WORKLIST ENTRIES (1):

LYSISCOLICIN View alignment     Colicin lysis protein signature
 Type of fingerprint: COMPOUND with 3  elements
Links:
   PRINTS; PR01295 CLOACIN; PR01296 CLOACNIMMNTY; PR01298 MICROCIN
   PRINTS; PR01299 PYOCIN; PR01300 PYOCINKILLER

 Creation date 17-FEB-2000

   1. COLE, S.T., SAINT-JOANIS, B. AND PUGSLEY, A.P.
   Molecular characterisation of the colicin E2 operon and identification
   of its products.
   MOL.GEN.GENET. 198 465-472 (1985). 

   2. WALEH, N.S. AND JOHNSON, P.H.
   Structural and functional organization of the colicin E1 operon.
   PROC.NATL.ACAD.SCI.U.S.A. 82 8389-8393 (1985). 

   3. VAN DEN ELZEN, P.J., GAASTRA, W., SPELT, C.E., DE GRAAF, F.K., VELTKAMP,
   E. AND NIJKAMP, H.J.
   Molecular structure of the immunity gene and immunity protein of the
   bacteriocinogenic plasmid Clo DF13.
   NUCLEIC ACIDS RES. 8 4349-4363 (1980). 

   The DNA sequence of the entire colicin E2 operon has been determined [1].
   The operon comprises the colicin activity gene (ceaB), the colicin immunity
   gene (ceiB) and the lysis gene (celB), which is essential for colicin
   release from producing cells [1]. A putative LexA binding site is located
   upstream from ceaB, and a rho-independent terminator structure is located
   downstream from celB [1]. Comparison of the amino acid sequences of colicin
   E2 and cloacin DF13 reveal extensive similarity. These colicins have
   different modes of action and recognise different cell surface receptors;
   the two major regions of heterology at the C-terminus, and in the C-terminal
   end of the central region are thought to correspond to the catalytic and 
   receptor-recognition domains, respectively [1]. 
  
   Sequence similarities between colicins E2, A and E1 [2] are less striking.
   The colicin E2 (pyocin) immunity protein does not share similarity with
   either the colicin E3 or cloacin DF13 [3] immunity proteins. By contrast,
   the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost
   identical except in the N-terminal regions, which themselves are similar to
   lipoprotein signal peptides [1]. Processing of the ColE2 prolysis protein
   to the mature form is prevented by globomycin, a specific inhibitor of the
   lipoprotein signal peptidase [1]. The mature ColE2 lysis protein is located
   in the cell envelope [1].
  
   LYSISCOLICIN is a 3-element fingerprint that provides a signature for 
   colcin lysis proteins. The fingerprint was derived from an initial alignment
   of 12 sequences: the motifs were drawn from conserved regions spanning the
   full alignment length - motif lies within the putative signal sequence; and
   motifs 2 and 3 span the rest of the polypeptide chain. Two iterations on
   SPTR37_10f were required to reach convergence, at which point a true set
   comprising 17 sequences was identified. A single partial match was also
   found, O24683, a colicin U lytic protein from Shigella boydii that fails
   to match motif 1.

  SUMMARY INFORMATION
     17 codes involving  3 elements
      1 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    3|  17   17   17  
    2|   0    1    1  
   --+----------------
     |   1    2    3  

True positives..
 LYS9_ECOLI     LYS5_ECOLI     LYS7_ECOLI     LYS6_ECOLI     
 Q47111         LYS8_ECOLI     LYS2_ECOLI     Q57131         
 Q47127         Q46785         LYS3_ECOLI     LYS0_ECOLI     
 LYS3_SHISO     Q51611         O52991         LYS4_ECOLI     
 LYS1_CITFR     
Subfamily:  Codes involving 2 elements
 Subfamily True positives..
 O24683         


