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PR00953

Identifier
TYPE3IMRPROT  [View Relations]  [View Alignment]  
Accession
PR00953
No. of Motifs
4
Creation Date
04-SEP-1998  (UPDATE 05-APR-2000)
Title
Type III secretion system inner membrane R protein family signature
Database References

PFAM; PF01311 Bac_export_1
INTERPRO; IPR002010
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]. 
One such set of inner membrane proteins, labeled "R" here for nomenclature 
purposes, includes the Salmonella and Shigella SpaR, the Yersinia YscT, 
Rhizobium Y4YN, and the Erwinia HrcT genes [4]. The flagellar protein FliR 
also shares similarity, probably due to evolution of the type III secretion 
system from the flagellar biosynthetic pathway. 
 
TYPE3IMRPROT is a 4-element fingerprint that provides a signature for the
type III secretion system inner membrane R protein family. The fingerprint
was derived from an initial alignment of 7 sequences: the motifs were drawn
from short conserved regions spanning virtually the full alignment length - 
motifs 1 and 2 include the C-terminal portions of putative TM domains 1 and
3; motif 3 encodes putative TM domain 6; and motif 4 includes the N-terminal
residues of putative TM domain 7. Three iterations on OWL30.2 were required 
to reach convergence, at which point a true set comprising 17 sequences was
identified. Several partial matches were also found, all of which are 
homologues that fail to match one or more motifs. 
 
An update on SPTR37_9f identified a true set of 22 sequences, and 3
partial matches.
Summary Information
  22 codes involving  4 elements
0 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
422222222
30000
20213
1234
True Positives
FLIR_BACSU    FLIR_CAUCR    FLIR_ECOLI    FLIR_ERWCA    
FLIR_SALTY FLIR_TREPA O24978 O67773
O84568 O85097 O85135 P72277
Q46648 Q47858 Q52497 Q56786
Q60238 SPAR_SALTY SPAR_SHIFL SSAT_SALTY
Y4YN_RHISN YSCT_YERPS
True Positive Partials
Codes involving 2 elements
FLIR_BORBU O52129 O85641
Sequence Titles
FLIR_BACSU  FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - BACILLUS SUBTILIS. 
FLIR_CAUCR FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - CAULOBACTER CRESCENTUS.
FLIR_ECOLI FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - ESCHERICHIA COLI.
FLIR_ERWCA FLAGELLAR BIOSYNTHETIC PROTEIN FLIR (FLAGELLAR BIOSYNTHETIC PROTEIN MOPE) - ERWINIA CAROTOVORA.
FLIR_SALTY FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - SALMONELLA TYPHIMURIUM.
FLIR_TREPA FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - TREPONEMA PALLIDUM.
O24978 FLAGELLAR BIOSYNTHETIC PROTEIN (FLIR) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O67773 FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - AQUIFEX AEOLICUS.
O84568 YOPT TRANLOCATION T - CHLAMYDIA TRACHOMATIS.
O85097 HRCT - PSEUDOMONAS SYRINGAE (PV. PHASEOLICOLA).
O85135 FLAGELLAR PROTEIN FLIR - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
P72277 NODULATION PROTEIN (NOLX, NOLW, NOLB, NOLT, NOLU, NOLV), PUTATIVE ATPASE (HRCN), HRCQ, HRCR, HRCS, HRCT GENES, COMPLETE CDS AND HRCU (HRCN) - RHIZOBIUM FREDII.
Q46648 HRCT - ERWINIA AMYLOVORA.
Q47858 HRCO, HRCP, HRCQ, HRCR, HRCS, HRCT & HRCU GENES - ERWINIA HERBICOLA.
Q52497 HRPC - BURKHOLDERIA SOLANACEARUM (PSEUDOMONAS SOLANACEARUM).
Q56786 HRPB8 - XANTHOMONAS CAMPESTRIS.
Q60238 HRPX - PSEUDOMONAS SYRINGAE.
SPAR_SALTY SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAR - SALMONELLA TYPHIMURIUM.
SPAR_SHIFL SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAR (SPA29 PROTEIN) - SHIGELLA FLEXNERI, AND SHIGELLA SONNEI.
SSAT_SALTY SECRETION SYSTEM APPARATUS PROTEIN SSAT - SALMONELLA TYPHIMURIUM.
Y4YN_RHISN PROBABLE TRANSLOCATION PROTEIN Y4YN - RHIZOBIUM SP. (STRAIN NGR234).
YSCT_YERPS YOP PROTEINS TRANSLOCATION PROTEIN T - YERSINIA PSEUDOTUBERCULOSIS.

