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PR00952

Identifier
TYPE3IMQPROT  [View Relations]  [View Alignment]  
Accession
PR00952
No. of Motifs
3
Creation Date
03-SEP-1998  (UPDATE 03-APR-2000)
Title
Type III secretion system inner membrane Q protein family signature
Database References

PFAM; PF01313 Bac_export_3
INTERPRO; IPR002191
Literature References
1. MECSAS, J. AND STRAUSS, E.J.
Molecular mechanisms of bacterial virulence: type III secretion and 
pathogenicity islands.
EMERG.INFECT.DIS. 2 271-288 (1996).
 
2. GALAN, J. AND COLLMER, A.
Type III secretion machines; bacterial devices for protein delivery into
host cells.
SCIENCE 284 1322-1328 (1999).
 
3. KOMORIYA, K., SHIBANO, N., HIGANO, T., AZUMA, N., YAMAGUCHI, S.
AND AIZAWA, S.
Flagellar proteins and type III-exported virulence factors are the 
predominant proteins secreted into the culture media of Salmonella 
typhimurium.
MOL.MICROBIOL. 34 767-779 (1999).
 
4. HUECK, C.J.
Type III protein secretion systems in bacterial pathogens of animals
and plants.
MICROBIOL.MOL.BIOL.REV. 379-433 (1998).

Documentation
Secretion of virulence factors in Gram-negative bacteria involves 
transportation of the protein across two membranes to reach the cell 
exterior [1]. There have been four secretion systems described in 
animal enteropathogens such as Salmonella and Yersinia, with further 
sequence similarities in plant pathogens like Ralstonia and Erwinia [1]. 
 
The type III secretion system is of great interest, as it is used to 
transport virulence factors from the pathogen directly into the host cell 
[2] and is only triggered when the bacterium comes into close contact with
the host. The protein subunits of the system are very similar to those of 
bacterial flagellar biosynthesis [3]. However, while the latter forms a
ring structure to allow secretion of flagellin and is an integral part of
the flagellum itself [3], type III subunits in the outer membrane
translocate secreted proteins through a channel-like structure.
 
It is believed that the family of type III inner membrane proteins are 
used as structural moieties in a complex with several other subunits [4], 
including the ATPase necessary for driving the secretion system. One such
set of inner membrane proteins, termed "Q" here for nomenclature purposes,
includes the Salmonella and Shigella SpaQ, the Yersinia YscS, the Rhizobium 
Y4YM, and the Erwinia HrcS genes [4]. The flagellar protein FliQ also shares 
similarity, probably due to evolution of the type III secretion system from
the flagellar biosynthetic pathway.
 
TYPE3IMQPROT is a 3-element fingerprint that provides a signature for the
type III secretion system inner membrane Q protein family. The fingerprint
was derived from an initial alignment of 9 sequences: the motifs were drawn
from short conserved regions spanning the full alignment length - motifs 1
and 3 each encode a putative TM region. Three iterations on OWL30.2 were 
required to reach convergence, at which point a true set comprising 21
sequences was identified. 
 
