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PR01022

Identifier
OUTRMMBRANEA  [View Relations]  [View Alignment]  
Accession
PR01022
No. of Motifs
7
Creation Date
08-DEC-1998  (UPDATE 28-JUL-1999)
Title
Outer membrane protein A signature
Database References
PRINTS; PR01021 OMPADOMAIN
PFAM; PF00691 OmpA
INTERPRO; IPR002368
Literature References
1. DE MOT, R., SCHOOFS, G., ROELANDT, A., DECLERCK, P., PROOST, P.,
VAN DAMME, J. AND VANDERLEYDEN, J.
Molecular characterization of the major outer-membrane protein OprF from
plant root-colonizing Pseudomonas fluorescens.
MICROBIOLOGY 140(6) 1377-87 (1994). 
 
2. HARDHAM, J.M. AND STAMM, L.V.
Identification and characterization of the Treponema pallidum tpn50 gene,
an ompA homolog.
INFECT.IMMUN. 62 1015-1025 (1994).
 
3. CHEN, R., SCHMIDMAYR, W., KRAMER, C., CHEN-SCHMEISSER, U. AND HENNING, U.
Primary structure of major outer membrane protein II (ompA protein) of
Escherichia coli K-12.
PROC.NATL.ACAD.SCI.U.S.A. 77 4592-4596 (1980). 
 
4. FREUDL, R. AND COLE, S.T.
Cloning and molecular characterization of the ompA gene from Salmonella
typhimurium.
EUR.J.BIOCHEMISTRY 134 497-502 (1983). 

Documentation
The outer membrane proteins of several Gram-negative organisms share a 
C-terminal domain of about 45 residues [1,2]: these include, outer membrane
protein ompA from enterobacteria such as E.coli; outer membrane protein P5
from Haemophilus influenzae; outer membrane protein P.III/class IV from 
Neisseria; outer membrane porin F (gene oprF) from Pseudomonas; protein
TpN50 from Treponema pallidum; peptidoglycan-associated lipoprotein (gene 
pal) from Escherichia coli, Haemophilus influenzae, Legionella pneumophila
and Pseudomonas putida; outer membrane lipoprotein P6 from Haemophilus 
influenzae; Escherichia coli hypothetical lipoprotein yiaD; and Vibrio 
parahaemolyticus sodium-type flagellar protein motY.
 
Apart from this domain, these proteins are not otherwise structurally 
related: most are porin-like integral membrane proteins (such as ompA),
but some are small lipid-anchored proteins (such as pal).
 
The amino acid sequence of major outer membrane protein II (ompA) from
E.coli K-12 has been determined [3]. The polypeptide contains 325 residues,
the transmembrane (TM) component being located between residues 1-177. In 
this region, a predominantly lipophilic 27-residue segment exists that may
span the membrane in a mostly alpha-helical conformation, or a 19-residue 
stretch of this segment might traverse the membrane linearly [3]. Inside 
the outer membrane, there exists an -APAPAPAP- sequence that, by analogy 
with the -CPPCP- sequence in the hinge region of immunoglobulin, could 
assume a polyproline helical conformation [3]. 
 
OmpA is required for the action of colicins K and L, and for stabilisation 
of mating aggregates in conjugation [4]. The protein serves as a receptor
for a number of phages, and also acts as a porin with low permeability,
allowing slow penetration of small solutes [4]. The size of the OmpA channel
is thought to be rather similar to that of E.coli OmpF and OmpC porins 
(i.e., about 1nm in diameter). 
 
OUTRMMBRANEA is a 7-element fingerprint that provides a signature for
outer membrane protein A. The fingerprint was derived from an initial
alignment of 10 sequences: the motifs were drawn from conserved regions
spanning the central and C-teminal portions of the alignment, focusing on
those regions that characterise ompA proteins but distinguish them from
general ompA-domain containing polypeptides - motif 1 encodes the fifth
putative TM region; motif 2 includes the C-terminal portion of putative TM 
domain 7; motif 3 spans putative TM domain 8; and motif 6 lies within the
ompA domain, and encodes part of the region encoded by PROSITE pattern OMPA
(PS01068). Two iterations on OWL30.2 were required to reach convergence,
at which point a true set comprising 18 sequences was identified. Several
partial matches were also found, all of which are outer membrane protein 
AII or P5 homologues.
 
