SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR00955

Identifier
FLGMOTORFLIM  [View Relations]  [View Alignment]  
Accession
PR00955
No. of Motifs
4
Creation Date
01-SEP-1998  (UPDATE 07-JUN-1999)
Title
Flagellar motor switch protein FliM signature
Database References

INTERPRO; IPR001689
Literature References
1. ROMAN, S.J., FRANTZ, B.B. AND MATSUMURA, P.
Gene sequence, overproduction, purification and determination of the
wild-type level of the Escherichia coli flagellar switch protein FliG. 
GENE 133 103-108 (1993). 
 
2. MARYKWAS, D.L. AND BERG, H.C.
A mutational analysis of the interaction between FliG and FliM, two
components of the flagellar motor of Escherichia coli. 
J.BACTERIOL. 178 1289-1294 (1996). 
 
3. KIHARA, M., HOMMA, M., KUTSUKAKE, K. AND MACNAB, R.M.
Flagellar switch of Salmonella typhimurium: gene sequences and deduced 
protein sequences. 
J.BACTERIOL. 171 3247-3257 (1989). 
 
4. FRANCIS, N.R., IRIKURA, V.M., YAMAGUCHI, S., DEROSIER, D.J.
AND MACNAB, R.M.
Localization of the Salmonella typhimurium flagellar switch protein FliG to
the cytoplasmic M-ring face of the basal body. 
PROC.NATL.ACAD.SCI.U.S.A. 89 6304-6308 (1992). 

Documentation
The flagellar motor switch in E.coli and S.typhimurium regulates the 
direction of flagellar rotation and hence controls swimming behaviour [1].
The switch is a complex apparatus that responds to signals transduced by the
chemotaxis sensory signalling system during chemotactic behaviour [1]. CheY,
the chemotaxis response regulator, is believed to act directly on the switch
to induce tumbles in the swimming pattern, but no physical interactions of 
CheY and switch proteins have yet been demonstrated. 
 
The switch complex comprises at least three proteins - FliG, FliM and FliN.
It has been shown that FliG interacts with FliM, FliM interacts with itself,
and FliM interacts with FliN [2]. Several residues within the middle third
of FliG appear to be strongly involved in the FliG-FliM interaction, with
residues near the N- or C-termini being less important [2]. Such clustering
suggests that FliG-FliM interaction plays a central role in switching. 
 
Analysis of the FliG, FliM and FliN sequences shows that none are especially
hydrophobic or appear to be integral membrane proteins [3]. This result is
consistent with other evidence suggesting that the proteins may be 
peripheral to the membrane, possibly mounted on the basal body M ring [3,4]. 
 
FLGMOTORFLIM is a 4-element fingerprint that provides a signature for
flagellar motor switch FliM proteins. The fingerprint was derived from
an initial alignment of 5 sequences: the motifs were drawn from short
conserved regions spanning the central portion of alignment. Two iterations 
on OWL30.2 were required to reach convergence, at which point a true set
comprising 7 sequences was identified. A single partial matches was also
found, TPU324754, a fragment from Treponema phagedenis that matches motifs
1 and 2.
 
An update on SPTR37_9f identified a true set of 7 sequences.
Summary Information
7 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
47777
30000
20000
1234
True Positives
FLIM_BACSU    FLIM_BORBU    FLIM_CAUCR    FLIM_ECOLI    
FLIM_SALTY O25675 P74927
Sequence Titles
FLIM_BACSU  FLAGELLAR MOTOR SWITCH PROTEIN FLIM - BACILLUS SUBTILIS. 
FLIM_BORBU FLAGELLAR MOTOR SWITCH PROTEIN FLIM - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
FLIM_CAUCR FLAGELLAR MOTOR SWITCH PROTEIN FLIM - CAULOBACTER CRESCENTUS.
FLIM_ECOLI FLAGELLAR MOTOR SWITCH PROTEIN FLIM - ESCHERICHIA COLI.
FLIM_SALTY FLAGELLAR MOTOR SWITCH PROTEIN FLIM - SALMONELLA TYPHIMURIUM.
O25675 FLAGELLAR MOTOR SWITCH PROTEIN (FLIM) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
P74927 FLAGELLAR SWITCH PROTEIN (FLIM) - TREPONEMA PALLIDUM.
Scan History
OWL30_2    2  100  NSINGLE    
SPTR37_9f 2 8 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
DSILSQAEIDALLN FLIM_SALTY 3 3 -
GEVLSQNEIDALLS FLIM_BACSU 3 3 -
TEVLSQDEIDQLLT TPU282195 2 2 -
ERILNQDEIDSLLG FLIM_CAUCR 49 49 -
DSILSQAEIDALLN FLIM_ECOLI 3 3 -