FLIR_BORBU FLAGELLAR BIOSYNTHETIC PROTEIN FLIR - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O52129 ESCT - ESCHERICHIA COLI.
O85641 L0047 - ESCHERICHIA COLI.
Scan History
OWL30_2    3  100  NSINGLE    
SPTR37_9f 2 26 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
RVFALMFTVPLLSVRSVSRVVR JC4509 21 21 -
RLYPCFILVPIFSFNILQGMVR EHHRC6 22 22 -
RILALISTAPVFNERAIGNRVK MOPE_ERWCA 22 22 -
RVGAMVMTMPGIGDQAIPARIR I40671 19 19 -
RVLALISTAPILSERSVPKRVK FLIR_ECOLI 22 22 -
RVRALISTAPILSERAIPKRVK FLIR_SALTY 22 22 -
RVAPIFFFLPFLNSGVLSGAPR SPAR_SALTY 22 22 -
RISAFFVTIPLFGHRNVPAVHR FLIR_BACSU 17 17 -

Motif 2 width=20
Element Seqn Id St Int Rpt
IGLMIGSVLRLFMTSLTTAG I40671 79 38 -
IGIALGFTMQFAFAAVRTAG FLIR_ECOLI 80 36 -
IGIALGFTMQFAFAAVRTAG FLIR_SALTY 80 36 -
VGVMLGCLLSWPFWVMHALG SPAR_SALTY 80 36 -
VGLCLGLIAYMMIAAVQIAG FLIR_BACSU 75 36 -
LGILTGFFISVIFTTFSAAG JC4509 81 38 -
IGILLGLVMSMPFWLFQSVG EHHRC6 82 38 -
IGVTLGLSMQLAFAAIRHAG MOPE_ERWCA 80 36 -

Motif 3 width=23
Element Seqn Id St Int Rpt
FLNGLMLALPLITLLLTLNLALG FLIR_ECOLI 180 80 -
FSHIIIYAGPLVALLLMMDFSIA EHHRC6 184 82 -
FINGLMLALPIITLLLTINLALG MOPE_ERWCA 180 80 -
FSLGVQLAAPVIVFSLVFNLATG I40671 179 80 -
FLNGLMLALPVITLLLTLNLALG FLIR_SALTY 180 80 -
AQNALVLASPVVLVLLLSEVFLG SPAR_SALTY 178 78 -
FIIAFQMSAPVVASLFLVDLALG FLIR_BACSU 178 83 -
FLHAMTIALPIMGALLLIHVSMG JC4509 183 82 -

