WORKLIST ENTRIES (1):

SSPAMPROTEIN View alignment     Salmonella surface presentation of antigen gene type M signature
 Type of fingerprint: COMPOUND with 8  elements
Links:
   PRINTS; PR01305 SSPAKPROTEIN; PR01306 SSPANPROTEIN; PR01344 INVEPROTEIN
   INTERPRO; IPR002954

 Creation date 06-JAN-2000

   1. GROISMAN, E.A. AND OCHMAN, H.
   Cognate gene clusters govern invasion of host epithelial cells by 
   Salmonella typhimurium and Shigella flexneri.
   EMBO J. 12 3779-3787 (1993).

   2. COLLAZO, C.M., ZIERLER, M.K. AND GALAN, J.E.
   Functional analysis of the Salmonella typhimurium invasion genes InvI    
   and InVJ and identification of a target of the protein secretion   
   apparatus encoded in the inv locus. 
   MOL.MICROBIOL. 15 25-38 (1995).

   3. LINDBERG, A.A. 
   Vaccination against enteric pathogens: from science to vaccine trials.
   CURR.OPIN.MICROBIOL. 1 116-124 (1998).

   4. BOYD, E.F., LI, J., OCHMAN, H., AND SELANDER, R.K.
   Comparative genetics of the inv-spa invasion gene complex of Salmonella 
   enterica.
   J.BACTERIOL. 179 1985-1991 (1997).

   5. COLLAZO, C.M. AND GALAN, J.E.
   Requirement for exported proteins in secretion through the invasion - 
   associated type III system of Salmonella typhimurium.
   INFECT.IMMUN. 64(9) 3524-3531 (1996).

   The Salmonella typhimurium surface presentation of antigens M gene (SpaM)
   is one of 12 that form a cluster responsible for invasion properties [1].
   The gene product is required for entry by the bacterium into epithelial
   cells, and is thus considered to be a virulence factor [1]. Other Spa genes 
   in the cluster are related to invasion (Inv) genes in similar Salmonella 
   and Shigella species [2], and to flagella biosynthesis genes in Helicobacter
   pylori [3].
       
   A homologue of this protein has been found recently in Salmonella enterica
   [4]. The protein, named InvI, is required by the organism to gain access to
   mammalian epithelial cells, and cellular mutants (InvI-) failed to
   successfully infect these cells. It has also been found that the inv-spa 
   loci of this particular species encode for a type III protein secretion
   system, essential in the bacterium's host cell invasion process [5].
   
   SSPAMPROTEIN is an 8-element fingerprint that provides a signature for the
   spa-inv family of proteins in Salmonella. The fingerprint was derived from
   an initial alignment of 5 sequences: the motifs were drawn from conserved
   regions spanning the full alignment length (~147 amino acid residues). Two
   iterations on SPTR37_10f were required to reach convergence, at which
   point a true set of 12 sequences was identified.

  SUMMARY INFORMATION
     12 codes involving  8 elements
      0 codes involving  7 elements
      0 codes involving  6 elements
      0 codes involving  5 elements
      0 codes involving  4 elements
      0 codes involving  3 elements
      0 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    8|  12   12   12   12   12   12   12   12  
    7|   0    0    0    0    0    0    0    0  
    6|   0    0    0    0    0    0    0    0  
    5|   0    0    0    0    0    0    0    0  
    4|   0    0    0    0    0    0    0    0  
    3|   0    0    0    0    0    0    0    0  
    2|   0    0    0    0    0    0    0    0  
   --+-----------------------------------------
     |   1    2    3    4    5    6    7    8  

True positives..
 Q54047         Q54045         Q54058         Q54055         
 Q54064         Q54062         Q57080         SPAM_SALTY     
 Q54043         Q54049         Q54051         Q57351         


  PROTEIN TITLES
   Q54047           SPAM - SALMONELLA TYPHIMURIUM.
   Q54045           SPAM - SALMONELLA TYPHIMURIUM.
   Q54058           SPAM - SALMONELLA TYPHIMURIUM.
   Q54055           SPAM - SALMONELLA TYPHIMURIUM.
   Q54064           SPAM - SALMONELLA TYPHIMURIUM.
   Q54062           SPAM - SALMONELLA TYPHIMURIUM.
   Q57080           SPAM - SALMONELLA TYPHIMURIUM.
   SPAM_SALTY       SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAM (INVASION PROT
   Q54043           SPAM - SALMONELLA TYPHIMURIUM.
   Q54049           SPAM - SALMONELLA TYPHIMURIUM.
   Q54051           SPAM - SALMONELLA TYPHIMURIUM.
   Q57351           SPAM - SALMONELLA TYPHIMURIUM.

