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PR00951

Identifier
FLGBIOSNFLIP  [View Relations]  [View Alignment]  
Accession
PR00951
No. of Motifs
6
Creation Date
17-MAR-2000
Title
Flagellar biosynthetic protein FliP signature
Database References
PRINTS; PR01302 TYPE3IMPPROT
INTERPRO; IPR002039
Literature References
1. MALAKOOTI, J., ELY, B. AND MATSUMURA, P.
Molecular characterization, nucleotide-sequence, and expression of 
the flio, flip, fliq and flir genes of Escherichia coli.
J.BACTERIOL. 176 189-197 (1994).

Documentation
The fliL operon of Escherichia coli contains seven genes (including fliO,
fliP, fliQ and fliR) involved in the biosynthesis and functioning of the
flagellar organelle [1]. The fliO, fliP, fliQ and fliR genes encode highly
hydrophobic polypeptides. On the basis of DNA sequence analysis and in vivo
protein expression, the fliP gene product appears to be synthesised as a 
precursor, with an N-terminal signal peptide of 21 amino acids [1]. The FliP
protein shows similarity to proteins encoded by a DNA sequence upstream of
the flaA gene of Rhizobium meliloti, to a gene involved in pathogenicity in
Xanthomonas campestris pv. glycines and to the spa24 gene of the Shigella
flexneri [1]. The gene products of the latter two appear to be involved in
protein translocation, suggesting a similar function in FliP [1]. 
 
FliP is an ~30Kd protein containing three or four transmembrane (TM) regions.
Proteins sharing an evolutionary relationship with FliP have been found in 
a wide range of bacteria and are involved in a variety of signal-peptide 
independent secretion systems (e.g., mopC, hrcR, hrpW, spaP, yscR).
 
FLGBIOSNFLIP is a 6-element fingerprint that provides a signature for
the flagellar biosynthetic FliP proteins. The fingerprint was derived from
an initial alignment of 8 sequences: the motifs were drawn from short 
conserved regions spanning virtually the full alignment length, focusing
on those sections that characterise the Flip proteins but distinguish 
them from the type III secretion system inner membrane P protein family - 
motif 1 spans the N-terminus of putative TM domain 1; motif 2 spans the
C-terminus of TM domain 2 and part of the following loop; and motifs 3 and
4 reside in the loop between TM domains 2 and 3. Two iterations on 
SPTR37_10f were required to reach convergence, at which point a true set 
comprising 9 sequences was identified. Several partial matches were also 
found, all of which are FliP proteins that fail to match one or more motifs.
Summary Information
   9 codes involving  6 elements
0 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
6999999
5000000
4011110
3120021
2001010
123456
True Positives
FLIP_AGRTU    FLIP_BACSU    FLIP_BORBU    FLIP_CAUCR    
FLIP_ECOLI FLIP_ERWCA FLIP_RHIME FLIP_SALTY
FLIP_TREPA
True Positive Partials
Codes involving 4 elements
Q9ZLF5
Codes involving 3 elements
O67750 Q9Z6F8
Codes involving 2 elements
O85133
Sequence Titles
FLIP_AGRTU  FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - AGROBACTERIUM TUMEFACIENS. 
FLIP_BACSU FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - BACILLUS SUBTILIS.
FLIP_BORBU FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - BORRELIA BURGDORFERI (LYME DISEASE SPIROCH
FLIP_CAUCR FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - CAULOBACTER CRESCENTUS.
FLIP_ECOLI FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - ESCHERICHIA COLI.
FLIP_ERWCA FLAGELLAR BIOSYNTHETIC PROTEIN FLIP (FLAGELLAR BIOSYNTHETIC PROTEIN MOPC) - ERWI
FLIP_RHIME FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - RHIZOBIUM MELILOTI.
FLIP_SALTY FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - SALMONELLA TYPHIMURIUM.
FLIP_TREPA FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - TREPONEMA PALLIDUM.

Q9ZLF5 FLAGELLAR BIOSYNTHESIS PROTEIN - HELICOBACTER PYLORI J99.