Motif 4 width=20
Element Seqn Id St Int Rpt
GLVGRIMPAFQIFFVASPLS I40671 201 -1 -
GLLNRMAPQLSIFVIGFPLT FLIR_SALTY 202 -1 -
GLLSRFAPQMNAFAISLTVK SPAR_SALTY 200 -1 -
GIVARTVPQLNVFVVGLPLK FLIR_BACSU 200 -1 -
GLLTKAAPQMNLLSEGLPLT JC4509 205 -1 -
AILSLYSPQLQAFVLSVPAK EHHRC6 206 -1 -
GMLNRVAPQLSIFVVGFPIT MOPE_ERWCA 202 -1 -
GLLNRMAPQLSIFVIGFPLT FLIR_ECOLI 202 -1 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
RVLALISTAPILSERSVPKRVK FLIR_ECOLI 22 22 -
RVRALISTAPILSERAIPKRVK FLIR_SALTY 22 22 -
RIYPCLILMPVFSFNILKGMVR Q46648 22 22 -
RILALISTAPVFNERAIGNRVK FLIR_ERWCA 22 22 -
RLLPCMLLVPAFCFKYLKGPLR O85097 21 21 -
RLYPCFILVPIFSFNILQGMVR Q47858 22 22 -
RLMPCMLLVPAFCFKYLKGPLR Q60238 21 21 -
RVAPIFFFLPFLNSGVLSGAPR SPAR_SALTY 22 22 -
RISAFFVTIPLFGHRNVPAVHR FLIR_BACSU 17 17 -
RLAPLFFFLPFLNNGIISPSIR SPAR_SHIFL 23 23 -
RFMACFVILPVLSKQLLGGVLL YSCT_YERPS 19 19 -
RIGAFLIASPAFGGRFVPLPVR O85135 28 28 -
RALGIMLILPVFTRSQIGGLIR P72277 28 28 -
RALGIMLILPVFTRSQIGGLIR Y4YN_RHISN 28 28 -
RIMTLFSILPATNDQMLTGIAR Q52497 31 31 -
RVFALMFTVPLLSVRSVSRVVR FLIR_TREPA 21 21 -
RPLSLSLLLPLLKSGSLGAALL SSAT_SALTY 18 18 -
RILSMLSIIPFLGAKLFPSPIK O84568 37 37 -
RVFVMFIVLPATAQDSLPGIAR Q56786 28 28 -
RIVSFLFTFPFYGSFLIPNTIR O67773 19 19 -
RVGAMVMTMPGIGDQAIPARIR FLIR_CAUCR 19 19 -
RVSGVLSFFPFFENHLVPLSVR O24978 22 22 -

Motif 2 width=20
Element Seqn Id St Int Rpt
IGIALGFTMQFAFAAVRTAG FLIR_ECOLI 80 36 -
IGIALGFTMQFAFAAVRTAG FLIR_SALTY 80 36 -
IGILLGLLLGMPFWLFQSAG Q46648 82 38 -
IGVTLGLSMQLAFAAIRHAG FLIR_ERWCA 80 36 -
LGTLLGLLLYAPFWMFASVG O85097 81 38 -
IGILLGLVMSMPFWLFQSVG Q47858 82 38 -
LGTLLGLLLYAPFWMFASVG Q60238 81 38 -
VGVMLGCLLSWPFWVMHALG SPAR_SALTY 80 36 -
VGLCLGLIAYMMIAAVQIAG FLIR_BACSU 75 36 -
VGLLLSFCLSLPFWIFHAVG SPAR_SHIFL 81 36 -
LGLLIGFVATIPFWALESAG YSCT_YERPS 79 38 -
VGLSAGLVLTILFSAAALAG O85135 87 37 -
VGVLLGTFLGIPLWGLQAAG P72277 90 40 -
VGVLLGTFLGIPLWGLQAAG Y4YN_RHISN 90 40 -
LGACLGFAASTVFWVAETAG Q52497 90 37 -
LGILTGFFISVIFTTFSAAG FLIR_TREPA 81 38 -
IGFSIGFCAAVPFWAVDMAG SSAT_SALTY 80 40 -
IGVLIGFLFSFPFYAAQSAG O84568 98 39 -
VGLLIGFAASTVFWIAESVG Q56786 87 37 -
FGFSAGLILRLLFDALIIAG O67773 78 37 -
IGLMIGSVLRLFMTSLTTAG FLIR_CAUCR 79 38 -
LGVCASVFLQIVFASLVFAT O24978 80 36 -