An update on SPTR37_9f identified a true set of 28 sequences.
Summary Information
28 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3282828
2000
123
True Positives
FLIQ_BACSU    FLIQ_BORBU    FLIQ_CAUCR    FLIQ_ECOLI    
FLIQ_ERWCA FLIQ_SALTY FLIQ_TREPA O25964
O52128 O67774 O84567 O85096
O85134 P72276 Q46647 Q47304
Q47857 Q52487 Q54013 Q57117
Q57533 Q60237 SPAQ_SALTY SPAQ_SHIFL
SSAS_SALTY Y4YM_RHISN YSCS_YERPE YSCS_YERPS
Sequence Titles
FLIQ_BACSU  FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - BACILLUS SUBTILIS. 
FLIQ_BORBU FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
FLIQ_CAUCR FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - CAULOBACTER CRESCENTUS.
FLIQ_ECOLI FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - ESCHERICHIA COLI.
FLIQ_ERWCA FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ (FLAGELLAR BIOSYNTHETIC PROTEIN MOPD) - ERWINIA CAROTOVORA.
FLIQ_SALTY FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - SALMONELLA TYPHIMURIUM.
FLIQ_TREPA FLAGELLAR BIOSYNTHETIC PROTEIN FLIQ - TREPONEMA PALLIDUM.
O25964 FLAGELLAR BIOSYNTHETIC PROTEIN (FLIQ) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI), AND HELICOBACTER PYLORI J99.
O52128 ESCS - ESCHERICHIA COLI.
O67774 FLAGELLAR BIOSYNTHESIS PROTEIN FLIQ - AQUIFEX AEOLICUS.
O84567 YOPS/FLIQ TRANSLOCATION PROTEIN - CHLAMYDIA TRACHOMATIS.
O85096 HRCS - PSEUDOMONAS SYRINGAE (PV. PHASEOLICOLA).
O85134 FLAGELLAR PROTEIN FLIQ - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
P72276 NODULATION PROTEIN (NOLX, NOLW, NOLB, NOLT, NOLU, NOLV), PUTATIVE ATPASE (HRCN), HRCQ, HRCR, HRCS, HRCT GENES, COMPLETE CDS AND HRCU (HRCN) - RHIZOBIUM FREDII.
Q46647 HRCS - ERWINIA AMYLOVORA.
Q47304 INVX PRECURSOR - ESCHERICHIA COLI.
Q47857 HRCO, HRCP, HRCQ, HRCR, HRCS, HRCT & HRCU GENES - ERWINIA HERBICOLA.
Q52487 HRPU - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
Q54013 SPAQ - SALMONELLA TYPHIMURIUM.
Q57117 SPAQ - SALMONELLA TYPHIMURIUM.
Q57533 SPAQ - SALMONELLA ENTERITIDIS, SALMONELLA DUBLIN, SALMONELLA SENFTENBERG, SALMONELLA GALLINARUM, SALMONELLA TYPHIMURIUM, SALMONELLA TYPHISUIS, AND SALMONELLA TYPHI.
Q60237 HRPO - PSEUDOMONAS SYRINGAE.
SPAQ_SALTY SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAQ - SALMONELLA TYPHIMURIUM.
SPAQ_SHIFL SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAQ (SPA9 PROTEIN) - SHIGELLA FLEXNERI, AND SHIGELLA SONNEI.
SSAS_SALTY SECRETION SYSTEM APPARATUS PROTEIN SSAS - SALMONELLA TYPHIMURIUM.
Y4YM_RHISN PROBABLE TRANSLOCATION PROTEIN Y4YM - RHIZOBIUM SP. (STRAIN NGR234).
YSCS_YERPE YOP PROTEINS TRANSLOCATION PROTEIN S - YERSINIA PESTIS.
YSCS_YERPS YOP PROTEINS TRANSLOCATION PROTEIN S - YERSINIA PSEUDOTUBERCULOSIS.
Scan History
OWL30_2    3  100  NSINGLE    
SPTR37_9f 2 29 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
LMISGPLLAIALLVGLIVSIFQ FLIQ_BACSU 18 18 -
IILSAPMLIIALIVGLLISIFQ B70134 18 18 -
LALAAPPLMAALLSGLLISLLQ MOPD_ERWCA 18 18 -
LMISLPVLLAGLVVGLLVSIFQ C64697 17 17 -
LQLCAPVLIVGLVVGVIIGLFQ I40670 18 18 -
VLLVAPVLCTALVVGLIVAIFQ JC4508 19 19 -
LVLSMPPVLVAAVVGTLVSLVQ YSCS_YERPE 18 18 -
LALAAPLLLVALVTGLIISILQ FLIQ_ECOLI 18 18 -
LALAAPLLLVALITGLIISILQ FLIQ_SALTY 18 18 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QAVTSIQEQTLTFVPK JC4508 40 -1 -
QALTQIQEQTLGFVIK YSCS_YERPE 39 -1 -
QAATQINEMTLSFIPK FLIQ_ECOLI 39 -1 -
QAATQINEMTLSFIPK FLIQ_SALTY 39 -1 -
QATTQIQEQTLAFIPK FLIQ_BACSU 39 -1 -
QAATQINEMTLSFIPK MOPD_ERWCA 39 -1 -
QATTQINEMTLSFVPK C64697 38 -1 -
QALTQIQEATLVYAPK I40670 39 -1 -
QAITSIQDQTLSFIPK B70134 39 -1 -

