRVEKFKQRY RL31_HELPY 46 -1 -
GKLRTVASEGNVARFTQRF YKGM_ECOLI 59 -1 -
DSQTIIDSEGRVERFMKKY RK31_ODOSI 47 -1 -
GQLTKQTVHGRAEKLSQKF RL31_MYCGE 48 -1 -
GELTKQTVHGRAEKLSGKF RL31_MYCPN 48 -1 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
KANIHPAYAETTVVCGCG RL31_MYCLE 2 2 -
KSDIHPAYEETTVVCGCG RL31_MYCTU 2 2 -
KQGIHPEYKEITATCSCG RL31_HAEDU 2 2 -
KQGIHPEYKEITATCSCG RL31_HAEIN 2 2 -
KKDIHPKYEEITASCSCG RL31_ECOLI 2 2 -
KKGLHPRYEETKVVCACG RL31_TREPA 2 2 -
KADIHPTWYPDAKVTCNG RL31_SYNY3 3 3 -
KAGIHPNFKKATVKCACG RL31_BACSU 2 2 -
KQNLHPKWYAEAKVYCDG RK31_GUITH 3 3 -
KVDIHPIWYPDAKVYCDG RK31_PORPU 3 3 -
KKGIHPEYIPCKVTCVTS RL31_HELPY 2 2 -
KKNTHPEYRQVLFVDSST Q9Z969 2 2 -
KKNTHPEYRQVLFVDSST O84025 2 2 -
KTGIHPEYRPVVFVDTST Q9ZH28 2 2 -
KEGIHPKNHKVIFQDVNS YTIA_BACSU 2 2 -
KPNIHPEYRTVVFHDTSV YKGM_ECOLI 2 2 -
KPEIHPTWFNETPIVCDG RK31_ODOSI 3 3 -
RKDIHPKNNLVVFKDGSN RL31_BORBU 2 2 -
KKAIHFQSQPVVFNCASC RL31_MYCGE 2 2 -
KKDFHFPSQSVSFKCASC RL31_MYCPN 2 2 -

Motif 2 width=16
Element Seqn Id St Int Rpt
RIVVEVCSQCHPFYTG RL31_MYCLE 32 12 -
RIVVEVCSQCHPFYTG RL31_MYCTU 32 12 -
NLNLDVCGNCHPFYTG RL31_HAEDU 31 11 -
DINLDVCGNCHPFYTG RL31_HAEIN 31 11 -
DLNLDVCSKCHPFFTG RL31_ECOLI 31 11 -
DLRVEICSACHPFFTG RL31_TREPA 30 10 -
EINVEIWSGNHPFYTG RL31_SYNY3 32 11 -
EVRVEICSECHPFYTG RL31_BACSU 30 10 -
ELNVDIWSGNHPFYTG RK31_GUITH 32 11 -
ELHVDIWSGNHPFFTG RK31_PORPU 32 11 -
EMRIDISSFCHPFYTG RL31_HELPY 31 11 -
VCYVSVSSSSHPFFTG Q9Z969 44 24 -
VCYVSVSSSSHPFFTG O84025 44 24 -
LLRVEISSDSHPFYTG Q9ZH28 45 25 -
VIKVEVSSDTHPFYTG YTIA_BACSU 45 25 -
YVTIDVSSKSHPFYTG YKGM_ECOLI 44 24 -
ELQVDIWLANHPFYTD RK31_ODOSI 32 11 -
LVTVEITSKSHPFYTG RL31_BORBU 45 25 -
DLAIDICGKCHPFYIG RL31_MYCGE 33 13 -
EITIDICGKCHPFYIG RL31_MYCPN 33 13 -

Motif 3 width=19
Element Seqn Id St Int Rpt
GKQKILDSGGRVARFEKRY RL31_MYCLE 47 -1 -
GKQKILDSGGRVARFEKRY RL31_MYCTU 47 -1 -
GKQRVVDTGGRVERFNKRF RL31_HAEDU 46 -1 -
GKQRVVDTGGRVERFNSRF RL31_HAEIN 46 -1 -
GKQRDVATGGRVDRFNKRF RL31_ECOLI 46 -1 -
GKQKLVDSAGRIDRFNRRY RL31_TREPA 45 -1 -
GTQKIIDTEGRVDRFMRKY RL31_SYNY3 47 -1 -
GRQKFASADGRVDRFNKKY RL31_BACSU 45 -1 -
GSQKMLDTEGRVERFMRKY RK31_GUITH 47 -1 -
GSQRIIDTEGRVERFMRKY RK31_PORPU 47 -1 -
GSDKIADTAGRVEKFKQRY RL31_HELPY 46 -1 -
GSKKFVDAEGRVDKFLKRY Q9Z969 59 -1 -
GSKKLVDAEGRVDKFLKRY O84025 59 -1 -
GKQKHATQTAVWTAFNKKY Q9ZH28 60 -1 -
GRQKFNEKGGRVEQFKKRY YTIA_BACSU 60 -1 -
GKLRTVASEGNVARFTQRF YKGM_ECOLI 59 -1 -
DSQTIIDSEGRVERFMKKY RK31_ODOSI 47 -1 -
GQQKFVDAAGRIDKFNKRY RL31_BORBU 60 -1 -
GQLTKQTVHGRAEKLSQKF RL31_MYCGE 48 -1 -
GELTKQTVHGRAEKLSGKF RL31_MYCPN 48 -1 -