Identifier | TYPE3IMRPROT  [View Relations]  [View Alignment]  
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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
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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).
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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.
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Summary Information | 22 codes involving 4 elements 0 codes involving 3 elements 3 codes involving 2 elements
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Composite Feature Index | |
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 | |
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.
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Scan History | OWL30_2 3 100 NSINGLE SPTR37_9f 2 26 NSINGLE
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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 -
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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 -
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