Motif 3 width=23
Element Seqn Id St Int Rpt
KIVAVLLALIFFGPWMLSTILSF FLIQ_BACSU 54 -1 -
KIIVILLVIVIFGPWILNKLMQF B70134 54 -1 -
KILTVFFTLVIAGPWMLNLMLDY MOPD_ERWCA 54 -1 -
KILAVIGVLILTMPWMTNMLLDY C64697 53 -1 -
KIVAIFISLLIFLPLMGSLMSGF I40670 54 -1 -
KMLTILGMIALLGGWMLTMLQNY JC4508 55 -1 -
KLIAVVVTLFATASWLGNELHSF YSCS_YERPE 54 -1 -
KIIAVFIAIIIAGPWMLNLLLDY FLIQ_ECOLI 54 -1 -
KIVAVFIAIIVAGPWMLNLLLDY FLIQ_SALTY 54 -1 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
LILSGWPTIVATVIGLLVGLFQ Q54013 16 16 -
LILSGWPTIVATIIGLLVGLFQ Q57117 16 16 -
LILSGWPTIVATIIGLLVGLFQ Q57533 16 16 -
LILSGWPTIVATIIGLLVGLFQ SPAQ_SALTY 12 12 -
VLLSAPPLLVAVIVGVLVSLLQ Q46647 15 15 -
VLLSAPPLLVAVIVGVLVSLLQ Q47857 12 12 -
LVLSMPPVLVAAVVGTLVSLVQ YSCS_YERPE 18 18 -
LVLSMPPVLVAAVVGTLVSLVQ YSCS_YERPS 18 18 -
LIFSLWPVGIATVIGLTIGLLQ Q47304 16 16 -
LIFSLWPVGIATVIGLSIGLLQ SPAQ_SHIFL 16 16 -
VILTAPPLGVAVLVGVLTSLLQ O85096 15 15 -
LALAAPLLLVALVTGLIISILQ FLIQ_ECOLI 18 18 -
VILTAPPLAVAVLVGVVTSLLQ Q60237 15 15 -
LALAAPLLLVALITGLIISILQ FLIQ_SALTY 18 18 -
LMISGPLLAIALLVGLIVSIFQ FLIQ_BACSU 18 18 -
LMISLPVLLAGLVVGLLVSIFQ O25964 17 17 -
LALAAPPLMAALLSGLLISLLQ FLIQ_ERWCA 18 18 -
LFTSMPVVLVASVVGVIVSLVQ SSAS_SALTY 18 18 -
IILSAPMLIIALIVGLLISIFQ FLIQ_BORBU 18 18 -
FILSLPTVIAASVIGIIISLVQ O52128 18 18 -
LIISAPPIILASVVGIMVAIFQ O84567 24 24 -
LLLALPVLLSTFVVGLVVSIFQ O67774 18 18 -
VLLVAPVLCTALVVGLIVAIFQ FLIQ_TREPA 19 19 -
LQLCAPVLIVGLVVGVIIGLFQ FLIQ_CAUCR 18 18 -
LLTAGPVLGVALAVGLVIGILQ O85134 18 18 -
MIWILPPLIASVIVGLTIGIIQ P72276 19 19 -
MIWILPPLIASVIVGLTIGIIQ Y4YM_RHISN 18 18 -
LLVSLPAVGVAAIAGLLISFLQ Q52487 18 18 -