  PROTEIN TITLES
   LYS9_ECOLI       LYSIS PROTEIN FOR COLICIN E9 PRECURSOR - ESCHERICHIA COLI.
   LYS5_ECOLI       LYSIS PROTEIN FOR COLICIN E5 PRECURSOR - ESCHERICHIA COLI.
   LYS7_ECOLI       LYSIS PROTEIN FOR COLICIN E7 PRECURSOR - ESCHERICHIA COLI.
   LYS6_ECOLI       LYSIS PROTEIN FOR COLICIN E6 PRECURSOR - ESCHERICHIA COLI.
   Q47111           LYSIS PROTEIN PRECURSOR - ESCHERICHIA COLI.
   LYS8_ECOLI       LYSIS PROTEIN FOR COLICIN E8 PRECURSOR - ESCHERICHIA COLI.
   LYS2_ECOLI       LYSIS PROTEIN FOR COLICINS E2 AND E3 PRECURSOR - ESCHERICHIA
   Q57131           COLICIN 5 LYSIS PROTEIN - ESCHERICHIA COLI.
   Q47127           COLICIN 10 LYSIS PROTEIN - ESCHERICHIA COLI.
   Q46785           COLICIN K LYSIS PROTEIN - ESCHERICHIA COLI.
   LYS3_ECOLI       LYSIS PROTEIN FOR COLICIN E1 PRECURSOR - ESCHERICHIA COLI.
   LYS0_ECOLI       LYSIS PROTEIN PRECURSOR (PROTEIN H) - ESCHERICHIA COLI.
   LYS3_SHISO       LYSIS PROTEIN FOR COLICIN E1* PRECURSOR - SHIGELLA SONNEI.
   Q51611           KIL PROTEIN - ESCHERICHIA COLI.
   O52991           COLICIN D-157 LYSIS PROTEIN - ESCHERICHIA COLI.
   LYS4_ECOLI       LYSIS PROTEIN FOR COLICIN N PRECURSOR - ESCHERICHIA COLI.
   LYS1_CITFR       LYSIS PROTEIN FOR COLICIN A PRECURSOR - CITROBACTER FREUNDII
 
   O24683           COLICIN U LYTIC PROTEIN - SHIGELLA BOYDII.

