WORKLIST ENTRIES (1):
CLOACIN View alignment View Structure Cloacin signature
Type of fingerprint: COMPOUND with 8 elements
Links:
PRINTS; PR01296 CLOACNIMMNTY; PR01297 LYSISCOLICIN; PR01298 MICROCIN
PRINTS; PR01299 PYOCIN; PR01300 PYOCINKILLER; PR00280 CHANLCOLICIN
Creation date 17-FEB-2000
1. VAN DEN ELZEN, P.J., WALTERS, H.H., VELTKAMP, E. AND NIJKAMP, H.J.
Molecular structure and function of the bacteriocin gene and bacteriocin
protein of plasmid Clo DF13.
NUCLEIC ACIDS RES. 11 2465-2477 (1983).
Colicins are polypeptide toxins produced by, and active against, Escherichia
coli and closely related bacteria. The bacteriocin cloacin DF13 inactivates
ribosomes by hydrolysing 16S RNA in 30S ribosomes at a specific site. The
protein consists of 561 amino acids and has a molecular weight of ~59kD.
Sequence analysis reveals the N-terminal third of the cloacin molecule,
which is involved in translocation of the protein across the cell membrane,
to be relatively hydrophobic and rich in glycine [1]. The C-terminal portion
is rich in positively charged amino acids, possibly reflecting the RNase
activity located within this domain [1]. Sequence comparisons reveal
similarities with colicin E3 and E6, but not with Col E1, despite striking
similarities in codon usage [1].
CLOACIN is an 8-element fingerprint that provides a signature for cloacins.
The fingerprint was derived from an initial alignment of 3 sequences: the
motifs were drawn from conserved regions spanning the central portion of the
alignment - motifs 1-4 were drawn from the domain thought to be involved in
translocation of the protein across the cell membrane; and motifs 5-8 reside
within the domain responsible for the receptor binding activity. Two
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 6 sequences was identified.
SUMMARY INFORMATION
6 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| 6 6 6 6 6 6 6 6
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..
CEA3_ECOLI CEA6_ECOLI CEA2_ECOLI CEAC_ECOLI
CEA9_ECOLI Q51604
PROTEIN TITLES
CEA3_ECOLI COLICIN E3 (EC 3.1.-.-) (COLICIN E3 A CHAIN) (RIBONUCLEASE)
CEA6_ECOLI COLICIN E6 (EC 3.1.-.-) (RIBONUCLEASE) - ESCHERICHIA COLI.
CEA2_ECOLI COLICIN E2 (EC 3.1.21.1) - ESCHERICHIA COLI.
CEAC_ECOLI CLOACIN (EC 3.1.-.-) (RIBONUCLEASE) - ESCHERICHIA COLI.
CEA9_ECOLI COLICIN E9 (EC 3.1.21.1) - ESCHERICHIA COLI.
Q51604 COLICIN E7 - ESCHERICHIA COLI.
SCAN HISTORY
SPTR37_10f 1 30 NSINGLE
INITIAL MOTIF SETS
CLOACIN1 Length of motif = 22 Motif number = 1
Cloacin motif I - 1
PCODE ST INT
AAPVAFGFPALSTPGAGGLAVS CEA3_ECOLI 85 85
AAPVAFGFPALSTPGAGGLAVS CEA6_ECOLI 85 85
ATAMAFGLPALATPGAEGPALS CEAC_ECOLI 94 94
CLOACIN2 Length of motif = 17 Motif number = 2
Cloacin motif II - 1
PCODE ST INT
SAGALSAAIADIMAALK CEA3_ECOLI 108 1
SAGALSAAIADIMAALK CEA6_ECOLI 108 1
SGDALSSAVADVLAALK CEAC_ECOLI 117 1
CLOACIN3 Length of motif = 20 Motif number = 3
Cloacin motif III - 1
PCODE ST INT
FKFGLWGVALYGVLPSQIAK CEA3_ECOLI 127 2
FKFGLWGVALYGVLPSQIAK CEA6_ECOLI 127 2
FKFGLWGIAIYGVLPSEIAK CEAC_ECOLI 136 2
CLOACIN4 Length of motif = 18 Motif number = 4
Cloacin motif IV - 1
PCODE ST INT
SLPADDITESPVSSLPLD CEA3_ECOLI 158 11
SLPADDITESPVSSLPLD CEA6_ECOLI 158 11
SLPADTVTETPASTLPLD CEAC_ECOLI 167 11
CLOACIN5 Length of motif = 20 Motif number = 5
Cloacin motif V - 1