O67750 FLAGELLAR BIOSYNTHETIC PROTEIN FLIP - AQUIFEX AEOLICUS.
Q9Z6F8 POLAR FLAGELLAR ASSEMBLY PROTEIN - VIBRIO PARAHAEMOLYTICUS.

O85133 FLAGELLAR PROTEIN FLIP - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
QTLVFITSLT FLIP_ECOLI 43 43 -
QTLVFITSLT FLIP_SALTY 43 43 -
RTFGLLTVLS FLIP_AGRTU 42 42 -
RTFGLLTVLS FLIP_RHIME 42 42 -
KLLLLLTVFS FLIP_BACSU 21 21 -
QLVGLMTVLS FLIP_CAUCR 60 60 -
QLLILLTIIT FLIP_BORBU 50 50 -
QLLLLLTLIS FLIP_TREPA 68 68 -

Motif 2 width=13
Element Seqn Id St Int Rpt
PVIDKIYVDAYQP FLIP_ECOLI 103 50 -
PVIDKIYVDAYQP FLIP_SALTY 103 50 -
PTFDKAWTDGVQP FLIP_AGRTU 102 50 -
PTFDRAWRDGIDP FLIP_RHIME 102 50 -
PTFSEINKEALTP FLIP_BACSU 81 50 -
PTFERSYDAGIKP FLIP_CAUCR 120 50 -
PTFNSIYEQAYLP FLIP_BORBU 110 50 -
PVFTEIYAKSFKP FLIP_TREPA 128 50 -

Motif 3 width=15
Element Seqn Id St Int Rpt
PFSEEKISMQEALEK FLIP_ECOLI 115 -1 -
PFSEQKISMQEALDK FLIP_SALTY 115 -1 -
PLLQNQINEQQAVQR FLIP_AGRTU 114 -1 -
PLLKNEISETDAIQR FLIP_RHIME 114 -1 -
PLMDNKISLDEAYTK FLIP_BACSU 93 -1 -
PLLDQQMELPEAFEA FLIP_CAUCR 132 -1 -
PLKESKINFNEFYNK FLIP_BORBU 122 -1 -
PLTDGQVDIQTAYTE FLIP_TREPA 140 -1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
READLGLFARLAN FLIP_ECOLI 143 13 -
READLALFARLAN FLIP_SALTY 143 13 -
RDKDLKLFVDIAR FLIP_AGRTU 142 13 -
RDKDLQLFIDIAR FLIP_RHIME 142 13 -
RQKDLALFMNYAK FLIP_BACSU 121 13 -
DRDDLALFVRLSK FLIP_CAUCR 160 13 -
RHEEIRLFMSMSN FLIP_BORBU 153 16 -
DPSSVRLCMSMAK FLIP_TREPA 170 15 -

Motif 5 width=13
Element Seqn Id St Int Rpt
VPMRILLPAYVTS FLIP_ECOLI 165 9 -
VPMRILLPAYVTS FLIP_SALTY 165 9 -
VDYRVLVPAFMLS FLIP_AGRTU 166 11 -
VDLRAVVPAFMIS FLIP_RHIME 166 11 -
IPLTTMVPAFAIS FLIP_BACSU 143 9 -
TPLRVVTPAFMIS FLIP_CAUCR 182 9 -
VPTHVLIAAFILH FLIP_BORBU 175 9 -
VPTYVLIPAFILH FLIP_TREPA 192 9 -

Motif 6 width=11
Element Seqn Id St Int Rpt
QLLVGSLAQSF FLIP_ECOLI 233 55 -
QLLMGSLAQSF FLIP_SALTY 233 55 -
NLLVGSLVRSF FLIP_AGRTU 234 55 -
NLLVGSLVRSF FLIP_RHIME 234 55 -
YLIVKSLLQSF FLIP_BACSU 211 55 -
RLVAGSLVESF FLIP_CAUCR 250 55 -
TLITSGLIKSF FLIP_BORBU 243 55 -
NLLIDRLFHSF FLIP_TREPA 260 55 -
Final Motifs
Motif 1  width=10
Element Seqn Id St Int Rpt
QTLVFITSLT FLIP_ECOLI 43 43 -
QTLVFITSLT FLIP_SALTY 43 43 -
QTLVLLTSLT FLIP_ERWCA 56 56 -
RTFGLLTVLS FLIP_AGRTU 42 42 -
RTFGLLTVLS FLIP_RHIME 42 42 -
KLLLLLTVFS FLIP_BACSU 21 21 -
QLVGLMTVLS FLIP_CAUCR 60 60 -
QLLILLTIIT FLIP_BORBU 50 50 -
QLLLLLTLIS FLIP_TREPA 68 68 -