Motif 2 width=16
Element Seqn Id St Int Rpt
QTVTQLQEQTLPFGIK Q54013 37 -1 -
QTVTQLQEQTLPFGIK Q57117 37 -1 -
QTVTQLQEQTLPFGIK Q57533 37 -1 -
QTVTQLQEQTLPFGIK SPAQ_SALTY 33 -1 -
QAVMQLQDQTLPFAIK Q46647 36 -1 -
QAVMQLQDQTLPFAIK Q47857 33 -1 -
QALTQIQEQTLGFVIK YSCS_YERPE 39 -1 -
QALTQIQEQTLGFVIK YSCS_YERPS 39 -1 -
QTVTQLQEQTLPFGIK Q47304 37 -1 -
QTVTQLQEQTLPFGIK SPAQ_SHIFL 37 -1 -
QALMQIQDQTLPFGIK O85096 36 -1 -
QAATQINEMTLSFIPK FLIQ_ECOLI 39 -1 -
QALMQIQDQTLPFGIK Q60237 36 -1 -
QAATQINEMTLSFIPK FLIQ_SALTY 39 -1 -
QATTQIQEQTLAFIPK FLIQ_BACSU 39 -1 -
QATTQINEMTLSFVPK O25964 38 -1 -
QAATQINEMTLSFIPK FLIQ_ERWCA 39 -1 -
QALTQIQDQTLQFMIK SSAS_SALTY 39 -1 -
QAITSIQDQTLSFIPK FLIQ_BORBU 39 -1 -
QAITQLQDQTLPFLLK O52128 39 -1 -
QAATQIQEQTFAFAIK O84567 45 -1 -
QAATQIQEMTLSYIPK O67774 39 -1 -
QAVTSIQEQTLTFVPK FLIQ_TREPA 40 -1 -
QALTQIQEATLVYAPK FLIQ_CAUCR 39 -1 -
QAATSINESTLSFVPK O85134 39 -1 -
QAATQIQDESLPLTVK P72276 40 -1 -
QAATQIQDESLPLTVK Y4YM_RHISN 39 -1 -
QAITSLQDSSISHGLK Q52487 39 -1 -

Motif 3 width=23
Element Seqn Id St Int Rpt
KLLGVCLCLFLLSGWYGEVLLSY Q54013 52 -1 -
KLLGVCLCLFLLSGWYGEVLLSY Q57117 52 -1 -
KLLGVCLCLFLLSGWYGEVLLSY Q57533 52 -1 -
KLLGVCLCLFLLSGWYGEVLLSY SPAQ_SALTY 48 -1 -
KLVAVGIALALSGRWIGVELLEL Q46647 51 -1 -
KLVAVGIALALSGRWIGVELLEL Q47857 48 -1 -
KLIAVVVTLFATASWLGNELHSF YSCS_YERPE 54 -1 -
KLIAVVVTLFATASWLGNELHSF YSCS_YERPS 54 -1 -
KLIGVSISLLLLSGWYGEVLLSF Q47304 52 -1 -
KLIGVSISLLLLSGWYGEVLLSF SPAQ_SHIFL 52 -1 -
KLGAVGLTLAMTGRWIGVELIQF O85096 51 -1 -
KIIAVFIAIIIAGPWMLNLLLDY FLIQ_ECOLI 54 -1 -
KLGAVGLTLAMTGRWIGVELIQF Q60237 51 -1 -
KIVAVFIAIIVAGPWMLNLLLDY FLIQ_SALTY 54 -1 -
KIVAVLLALIFFGPWMLSTILSF FLIQ_BACSU 54 -1 -
KILAVIGVLILTMPWMTNMLLDY O25964 53 -1 -
KILTVFFTLVIAGPWMLNLMLDY FLIQ_ERWCA 54 -1 -
KLLAIAITLMVSYPWLSGILLNY SSAS_SALTY 54 -1 -
KIIVILLVIVIFGPWILNKLMQF FLIQ_BORBU 54 -1 -
KIIAVFATLALTYHWMGTTIINF O52128 54 -1 -
KLVVIFGTLMITGGWLCSMILRF O84567 60 -1 -
KVITAFLVIFLLGGWMMRKLVDF O67774 54 -1 -
KMLTILGMIALLGGWMLTMLQNY FLIQ_TREPA 55 -1 -
KIVAIFISLLIFLPLMGSLMSGF FLIQ_CAUCR 54 -1 -
KLAIVLLTMALASSFMLTRMTDY O85134 54 -1 -
KLLVVVAVIGLFAPVLSAPLIEL P72276 55 -1 -
KLLVVVAVIGLFAPVLSAPLIEL Y4YM_RHISN 54 -1 -
KLIIVSLVIVVAAPWGAAAILQF Q52487 54 -1 -