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PR00281

Identifier
HOKGEFTOXIC  [View Relations]  [View Alignment]  
Accession
PR00281
No. of Motifs
2
Creation Date
18-JUL-1994  (UPDATE 27-JUN-1999)
Title
Hok/Gef cell toxic protein family signature
Database References

PROSITE; PS00556 HOK_GEF
BLOCKS; BL00556
INTERPRO; IPR000021
Literature References
1. GOLUB, E.I. AND PANZER, H.A.
The factor F of Escherichia coli carries a locus of stable plasmid 
inheritance stm, similar to the parB locus of plasmid RI.
MOL.GEN.GENET. 214(2) 353-357 (1988).
 
2. SAKIKAWA, T., AKIMOTO, S. AND OHNISHI, Y.
The pnd gene in E.coli plasmid R16: nucleotide sequence and gene expression
leading to cell Mg2+ release and stable RNA degradation.
BIOCHIM.BIOPHYS.ACTA 1007 158-166 (1989).
 
3. POULSEN, L.K., REFN, A., MOLIN, S. AND ANDERSSON, P.
Topographic analysis of the toxic Gef protein from Escherichia coli.
MOL.MICROBIOL. 5 1627-1637 (1991).

Documentation
The hok/gef family of Gram-negative bacterial proteins are toxic to cells
when over-expressed, killing the cells from within by interfering with a
vital function in the cell membrane [1]. Some family members (flm) increase
the stability of unstable RNA [1], some (pnd) induce the degradation of
stable RNA at higher than optimium growth temperatures [2], and others
affect the release of cellular magnesium by membrane alterations [2]. The
proteins are short (50-70 residues), consisting of an N-terminal hydro-
phobic (possibly membrane spanning) domain, and a C-terminal periplasmic
region, which contains the toxic domain. The C-terminal region contains a
conserved cysteine residue that mediates homo-dimerisation in the gef
protein, although dimerisation is not neccessary for the toxic effect [3].
 
HOKGEFTOXIC is a 2-element fingerprint that provides a signature for the
hok/gef family. The fingerprint was derived from an initial alignment of 6
sequences: motif 1 includes the hydrophobic, putative transmembrane region;
and motif 2 contains the periplasmic toxic region - together they span the
region encoded by PROSITE pattern HOK_GEF (PS00556), which contains the
conserved Cys residue involved in homo-dimerisation in the gef protein. Two
iterations on OWL23.2 were required to reach convergence, at which point a
true set comprising 7 sequences was identified.
 
An update on SPTR37_9f identified a true set of 11 sequences.
Summary Information
11 codes involving  2 elements
Composite Feature Index
21111
12
True Positives
FLMA_ECOLI    GEF_ECOLI     HOK_ECOLI     PND1_ECOLI    
PND2_ECOLI Q47655 RELF_ECOLI SRNB_ECOLI
YBDY_ECOLI YDCB_ECOLI YIAZ_ECOLI
Sequence Titles
FLMA_ECOLI  STABLE PLASMID INHERITANCE PROTEIN (F LEADING MAINTENANCE PROTEIN) - ESCHERICHIA COLI. 
GEF_ECOLI GEF PROTEIN - ESCHERICHIA COLI.
HOK_ECOLI HOK PROTEIN - ESCHERICHIA COLI.
PND1_ECOLI PND PROTEIN - ESCHERICHIA COLI.
PND2_ECOLI PND PROTEIN - ESCHERICHIA COLI.
Q47655 F FACTOR (STM) - ESCHERICHIA COLI.
RELF_ECOLI RELF PROTEIN - ESCHERICHIA COLI.
SRNB_ECOLI SRNB PROTEIN - ESCHERICHIA COLI.
YBDY_ECOLI HYPOTHETICAL 5.6 KD PROTEIN IN NFNB-ENTD INTERGENIC REGION - ESCHERICHIA COLI.
YDCB_ECOLI HYPOTHETICAL 5.6 KD PROTEIN IN CYBB-TRG INTERGENIC REGION - ESCHERICHIA COLI.
YIAZ_ECOLI HYPOTHETICAL 6.0 KD PROTEIN IN CSPA-GLYS INTERGENIC REGION - ESCHERICHIA COLI.
Scan History
OWL23_2    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
SLVWCVLIVCLTLLIFTYL FLMA_ECOLI 7 7 -
SLVWCVLIVCLTLLIFTYL HOK_ECOLI 7 7 -
TFLMMLIVVCVTILCFVWM PND1_ECOLI 5 5 -
AMLIALIVICLTVIVTALV RELF_ECOLI 6 6 -
YALIGLLAVCATVLCFSLI SRNB_ECOLI 23 23 -
AMIVALIVICITAVVAALV GEF_ECOLI 6 6 -

Motif 2 width=23
Element Seqn Id St Int Rpt
RKSLCEIRYRDGYREVAAFMAYE FLMA_ECOLI 27 1 -
RKSLCEIRYRDGHREVAAFMAYE HOK_ECOLI 27 1 -
RDSLCGFRIEQGNTVLVATLAYE PND1_ECOLI 25 1 -
RKDLCEVRIRTDQTEVAVFTAYE RELF_ECOLI 26 1 -
RERLCELNIHRGNTVVQVTLAYE SRNB_ECOLI 43 1 -
RKDLCEVHIRTGQTEVAVFTAYE GEF_ECOLI 26 1 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
SLVWCVLIVCLTLLIFTYL FLMA_ECOLI 7 7 -
SLVWCVLIVCLTLLIFTYL HOK_ECOLI 7 7 -
SLVWCVLIVCLTLLIFTYL Q47655 7 7 -
TFLMMLIVVCVTILCFVWM PND1_ECOLI 5 5 -
TFLMMLIVICVTILCFVWM PND2_ECOLI 5 5 -
AMLIALIVICLTVIVTALV RELF_ECOLI 6 6 -
YRLLSLIVICFTLLFFTWM YIAZ_ECOLI 5 5 -
PLVVCLLIICITILTFTLL YDCB_ECOLI 5 5 -
YALAAVIVLCLTVLGFTLL YBDY_ECOLI 5 5 -
YALIGLLAVCATVLCFSLI SRNB_ECOLI 23 23 -
AMIVALIVICITAVVAALV GEF_ECOLI 6 6 -

Motif 2 width=23
Element Seqn Id St Int Rpt
RKSLCEIRYRDGYREVAAFMAYE FLMA_ECOLI 27 1 -
RKSLCEIRYRDGHREVAAFMAYE HOK_ECOLI 27 1 -
RKSLCEIRYRDGYREVAAGYREV Q47655 27 1 -
RDSLCGFRIEQGNTVLVATLAYE PND1_ECOLI 25 1 -
RDSLCGLRLQQGNTVLVATLAYE PND2_ECOLI 25 1 -
RKDLCEVRIRTDQTEVAVFTAYE RELF_ECOLI 26 1 -
RDSLCELHIKQESYELAAFLACK YIAZ_ECOLI 25 1 -
RQTLYELRFRDGDKEVAALMACT YDCB_ECOLI 25 1 -
GDSLCEFTVKERNIEFKAVLAYE YBDY_ECOLI 25 1 -
RERLCELNIHRGNTVVQVTLAYE SRNB_ECOLI 43 1 -
RKDLCEVHIRTGQTEVAVFTAYE GEF_ECOLI 26 1 -