Motif 2 width=17
Element Seqn Id St Int Rpt
YEEFIRSIPNMTILNLF FLIM_BACSU 91 74 -
YEEFIRSIPTPSTLAVI TPU282195 90 74 -
YHEFARNLPVPTNLNLI FLIM_ECOLI 89 72 -
YHEFARNLPVPTNLNLI FLIM_SALTY 89 72 -
FGDYLNSIPLPGILAVF FLIM_CAUCR 128 65 -

Motif 3 width=20
Element Seqn Id St Int Rpt
AVLEVDPSITFSIIDRLFGG TPU282195 115 8 -
GLVVFSPSLVFIAVDNLFGG FLIM_ECOLI 114 8 -
GLVVFSPSLVFIAVDNLFGG FLIM_SALTY 114 8 -
IMMEVNPTIAYTMMDRVMGG FLIM_BACSU 116 8 -
GLLTVDSNLIYSIVDVLLGG FLIM_CAUCR 153 8 -

Motif 4 width=19
Element Seqn Id St Int Rpt
GVINLCIPHIVLEPLIPKL FLIM_BACSU 212 76 -
GRIELLLPYATLEPIRKML FLIM_CAUCR 252 79 -
GEFNICLPFSMIEPLRELL FLIM_ECOLI 213 79 -
GMMNFCIPYITIEPIISKL TPU282195 211 76 -
GEFNICLPFSMIEPLRELL FLIM_SALTY 213 79 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
TEVLSQDEIDQLLT P74927 2 2 -
DSILSQAEIDALLN FLIM_ECOLI 3 3 -
DSILSQAEIDALLN FLIM_SALTY 3 3 -
PGALSQDDIDSLLE FLIM_BORBU 5 5 -
ADILSQEEIDALLE O25675 2 2 -
GEVLSQNEIDALLS FLIM_BACSU 3 3 -
ERILNQDEIDSLLG FLIM_CAUCR 49 49 -

Motif 2 width=17
Element Seqn Id St Int Rpt
YEEFIRSIPTPSTLAVI P74927 90 74 -
YHEFARNLPVPTNLNLI FLIM_ECOLI 89 72 -
YHEFARNLPVPTNLNLI FLIM_SALTY 89 72 -
YEEFIRSIPNPTTLAII FLIM_BORBU 100 81 -
YGEFLMSLPSPTSFNVF O25675 91 75 -
YEEFIRSIPNMTILNLF FLIM_BACSU 91 74 -
FGDYLNSIPLPGILAVF FLIM_CAUCR 128 65 -

Motif 3 width=20
Element Seqn Id St Int Rpt
AVLEVDPSITFSIIDRLFGG P74927 115 8 -
GLVVFSPSLVFIAVDNLFGG FLIM_ECOLI 114 8 -
GLVVFSPSLVFIAVDNLFGG FLIM_SALTY 114 8 -
AIFEVDPTIAFAIVDRLFGG FLIM_BORBU 125 8 -
GVLEINPSIAFPMIDRLLGG O25675 116 8 -
IMMEVNPTIAYTMMDRVMGG FLIM_BACSU 116 8 -
GLLTVDSNLIYSIVDVLLGG FLIM_CAUCR 153 8 -

Motif 4 width=19
Element Seqn Id St Int Rpt
GMMNFCIPYITIEPIISKL P74927 211 76 -
GEFNICLPFSMIEPLRELL FLIM_ECOLI 213 79 -
GEFNICLPFSMIEPLRELL FLIM_SALTY 213 79 -
GLMNFCLPYITIEPIVSKL FLIM_BORBU 222 77 -
GMMNICYPVISIESILSKM O25675 212 76 -
GVINLCIPHIVLEPLIPKL FLIM_BACSU 212 76 -
GRIELLLPYATLEPIRKML FLIM_CAUCR 252 79 -