An update on SPTR37_9f identified a true set of 6 sequences, and 8
partial matches.
Summary Information
   6 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
5 codes involving 4 elements
3 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
76666666
60000000
50000000
40045155
30023103
20000000
1234567
True Positives
OMPA_ECOLI    OMPA_ENTAE    OMPA_KLEPN    OMPA_SALTY    
OMPA_SERMA OMPA_SHIDY
True Positive Partials
Codes involving 4 elements
O51841 OM51_HAEIN OM52_HAEIN OM53_HAEIN
Q44299
Codes involving 3 elements
P96773 P96774 Q44298
Sequence Titles
OMPA_ECOLI  OUTER MEMBRANE PROTEIN A PRECURSOR (OUTER MEMBRANE PROTEIN II*) - ESCHERICHIA COLI. 
OMPA_ENTAE OUTER MEMBRANE PROTEIN A PRECURSOR - ENTEROBACTER AEROGENES (AEROBACTER AEROGENES).
OMPA_KLEPN OUTER MEMBRANE PROTEIN A PRECURSOR (OUTER MEMBRANE PROTEIN II) - KLEBSIELLA PNEUMONIAE.
OMPA_SALTY OUTER MEMBRANE PROTEIN A PRECURSOR (OUTER MEMBRANE PROTEIN 33K) (OUTER MEMBRANE MAJOR HEAT-MODIFIABLE PROTEIN) - SALMONELLA TYPHIMURIUM.
OMPA_SERMA OUTER MEMBRANE PROTEIN A PRECURSOR - SERRATIA MARCESCENS.
OMPA_SHIDY OUTER MEMBRANE PROTEIN A PRECURSOR (OUTER MEMBRANE PROTEIN II) - SHIGELLA DYSENTERIAE.

O51841 OUTER MEMBRANE PROTEIN 34 PRECURSOR - ACTINOBACILLUS ACTINOMYCETEMCOMITANS (HAEMOPHILUS ACTINOMYCETEMCOMITANS).
OM51_HAEIN OUTER MEMBRANE PROTEIN P5 PRECURSOR (OMP P5) - HAEMOPHILUS INFLUENZAE.
OM52_HAEIN OUTER MEMBRANE PROTEIN P5 PRECURSOR (OMP P5) - HAEMOPHILUS INFLUENZAE.
OM53_HAEIN OUTER MEMBRANE PROTEIN P5 PRECURSOR (OMP P5) (FIMBRIN) - HAEMOPHILUS INFLUENZAE.
Q44299 OUTER MEMBRANE PROTEIN PRECURSOR - AEROMONAS SALMONICIDA.

P96773 MAJOR OUTER MEMBRANE PROTEIN - HAEMOPHILUS DUCREYI.
P96774 OMPA2 - HAEMOPHILUS DUCREYI.
Q44298 OUTER MEMBRANE PROTEIN PRECURSOR - AEROMONAS SALMONICIDA.
Scan History
OWL30_2    2  50   NSINGLE    
SPTR37_9f 3 50 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
PITDDLDIYTRLGGMVW OMPA_ENTAE 111 111 -
PITDDLDVYTRLGGMVW OMPA_SHIDY 107 107 -
PITDDLDIYTRLGGMVW OMPA_KLEPN 8 8 -
PITDDLDIYTRLGGMVW OMPA_ECOLI 107 107 -
PITDDLDIYTRLGGMVW OMPA_CITFR 8 8 -
PIYDDLDIYTRLGGMVW OMPA_ESCBL 8 8 -
PITDDLDIYTRLGGMVW OMPA_ESCFE 8 8 -
PITDELDIYTRLGGMVW OMPA_ESCHE 8 8 -
PIADDLDIYTRLGGMVW OMPA_SERMA 114 114 -
PITDDLDFYTRLGGMVW OMPA_SALTY 107 107 -

Motif 2 width=15
Element Seqn Id St Int Rpt
VNNIGDAGTVGTRPD OMPA_KLEPN 71 46 -
TNNIGDAHTIGTRPD OMPA_ECOLI 165 41 -
VSNIGDAGTVGARPD OMPA_SERMA 177 46 -
VNNIGDAGTVGVRPD OMPA_ENTAE 169 41 -
TNNIGDANTVGGRPD OMPA_CITFR 66 41 -
INNIGDAGTVGTRPD OMPA_ESCBL 69 44 -
TNNIGDANTIGTRPD OMPA_ESCFE 71 46 -
TNNIGDANTVGTRPD OMPA_ESCHE 70 45 -
TNNIGDANTIGTRPD OMPA_SALTY 169 45 -
TNNIGDAHTIGTRPD OMPA_SHIDY 170 46 -

