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PR01297

Identifier
LYSISCOLICIN  [View Relations]  [View Alignment]  
Accession
PR01297
No. of Motifs
3
Creation Date
17-FEB-2000
Title
Colicin lysis protein signature
Database References
Literature References
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). 

Documentation
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 Feature Index
3171717
2011
123
True Positives
LYS0_ECOLI    LYS1_CITFR    LYS2_ECOLI    LYS3_ECOLI    
LYS3_SHISO LYS4_ECOLI LYS5_ECOLI LYS6_ECOLI
LYS7_ECOLI LYS8_ECOLI LYS9_ECOLI O52991
Q46785 Q47111 Q47127 Q51611
Q57131
True Positive Partials
Codes involving 2 elements
O24683
Sequence Titles
LYS0_ECOLI  LYSIS PROTEIN PRECURSOR (PROTEIN H) - ESCHERICHIA COLI. 
LYS1_CITFR LYSIS PROTEIN FOR COLICIN A PRECURSOR - CITROBACTER FREUNDII.
LYS2_ECOLI LYSIS PROTEIN FOR COLICINS E2 AND E3 PRECURSOR - ESCHERICHIA COLI.
LYS3_ECOLI LYSIS PROTEIN FOR COLICIN E1 PRECURSOR - ESCHERICHIA COLI.
LYS3_SHISO LYSIS PROTEIN FOR COLICIN E1* PRECURSOR - SHIGELLA SONNEI.
LYS4_ECOLI LYSIS PROTEIN FOR COLICIN N PRECURSOR - ESCHERICHIA COLI.
LYS5_ECOLI LYSIS PROTEIN FOR COLICIN E5 PRECURSOR - ESCHERICHIA COLI.
LYS6_ECOLI LYSIS PROTEIN FOR COLICIN E6 PRECURSOR - ESCHERICHIA COLI.
LYS7_ECOLI LYSIS PROTEIN FOR COLICIN E7 PRECURSOR - ESCHERICHIA COLI.
LYS8_ECOLI LYSIS PROTEIN FOR COLICIN E8 PRECURSOR - ESCHERICHIA COLI.
LYS9_ECOLI LYSIS PROTEIN FOR COLICIN E9 PRECURSOR - ESCHERICHIA COLI.
O52991 COLICIN D-157 LYSIS PROTEIN - ESCHERICHIA COLI.
Q46785 COLICIN K LYSIS PROTEIN - ESCHERICHIA COLI.
Q47111 LYSIS PROTEIN PRECURSOR - ESCHERICHIA COLI.
Q47127 COLICIN 10 LYSIS PROTEIN - ESCHERICHIA COLI.
Q51611 KIL PROTEIN - ESCHERICHIA COLI.
Q57131 COLICIN 5 LYSIS PROTEIN - ESCHERICHIA COLI.

O24683 COLICIN U LYTIC PROTEIN - SHIGELLA BOYDII.
Scan History
SPTR37_10f 2  100  NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
IILLLLAAIILAAC LYS9_ECOLI 7 7 -
IILLLLAAIILAAC LYS5_ECOLI 7 7 -
IILLLLAVIILAAC LYS6_ECOLI 7 7 -
IILLLLAAIILAAC LYS7_ECOLI 7 7 -
IILLLLAVIILAAC LYS8_ECOLI 7 7 -
IILLLLAVIILSAC LYS2_ECOLI 7 7 -
IIIFLITILFCSGC Q46785 3 3 -
FFVGIFAINLLVGC LYS3_ECOLI 5 5 -
LFILIVSGFLLVAC LYS0_ECOLI 9 9 -
SMILVLAVLCLTAC O52991 8 8 -
ILLILFFIMTLSAC LYS4_ECOLI 5 5 -
ICVILLAIMLLAAC LYS1_CITFR 6 6 -

Motif 2 width=16
Element Seqn Id St Int Rpt
CQANYIRDVQGGTVSP LYS9_ECOLI 20 -1 -
CQANYIHDVQGGTVSP LYS5_ECOLI 20 -1 -
CQANYIRDVQGGTVSP LYS6_ECOLI 20 -1 -
CQANYIRDVQGGTVSP LYS7_ECOLI 20 -1 -
CQANYIRDVQGGTVSP LYS8_ECOLI 20 -1 -
CQANYIRDVQGGTVSP LYS2_ECOLI 20 -1 -
CQANYIRDVQGGTVAP Q46785 16 -1 -
CQANYIRDVQGGTIAP LYS3_ECOLI 18 -1 -
CQANYIRDVQGGTVAP LYS0_ECOLI 22 -1 -
CQANYVRDVQGGTIAP O52991 21 -1 -
CQVNHIRDVKGGTVAP LYS4_ECOLI 18 -1 -
CQVNNVRDTGGGSVSP LYS1_CITFR 19 -1 -

Motif 3 width=11
Element Seqn Id St Int Rpt
SSAELTGLATQ LYS9_ECOLI 37 1 -
SSAELTGLATQ LYS5_ECOLI 37 1 -
STAELTGVETQ LYS6_ECOLI 37 1 -
STAELTGVETQ LYS7_ECOLI 37 1 -
STAEVTGLATQ LYS8_ECOLI 37 1 -
STAEVTGLATQ LYS2_ECOLI 37 1 -
SSSELTGIAVQ Q46785 33 1 -
SSSKLTGIAVQ LYS3_ECOLI 35 1 -
SSSELTGIAVQ LYS0_ECOLI 39 1 -
SSSKLIGVAVQ O52991 38 1 -
SSSRLTGLKLS LYS4_ECOLI 35 1 -
PSSIVTGVSMG LYS1_CITFR 34 -1 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
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 -

Motif 2 width=16
Element Seqn Id St Int Rpt
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 -

Motif 3 width=11
Element Seqn Id St Int Rpt
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 -