PCODE ST INT
RQNISVVSGVPMSVPVVDAK CEA3_ECOLI 193 17
RQNISVVSGVPMSVPVVDAK CEA6_ECOLI 193 17
RQHIAVVAGRPMSVPVVDAK CEAC_ECOLI 202 17
CLOACIN6 Length of motif = 23 Motif number = 6
Cloacin motif VI - 1
PCODE ST INT
GVFTASIPGAPVLNISVNNSTPA CEA3_ECOLI 218 5
GVFTASIPGAPVLNISVNNSTPA CEA6_ECOLI 218 5
GVFSVSIPGLPALQVSVPKGVPA CEAC_ECOLI 227 5
CLOACIN7 Length of motif = 23 Motif number = 7
Cloacin motif VII - 1
PCODE ST INT
RDAVIRFPKDSGHNAVYVSVSDV CEA3_ECOLI 268 27
RDAVIRFPKDSGHNAVYVSVSDV CEA6_ECOLI 268 27
REAVIRFPKETGQKPVYVSVTDV CEAC_ECOLI 276 26
CLOACIN8 Length of motif = 20 Motif number = 8
Cloacin motif VIII - 1
PCODE ST INT
WDATHPVEAAERNYERARAE CEA3_ECOLI 310 19
WDATHPVEAAERNYERARAE CEA6_ECOLI 310 19
WDAAHPEEGLKREYDKAKAE CEAC_ECOLI 318 19
FINAL MOTIF SETS
CLOACIN1 Length of motif = 22 Motif number = 1
Cloacin motif I - 2
PCODE ST INT
AAPVAFGFPALSTPGAGGLAVS CEA3_ECOLI 85 85
AAPVAFGFPALSTPGAGGLAVS CEA6_ECOLI 85 85
AAPVAFGFPALSTPGAGGLAVS CEA2_ECOLI 85 85
ATAMAFGLPALATPGAEGPALS CEAC_ECOLI 94 94
AAPVAFGFPALSTPGAGGLAVS CEA9_ECOLI 85 85
AAPMAFGFPALAAPGAGTLGIS Q51604 80 80
CLOACIN2 Length of motif = 17 Motif number = 2
Cloacin motif II - 2
PCODE ST INT
SAGALSAAIADIMAALK CEA3_ECOLI 108 1
SAGALSAAIADIMAALK CEA6_ECOLI 108 1
SAGALSAAIADIMAALK CEA2_ECOLI 108 1
SGDALSSAVADVLAALK CEAC_ECOLI 117 1
SASELSAAIAGIIAKLK CEA9_ECOLI 108 1
SGEALSAAIADIFAALK Q51604 103 1
CLOACIN3 Length of motif = 20 Motif number = 3
Cloacin motif III - 2
PCODE ST INT
FKFGLWGVALYGVLPSQIAK CEA3_ECOLI 127 2
FKFGLWGVALYGVLPSQIAK CEA6_ECOLI 127 2
FKFGLWGVALYGVLPSQIAK CEA2_ECOLI 127 2
FKFGLWGIAIYGVLPSEIAK CEAC_ECOLI 136 2
LKFTPFGVVLSSLIPSEIAK CEA9_ECOLI 128 3
FKFSAWGIALYGILPSEIAK Q51604 122 2
CLOACIN4 Length of motif = 18 Motif number = 4
Cloacin motif IV - 2
PCODE ST INT
SLPADDITESPVSSLPLD CEA3_ECOLI 158 11
SLPADDITESPVSSLPLD CEA6_ECOLI 158 11
SLPADDITESPVSSLPLD CEA2_ECOLI 158 11
SLPADTVTETPASTLPLD CEAC_ECOLI 167 11
SLPADDITESPVSSLPLD CEA9_ECOLI 159 11
SLPAETVTNVQVSTLPLD Q51604 153 11
CLOACIN5 Length of motif = 20 Motif number = 5
Cloacin motif V - 2
PCODE ST INT
RQNISVVSGVPMSVPVVDAK CEA3_ECOLI 193 17
RQNISVVSGVPMSVPVVDAK CEA6_ECOLI 193 17
RQNISVVSGVPMSVPVVDAK CEA2_ECOLI 193 17
RQHIAVVAGRPMSVPVVDAK CEAC_ECOLI 202 17
RQNISVVSGVPMSVPVVDAK CEA9_ECOLI 194 17
RQHIAVVAGVPMSVPVVNAK Q51604 188 17
CLOACIN6 Length of motif = 23 Motif number = 6
Cloacin motif VI - 2
PCODE ST INT
GVFTASIPGAPVLNISVNNSTPA CEA3_ECOLI 218 5
GVFTASIPGAPVLNISVNNSTPA CEA6_ECOLI 218 5
GVFTASIPGAPVLNISVNNSTPE CEA2_ECOLI 218 5
GVFSVSIPGLPALQVSVPKGVPA CEAC_ECOLI 227 5
GVFTASIPGAPVLNISVNDSTPA CEA9_ECOLI 219 5
GVFHASFPGVPSLTVSTVKGLPV Q51604 213 5
CLOACIN7 Length of motif = 23 Motif number = 7
Cloacin motif VII - 2
PCODE ST INT
RDAVIRFPKDSGHNAVYVSVSDV CEA3_ECOLI 268 27
RDAVIRFPKDSGHNAVYVSVSDV CEA6_ECOLI 268 27
RDAVIRFPKDSGHNAVYVSVSDV CEA2_ECOLI 268 27
REAVIRFPKETGQKPVYVSVTDV CEAC_ECOLI 276 26
RDAVIRFPKDSGHNAVYVSVSDV CEA9_ECOLI 269 27
HEAVIRFPKESGQKPVYVSVTDV Q51604 263 27
CLOACIN8 Length of motif = 20 Motif number = 8
Cloacin motif VIII - 2
PCODE ST INT
WDATHPVEAAERNYERARAE CEA3_ECOLI 310 19
WDATHPVEAAERNYERARAE CEA6_ECOLI 310 19
WDATHPVEAAERNYERARAE CEA2_ECOLI 310 19
WDAAHPEEGLKREYDKAKAE CEAC_ECOLI 318 19
WDATHPVEAAERNYERARAE CEA9_ECOLI 311 19
WNDAHPVEVAERNYEQARAE Q51604 305 19
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