SCAN HISTORY SPTR37_10f 2 100 NSINGLE INITIAL MOTIF SETS LYSISCOLICIN1 Length of motif = 14 Motif number = 1 Colicin lysis protein motif I - 1 PCODE ST INT LFILIVSGFLLVAC LYS0_ECOLI 9 9 ICVILLAIMLLAAC LYS1_CITFR 6 6 IILLLLAVIILSAC LYS2_ECOLI 7 7 FFVGIFAINLLVGC LYS3_ECOLI 5 5 ILLILFFIMTLSAC LYS4_ECOLI 5 5 IILLLLAAIILAAC LYS5_ECOLI 7 7 IILLLLAVIILAAC LYS6_ECOLI 7 7 IILLLLAAIILAAC LYS7_ECOLI 7 7 IILLLLAVIILAAC LYS8_ECOLI 7 7 IILLLLAAIILAAC LYS9_ECOLI 7 7 IIIFLITILFCSGC Q46785 3 3 SMILVLAVLCLTAC O52991 8 8 LYSISCOLICIN2 Length of motif = 16 Motif number = 2 Colicin lysis protein motif II - 1 PCODE ST INT CQANYIRDVQGGTVAP LYS0_ECOLI 22 -1 CQVNNVRDTGGGSVSP LYS1_CITFR 19 -1 CQANYIRDVQGGTVSP LYS2_ECOLI 20 -1 CQANYIRDVQGGTIAP LYS3_ECOLI 18 -1 CQVNHIRDVKGGTVAP LYS4_ECOLI 18 -1 CQANYIHDVQGGTVSP LYS5_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS6_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS7_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS8_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS9_ECOLI 20 -1 CQANYIRDVQGGTVAP Q46785 16 -1 CQANYVRDVQGGTIAP O52991 21 -1 LYSISCOLICIN3 Length of motif = 11 Motif number = 3 Colicin lysis protein motif III - 1 PCODE ST INT SSSELTGIAVQ LYS0_ECOLI 39 1 PSSIVTGVSMG LYS1_CITFR 34 -1 STAEVTGLATQ LYS2_ECOLI 37 1 SSSKLTGIAVQ LYS3_ECOLI 35 1 SSSRLTGLKLS LYS4_ECOLI 35 1 SSAELTGLATQ LYS5_ECOLI 37 1 STAELTGVETQ LYS6_ECOLI 37 1 STAELTGVETQ LYS7_ECOLI 37 1 STAEVTGLATQ LYS8_ECOLI 37 1 SSAELTGLATQ LYS9_ECOLI 37 1 SSSELTGIAVQ Q46785 33 1 SSSKLIGVAVQ O52991 38 1 FINAL MOTIF SETS LYSISCOLICIN1 Length of motif = 14 Motif number = 1 Colicin lysis protein motif I - 2 PCODE ST INT IILLLLAAIILAAC LYS9_ECOLI 7 7 IILLLLAAIILAAC LYS5_ECOLI 7 7 IILLLLAVIILAAC LYS6_ECOLI 7 7 IILLLLAAIILAAC LYS7_ECOLI 7 7 IILLLFAAIILAAC Q47111 7 7 IILLLLAVIILAAC LYS8_ECOLI 7 7 IILLLLAVIILSAC LYS2_ECOLI 7 7 IIIFLITILFLSGC Q57131 3 3 ITFLIITILSLSGC Q47127 3 3 IIIFLITILFCSGC Q46785 3 3 FFVGIFAINLLVGC LYS3_ECOLI 5 5 LFILIVSGFLLVAC LYS0_ECOLI 9 9 FFVGIFAINLLVGC LYS3_SHISO 5 5 FFVGIFAINLLVGC Q51611 5 5 SMILVLAVLCLTAC O52991 8 8 ILLILFFIMTLSAC LYS4_ECOLI 5 5 ICVILLAIMLLAAC LYS1_CITFR 6 6 LYSISCOLICIN2 Length of motif = 16 Motif number = 2 Colicin lysis protein motif II - 2 PCODE ST INT CQANYIRDVQGGTVSP LYS9_ECOLI 20 -1 CQANYIHDVQGGTVSP LYS5_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS6_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS7_ECOLI 20 -1 CQANYIRDVQGGTVSP Q47111 20 -1 CQANYIRDVQGGTVSP LYS8_ECOLI 20 -1 CQANYIRDVQGGTVSP LYS2_ECOLI 20 -1 CQANYIRDVQGGTVAP Q57131 16 -1 CQANYIRDVQGGTVAP Q47127 16 -1 CQANYIRDVQGGTVAP Q46785 16 -1 CQANYIRDVQGGTIAP LYS3_ECOLI 18 -1 CQANYIRDVQGGTVAP LYS0_ECOLI 22 -1 CQANYIRDVQGGTVAP LYS3_SHISO 18 -1 CQANYIPDVQGGTIAP Q51611 18 -1 CQANYVRDVQGGTIAP O52991 21 -1 CQVNHIRDVKGGTVAP LYS4_ECOLI 18 -1 CQVNNVRDTGGGSVSP LYS1_CITFR 19 -1 LYSISCOLICIN3 Length of motif = 11 Motif number = 3 Colicin lysis protein motif III - 2 PCODE ST INT SSAELTGLATQ LYS9_ECOLI 37 1 SSAELTGLATQ LYS5_ECOLI 37 1 STAELTGVETQ LYS6_ECOLI 37 1 STAELTGVETQ LYS7_ECOLI 37 1 STAELTGVETQ Q47111 37 1 STAEVTGLATQ LYS8_ECOLI 37 1 STAEVTGLATQ LYS2_ECOLI 37 1 SSSELTGIAVQ Q57131 33 1 SSSELTGIAVQ Q47127 33 1 SSSELTGIAVQ Q46785 33 1 SSSKLTGIAVQ LYS3_ECOLI 35 1 SSSELTGIAVQ LYS0_ECOLI 39 1 SSSKLTGISVQ LYS3_SHISO 35 1 SSSKLTGIAVQ Q51611 35 1 SSSKLIGVAVQ O52991 38 1 SSSRLTGLKLS LYS4_ECOLI 35 1 PSSIVTGVSMG LYS1_CITFR 34 -1

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