Motif 2 width=13
Element Seqn Id St Int Rpt
PVIDKIYVDAYQP FLIP_ECOLI 103 50 -
PVIDKIYVDAYQP FLIP_SALTY 103 50 -
PVLNRVYDEAYLP FLIP_ERWCA 116 50 -
PTFDKAWTDGVQP FLIP_AGRTU 102 50 -
PTFDRAWRDGIDP FLIP_RHIME 102 50 -
PTFSEINKEALTP FLIP_BACSU 81 50 -
PTFERSYDAGIKP FLIP_CAUCR 120 50 -
PTFNSIYEQAYLP FLIP_BORBU 110 50 -
PVFTEIYAKSFKP FLIP_TREPA 128 50 -

Motif 3 width=15
Element Seqn Id St Int Rpt
PFSEEKISMQEALEK FLIP_ECOLI 115 -1 -
PFSEQKISMQEALDK FLIP_SALTY 115 -1 -
PFSQDQISMEVAIER FLIP_ERWCA 128 -1 -
PLLQNQINEQQAVQR FLIP_AGRTU 114 -1 -
PLLKNEISETDAIQR FLIP_RHIME 114 -1 -
PLMDNKISLDEAYTK FLIP_BACSU 93 -1 -
PLLDQQMELPEAFEA FLIP_CAUCR 132 -1 -
PLKESKINFNEFYNK FLIP_BORBU 122 -1 -
PLTDGQVDIQTAYTE FLIP_TREPA 140 -1 -

Motif 4 width=13
Element Seqn Id St Int Rpt
READLGLFARLAN FLIP_ECOLI 143 13 -
READLALFARLAN FLIP_SALTY 143 13 -
RETDLALFTRLAE FLIP_ERWCA 156 13 -
RDKDLKLFVDIAR FLIP_AGRTU 142 13 -
RDKDLQLFIDIAR FLIP_RHIME 142 13 -
RQKDLALFMNYAK FLIP_BACSU 121 13 -
DRDDLALFVRLSK FLIP_CAUCR 160 13 -
RHEEIRLFMSMSN FLIP_BORBU 153 16 -
DPSSVRLCMSMAK FLIP_TREPA 170 15 -

Motif 5 width=13
Element Seqn Id St Int Rpt
VPMRILLPAYVTS FLIP_ECOLI 165 9 -
VPMRILLPAYVTS FLIP_SALTY 165 9 -
VPMRVLLPAFVTS FLIP_ERWCA 178 9 -
VDYRVLVPAFMLS FLIP_AGRTU 166 11 -
VDLRAVVPAFMIS FLIP_RHIME 166 11 -
IPLTTMVPAFAIS FLIP_BACSU 143 9 -
TPLRVVTPAFMIS FLIP_CAUCR 182 9 -
VPTHVLIAAFILH FLIP_BORBU 175 9 -
VPTYVLIPAFILH FLIP_TREPA 192 9 -

Motif 6 width=11
Element Seqn Id St Int Rpt
QLLVGSLAQSF FLIP_ECOLI 233 55 -
QLLMGSLAQSF FLIP_SALTY 233 55 -
QLLLGSLAQSF FLIP_ERWCA 246 55 -
NLLVGSLVRSF FLIP_AGRTU 234 55 -
NLLVGSLVRSF FLIP_RHIME 234 55 -
YLIVKSLLQSF FLIP_BACSU 211 55 -
RLVAGSLVESF FLIP_CAUCR 250 55 -
TLITSGLIKSF FLIP_BORBU 243 55 -
NLLIDRLFHSF FLIP_TREPA 260 55 -