SCAN HISTORY SPTR37_10f 2 30 NSINGLE INITIAL MOTIF SETS SSPAMPROTEIN1 Length of motif = 13 Motif number = 1 Salmonella SPAM motif I - 1 PCODE ST INT QRRCTVFHSQCES SPAM_SALTY 11 11 QRRCTVFHSQCES Q54043 11 11 QRRCTVFHSQCES Q54047 11 11 QRRCTVFHSQCES Q54062 11 11 QRRCTVFHSQCES Q54064 11 11 SSPAMPROTEIN2 Length of motif = 13 Motif number = 2 Salmonella SPAM motif II - 1 PCODE ST INT RYQDEDRGLQAEE SPAM_SALTY 27 3 RYQDEDRGLQAEE Q54043 27 3 RYQDEDRRLQVEE Q54047 27 3 RYQDEDRRLQAEE Q54062 27 3 RYQDEDRRLQAEE Q54064 27 3 SSPAMPROTEIN3 Length of motif = 14 Motif number = 3 Salmonella SPAM motif III - 1 PCODE ST INT DTLRAENRQLSREE SPAM_SALTY 54 14 DTLRAENRQLSREE Q54043 54 14 DTLRAENRQLSREE Q54047 54 14 DTLRAENRQLSREE Q54062 54 14 DTLRAENRQLSREE Q54064 54 14 SSPAMPROTEIN4 Length of motif = 9 Motif number = 4 Salmonella SPAM motif IV - 1 PCODE ST INT RKQSIVRRQ SPAM_SALTY 73 5 RKQSIVRRQ Q54043 73 5 RKQSIVRRQ Q54047 73 5 RKQSIVRRQ Q54062 73 5 RKQSIVRRQ Q54064 73 5 SSPAMPROTEIN5 Length of motif = 12 Motif number = 5 Salmonella SPAM motif V - 1 PCODE ST INT EKRSELEKKREE SPAM_SALTY 94 10 EKRSELEKKREE Q54043 94 10 EKRSELEKKREE Q54047 94 10 EKRDELEKKRQE Q54062 94 10 EKRYELEKKRQE Q54064 94 10 SSPAMPROTEIN6 Length of motif = 7 Motif number = 6 Salmonella SPAM motif VI - 1 PCODE ST INT QKKSKYW SPAM_SALTY 107 1 QKKSKYW Q54043 107 1 QEKSKYW Q54047 107 1 QEKSKYW Q54062 107 1 QEKSKYW Q54064 107 1 SSPAMPROTEIN7 Length of motif = 9 Motif number = 7 Salmonella SPAM motif VII - 1 PCODE ST INT RKEGNYQRW SPAM_SALTY 115 1 RKEGNYQRW Q54043 115 1 RKEGNYQRW Q54047 115 1 RKEGNYQRW Q54062 115 1 RKEGNYQRW Q54064 115 1 SSPAMPROTEIN8 Length of motif = 10 Motif number = 8 Salmonella SPAM motif VIII - 1 PCODE ST INT IQQEEAESEE SPAM_SALTY 136 12 IQQEEAESEE Q54043 136 12 IQQEEAESEE Q54047 136 12 IQQEEAESEE Q54062 136 12 IQQEEAESEE Q54064 136 12 FINAL MOTIF SETS SSPAMPROTEIN1 Length of motif = 13 Motif number = 1 Salmonella SPAM motif I - 2 PCODE ST INT QRRCTVFHSQCES Q54045 11 11 QRRCTVFHSQCES Q54047 11 11 QRRCTVFHSQCES Q54058 11 11 QRRCTVFHSQCES Q54055 11 11 QRRCTVFHSQCES Q54064 11 11 QRRCTVFHSQCES Q54062 11 11 QRRCTVFHSQCES Q57080 11 11 QRRCTVFHSQCES Q54043 11 11 QRRCTVFHSQCES SPAM_SALTY 11 11 QRRCTVFHSQCES Q54049 11 11 QRRCTVFHSQCES Q54051 11 11 QRRCTVFHSQCES Q57351 11 11 SSPAMPROTEIN2 Length of motif = 13 Motif number = 2 Salmonella SPAM motif II - 2 PCODE ST INT RYQDEDRRLQVEE Q54045 27 3 RYQDEDRRLQVEE Q54047 27 3 RYQDEDRRLQDEE Q54058 27 3 RYQDEDRRLQAEE Q54055 27 3 RYQDEDRRLQAEE Q54064 27 3 RYQDEDRRLQAEE Q54062 27 3 RYQDEDRRLQDEE