Motif 3 width=23
Element Seqn Id St Int Rpt
FLNGLMLALPLITLLLTLNLALG FLIR_ECOLI 180 80 -
FLNGLMLALPVITLLLTLNLALG FLIR_SALTY 180 80 -
FTHIIIYAGPLVALLLLLDFSIA Q46648 184 82 -
FINGLMLALPIITLLLTINLALG FLIR_ERWCA 180 80 -
MQHMLLYAAPFIALLLLIEAAFA O85097 183 82 -
FSHIIIYAGPLVALLLMMDFSIA Q47858 184 82 -
MQHMLLYAAPFIALLLLIEAAFA Q60238 183 82 -
AQNALVLASPVVLVLLLSEVFLG SPAR_SALTY 178 78 -
FIIAFQMSAPVVASLFLVDLALG FLIR_BACSU 178 83 -
ASQAVILASPVMIVLLLSEVLLG SPAR_SHIFL 179 78 -
LLIAAVLAAPLLIAMFLAEFGLA YSCT_YERPS 181 82 -
FLLGLQIMMPVVAALILINVTIG O85135 187 80 -
MRTTLLVSGPVVFFLGLIDISMM P72277 193 83 -
MRTTLLVSGPVVFFLGLIDISMM Y4YN_RHISN 193 83 -
FSTAVKLAAPVMMTMLLIDAGIG Q52497 192 82 -
FLHAMTIALPIMGALLLIHVSMG FLIR_TREPA 183 82 -
YQLCISFSLPAIICMVLADLALG SSAT_SALTY 181 81 -
LIMTIQLSAPAAVAMLMSDLFLG O84568 205 87 -
MAAVVKLSAPVMLVLVLVDLAIG Q56786 189 82 -
FRLGVKIAMPLILTALILNLVLA O67773 177 79 -
FSLGVQLAAPVIVFSLVFNLATG FLIR_CAUCR 179 80 -
FVIGFSMAFPILCLVLLSDIIFG O24978 180 80 -

Motif 4 width=20
Element Seqn Id St Int Rpt
GLLNRMAPQLSIFVIGFPLT FLIR_ECOLI 202 -1 -
GLLNRMAPQLSIFVIGFPLT FLIR_SALTY 202 -1 -
AILSLYSPQLQVFVLSVPAK Q46648 206 -1 -
GMLNRVAPQLSIFVVGFPIT FLIR_ERWCA 202 -1 -
AIIGLYAQQLNVSILAMPAK O85097 205 -1 -
AILSLYSPQLQAFVLSVPAK Q47858 206 -1 -
AIIGLYAQQLNVSILAMPAK Q60238 205 -1 -
GLLSRFAPQMNAFAISLTVK SPAR_SALTY 200 -1 -
GIVARTVPQLNVFVVGLPLK FLIR_BACSU 200 -1 -
GVLSRFAPQMNAFSVSLTIK SPAR_SHIFL 201 -1 -
ALISRFAPSLNVFVLAMPIK YSCT_YERPS 203 -1 -
GIVTRSAPQLNVFSFGFPVT O85135 209 -1 -
MMLRRFAPQFKSGQLSPPIK P72277 215 -1 -
MMLRRFAPQFKSGQLSPPIK Y4YN_RHISN 215 -1 -
GFVARAADKLEPTSLGQPIK Q52497 214 -1 -
GLLTKAAPQMNLLSEGLPLT FLIR_TREPA 205 -1 -
GLLNRSAQQLNVFFFSMPLK SSAT_SALTY 203 -1 -
GIINRMAPQVQVIYLLSALK O84568 227 -1 -
GLVARAADKLEPSNLSQPIR Q56786 211 -1 -
AVVNRFIPQMNVFMVGLPLQ O67773 199 -1 -
GLVGRIMPAFQIFFVASPLS FLIR_CAUCR 201 -1 -
GMIMKTHPQFNLLAIGFPVK O24978 202 -1 -