Motif 3 width=15
Element Seqn Id St Int Rpt
DNGLLSVGVSYRFGQ OMPA_CITFR 80 -1 -
DNGMLSVGVSYRFGQ OMPA_ESCBL 83 -1 -
DNGLLSLGVSYRFGQ OMPA_ESCFE 85 -1 -
DNGLLSVGVSYRFGQ OMPA_ESCHE 84 -1 -
DNGMLSLGVSYRFGQ OMPA_ECOLI 179 -1 -
DNGMLSLGVSYRFGQ OMPA_KLEPN 85 -1 -
DNGLLSLGVSYRFGQ OMPA_SHIDY 184 -1 -
DNGLLSVGVSYRFGQ OMPA_SALTY 183 -1 -
DNGMLSVGVSYRFGQ OMPA_ENTAE 183 -1 -
DNTMLSLGVSYRFGQ OMPA_SERMA 191 -1 -

Motif 4 width=16
Element Seqn Id St Int Rpt
TTKTFTLKSDVLFNFN OMPA_ENTAE 215 17 -
ETKRFTLKSDVLFNFN OMPA_SERMA 222 16 -
QTKHFTLKSDVLFNFN OMPA_ESCHE 117 18 -
QTKHFTLKSDVLFNFN OMPA_ESCFE 117 17 -
QTKHFTLKSDVLFNFN OMPA_ESCBL 115 17 -
QTKHFTLKSDVLFNFN OMPA_CITFR 112 17 -
QTKHFTLKSDVLFNFN OMPA_ECOLI 211 17 -
ATKHFTLKSDVLFNFN OMPA_KLEPN 117 17 -
QTKHFTLKSDVLFNFN OMPA_SHIDY 216 17 -
QTKHFTLKSDVLFNFN OMPA_SALTY 215 17 -

Motif 5 width=20
Element Seqn Id St Int Rpt
QLYTQLSSMDPKDGSVVVLG OMPA_SERMA 251 13 -
QLYTQLSNMDPKDGSAVVLG OMPA_ENTAE 244 13 -
QMYTQLSNLDPKDGSVVVLG OMPA_ESCHE 146 13 -
QLYSQLSNLDPKDGSVVVLG OMPA_ESCFE 146 13 -
QLYTQLSNLDPKDGAVVVLG OMPA_ESCBL 144 13 -
QMYSQLSNLDPKDGSVVVLG OMPA_CITFR 141 13 -
QLYIQLSNLDPKDGSVVVLG OMPA_SALTY 244 13 -
QLYSQLSNLDPKDGSVVVLG OMPA_SHIDY 245 13 -
QLYTQLSNMDPKDGSAVVLG OMPA_KLEPN 146 13 -
QLYSQLSNLDPKDGSVVVLG OMPA_ECOLI 240 13 -

Motif 6 width=20
Element Seqn Id St Int Rpt
QSVVDYLISKGIPADKISAR OMPA_ESCFE 185 19 -
QSVVDYLISKGIPSDKISAR OMPA_CITFR 180 19 -
QSVVDYLISKGIPADKISAR OMPA_ECOLI 279 19 -
QSVVDYLVAKGIPAGKISAR OMPA_KLEPN 185 19 -
QSVVDYLISKGIPADKISAR OMPA_SHIDY 284 19 -
QSVVDYLISKGIPSDKISAR OMPA_SALTY 283 19 -
QSVVDYLVAKGIPANKISAR OMPA_ENTAE 283 19 -
QSVVDYLVSKGIPSDKISAR OMPA_SERMA 290 19 -
QSVVDYLISKGIPSDKISAR OMPA_ESCHE 185 19 -
QSVVDYLVSKGIPAGKITAQ OMPA_ESCBL 183 19 -