Q57080 27 3 RYQDEDRGLQAEE Q54043 27 3 RYQDEDRGLQAEE SPAM_SALTY 27 3 RYQDEDRRLQAEE Q54049 27 3 RYQDEDRRLQAEE Q54051 27 3 RYQDEDRMLHAEE Q57351 27 3 SSPAMPROTEIN3 Length of motif = 14 Motif number = 3 Salmonella SPAM motif III - 2 PCODE ST INT DTLRAENRQLSREE Q54045 54 14 DTLRAENRQLSREE Q54047 54 14 DTLRAENRQLSREE Q54058 54 14 DTLRAENRQLSREE Q54055 54 14 DTLRAENRQLSREE Q54064 54 14 DTLRAENRQLSREE Q54062 54 14 DTLRAENRQLSREE Q57080 54 14 DTLRAENRQLSREE Q54043 54 14 DTLRAENRQLSREE SPAM_SALTY 54 14 DTLRAEKRLLSREE Q54049 54 14 DTLRAEKRLLSREE Q54051 54 14 DTLRAENRQLSREE Q57351 54 14 SSPAMPROTEIN4 Length of motif = 9 Motif number = 4 Salmonella SPAM motif IV - 2 PCODE ST INT RKQSIVRRQ Q54045 73 5 RKQSIVRRQ Q54047 73 5 RKQSIVRRQ Q54058 73 5 RKQSIVRRQ Q54055 73 5 RKQSIVRRQ Q54064 73 5 RKQSIVRRQ Q54062 73 5 RKQSIVRRQ Q57080 73 5 RKQSIVRRQ Q54043 73 5 RKQSIVRRQ SPAM_SALTY 73 5 RKQSIIRRQ Q54049 73 5 RKQSIIRRQ Q54051 73 5 RRQSIVRRQ Q57351 73 5 SSPAMPROTEIN5 Length of motif = 12 Motif number = 5 Salmonella SPAM motif V - 2 PCODE ST INT EKRSELEKKREE Q54045 94 10 EKRSELEKKREE Q54047 94 10 EKRYELEKKREE Q54058 94 10 EQRDELEKKREE Q54055 94 10 EKRYELEKKRQE Q54064 94 10 EKRDELEKKRQE Q54062 94 10 EKRYELEKKREE Q57080 94 10 EKRSELEKKREE Q54043 94 10 EKRSELEKKREE SPAM_SALTY 94 10 EKRNELEKKREE Q54049 94 10 EKLNELEKKREE Q54051 94 10 EKRCELEKKTQE Q57351 94 10 SSPAMPROTEIN6 Length of motif = 7 Motif number = 6 Salmonella SPAM motif VI - 2 PCODE ST INT QEKSKYW Q54045 107 1 QEKSKYW Q54047 107 1 QEKSKYW Q54058 107 1 QEKSKYW Q54055 107 1 QEKSKYW Q54064 107 1 QEKSKYW Q54062 107 1 QEKSKYW Q57080 107 1 QKKSKYW Q54043 107 1 QKKSKYW SPAM_SALTY 107 1 QEKSKYW Q54049 107 1 QEKSKYW Q54051 107 1 QEKSKYW Q57351 107 1 SSPAMPROTEIN7 Length of motif = 9 Motif number = 7 Salmonella SPAM motif VII - 2 PCODE ST INT RKEGNYQRW Q54045 115 1 RKEGNYQRW Q54047 115 1 RKEGNYQRW Q54058 115 1 RKEGNYQRW Q54055 115 1 RKEGNYQRW Q54064 115 1 RKEGNYQRW Q54062 115 1 RKEGNYQRW Q57080 115 1 RKEGNYQRW Q54043 115 1 RKEGNYQRW SPAM_SALTY 115 1 RKEGNYQRW Q54049 115 1 RKEGNYQRW Q54051 115 1 RKEGNYQRW Q57351 115 1 SSPAMPROTEIN8 Length of motif = 10 Motif number = 8 Salmonella SPAM motif VIII - 2 PCODE ST INT IQQEEAESEE Q54045 136 12 IQQEEAESEE Q54047 136 12 IQQEEAESEE Q54058 136 12 IQQEEAESEE Q54055 136 12 IQQEEAESEE Q54064 136 12 IQQEEAESEE Q54062 136 12 IQQEEAESEE Q57080 136 12 IQQEEAESEE Q54043 136 12 IQQEEAESEE SPAM_SALTY 136 12 IQQEEAESEE Q54049 136 12 IQQEEAESEE Q54051 136 12 IQQEEAESEE Q57351 136 12

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