Motif 7 width=14
Element Seqn Id St Int Rpt
NVKARAALIDCLAP OMPA_CITFR 214 14 -
NVKKRAALIDCLAP OMPA_ESCBL 217 14 -
SGRATKAQIVCLAP OMPA_SERMA 326 16 -
NVKARAALIDCLAP OMPA_ENTAE 317 14 -
NVKPRAALIDCLAP OMPA_SALTY 317 14 -
NVKQRAALIDCLAP OMPA_SHIDY 318 14 -
NVKARAALIDCLAP OMPA_KLEPN 219 14 -
NVKQRAALIDCLAP OMPA_ECOLI 313 14 -
NVKQRAALIDCLAP OMPA_ESCFE 219 14 -
NVKPRAALIDCLAP OMPA_ESCHE 219 14 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
PITDDLDIYTRLGGMVW OMPA_ECOLI 107 107 -
PITDDLDIYTRLGGMVW OMPA_KLEPN 8 8 -
PITDDLDVYTRLGGMVW OMPA_SHIDY 107 107 -
PITDDLDFYTRLGGMVW OMPA_SALTY 107 107 -
PITDDLDIYTRLGGMVW OMPA_ENTAE 111 111 -
PIADDLDIYTRLGGMVW OMPA_SERMA 114 114 -

Motif 2 width=15
Element Seqn Id St Int Rpt
TNNIGDAHTIGTRPD OMPA_ECOLI 165 41 -
VNNIGDAGTVGTRPD OMPA_KLEPN 71 46 -
TNNIGDAHTIGTRPD OMPA_SHIDY 170 46 -
TNNIGDANTIGTRPD OMPA_SALTY 169 45 -
VNNIGDAGTVGVRPD OMPA_ENTAE 169 41 -
VSNIGDAGTVGARPD OMPA_SERMA 177 46 -

Motif 3 width=15
Element Seqn Id St Int Rpt
DNGMLSLGVSYRFGQ OMPA_ECOLI 179 -1 -
DNGMLSLGVSYRFGQ OMPA_KLEPN 85 -1 -
DNGLLSLGVSYRFGQ OMPA_SHIDY 184 -1 -
DNGLLSVGVSYRFGQ OMPA_SALTY 183 -1 -
DNGMLSVGVSYRFGQ OMPA_ENTAE 183 -1 -
DNTMLSLGVSYRFGQ OMPA_SERMA 191 -1 -

Motif 4 width=16
Element Seqn Id St Int Rpt
QTKHFTLKSDVLFNFN OMPA_ECOLI 211 17 -
ATKHFTLKSDVLFNFN OMPA_KLEPN 117 17 -
QTKHFTLKSDVLFNFN OMPA_SHIDY 216 17 -
QTKHFTLKSDVLFNFN OMPA_SALTY 215 17 -
TTKTFTLKSDVLFNFN OMPA_ENTAE 215 17 -
ETKRFTLKSDVLFNFN OMPA_SERMA 222 16 -

Motif 5 width=20
Element Seqn Id St Int Rpt
QLYSQLSNLDPKDGSVVVLG OMPA_ECOLI 240 13 -
QLYTQLSNMDPKDGSAVVLG OMPA_KLEPN 146 13 -
QLYSQLSNLDPKDGSVVVLG OMPA_SHIDY 245 13 -
QLYIQLSNLDPKDGSVVVLG OMPA_SALTY 244 13 -
QLYTQLSNMDPKDGSAVVLG OMPA_ENTAE 244 13 -
QLYTQLSSMDPKDGSVVVLG OMPA_SERMA 251 13 -

Motif 6 width=20
Element Seqn Id St Int Rpt
QSVVDYLISKGIPADKISAR OMPA_ECOLI 279 19 -
QSVVDYLVAKGIPAGKISAR OMPA_KLEPN 185 19 -
QSVVDYLISKGIPADKISAR OMPA_SHIDY 284 19 -
QSVVDYLISKGIPSDKISAR OMPA_SALTY 283 19 -
QSVVDYLVAKGIPANKISAR OMPA_ENTAE 283 19 -
QSVVDYLVSKGIPSDKISAR OMPA_SERMA 290 19 -

Motif 7 width=14
Element Seqn Id St Int Rpt
NVKQRAALIDCLAP OMPA_ECOLI 313 14 -
NVKARAALIDCLAP OMPA_KLEPN 219 14 -
NVKQRAALIDCLAP OMPA_SHIDY 318 14 -
NVKPRAALIDCLAP OMPA_SALTY 317 14 -
NVKARAALIDCLAP OMPA_ENTAE 317 14 -
SGRATKAQIVCLAP OMPA_SERMA 326 16 -