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PR00183

Identifier
ECOLIPORIN  [View Relations]  [View Alignment]  
Accession
PR00183
No. of Motifs
6
Creation Date
19-MAR-1993  (UPDATE 07-JUN-1999)
Title
E.coli/Salmonella-type porin signature
Database References
PRINTS; PR00182 ECOLNEIPORIN
INTERPRO; IPR001897
PDB; 1OMF
SCOP; 1OMF
CATH; 1OMF
Literature References
1. JAP, B.K. AND WALIAN, P.J.
Biophysics of the structure and function of porins.
Q.REV.BIOPHYS. 23 367-403 (1990).
 
2. NIKAIDO, H.
Porins and specific channels of bacterial outer membranes.
MOL.MICROBIOL. 6 435-442 (1992).
 
3. WEISS, M.S., KREUSCH, A., SCHILTZ, E., NESTEL, U., WELTE, W., 
WECKESSER, J. AND SCHULZ, G.E.
The structure of porin from Rhodobacter casulatus at 1.8A resolution.
FEBS LETT. 280 379-382 (1991).
 
4. PAUPTIT, R.A., SCHIRMER, T., JANSONIUS, J.N., ROSENBUSCH, J.P,
PARKER, M.W., TUCKER, A.D., TSERNOGLOU, D., WIESS, M.S. AND SCHULZ, G.E.
A common channel-forming motif in evolutionarily distant porins
J.STRUCT.BIOL. 107 136-145 (1991).
 
5. KREUSCH, A. AND SCHULZ, G.E. 
Refined structure of the porin from Rhodopseudomonas blastica. 
Comparison with the porin from Rhodobacter capsulatus.
J.MOL.BIOL. 243 891-905 (1994).
 
6. COWAN, S.W.
Bacterial porins: lessons from three high-resolution structures.
CURR.OPIN.STRUCT.BIOL. 3 501-507 (1993).

Documentation
Porins are found in the outer membranes of Gram-negative bacteria,
mitochondria and chloroplasts, where they form ion-selective channels for 
small hydrophilic molecules (up to ~600 Da) [1,2]. X-ray structure analyses
of several bacterial porins [3-5] have revealed a 16-stranded anti-parallel
beta-barrel structure enclosing the transmembrane pore, by contrast with
all other integral membrane proteins described to date, which are alpha-
helical. Three subunits form a trimer; the 3-fold axis is approximately
parallel to the barrel axes and is assumed to be perpendicular to the
membrane plane [6].  
 
From the range of porins now known, similarities have been observed between
porins from different species, and between porins of different specificity
within the same species. But most porins cannot be related to each other on
the basis of sequence alone, and this is reflected in the lengths of the 
known porin sequences, which range from 282-483 residues/monomer.
 
ECOLIPORIN is a 6-element fingerprint that provides a signature for porins
from E.coli, Salmonella, Klebsiella and so on. The fingerprint was derived
from an initial alignment of 4 sequences: the motifs were drawn from
conserved regions spanning virtually the full alignment length. Two
iterations on OWL19.1 were required to reach convergence, at which point
a true set comprising 12 sequences was identified. The fingerprint is
selective for this particular family, and there is no cross-reaction with
porins from Neisseria or with eukaryotic porins.
 
An update on SPTR37_9f identified a true set of 26 sequences, and 1
partial match.
Summary Information
  26 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
6262626262626
5000000
4000000
3000000
2110000
123456
True Positives
NMPC_ECOLI    O85030        O87753        O87754        
OMPC_ECOLI OMPC_KLEPN OMPC_SALTI OMPC_SALTY
OMPC_SERMA OMPF_ECOLI OMPF_SALTI OMPF_SALTY
OMPF_SERMA OMPF_XENNE OMPN_ECOLI OMS1_SALTI
OMS2_SALTI PHOE_CITFR PHOE_ECOLI PHOE_ENTCL
PHOE_KLEOX PHOE_KLEPN PHOE_SALTI PHOE_SALTY
PORI_BPPA2 YEDS_ECOLI
True Positive Partials
Codes involving 2 elements
P77519
Sequence Titles
NMPC_ECOLI  OUTER MEMBRANE PORIN PROTEIN NMPC PRECURSOR - ESCHERICHIA COLI. 
O85030 PORIN OMPN - ESCHERICHIA COLI.
O87753 OMPK35 PORIN PRECURSOR - KLEBSIELLA PNEUMONIAE.
O87754 OMPK37 PORIN PRECURSOR - KLEBSIELLA PNEUMONIAE.
OMPC_ECOLI OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) (OUTER MEMBRANE PROTEIN 1B) - ESCHERICHIA COLI.
OMPC_KLEPN OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) (PORIN OMPK36) - KLEBSIELLA PNEUMONIAE.
OMPC_SALTI OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SALMONELLA TYPHI.
OMPC_SALTY OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SALMONELLA TYPHIMURIUM.
OMPC_SERMA OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SERRATIA MARCESCENS.
OMPF_ECOLI OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBRANE PROTEIN 1A, IA, OR B) - ESCHERICHIA COLI.
OMPF_SALTI OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBRANE PROTEIN S3) - SALMONELLA TYPHI.
OMPF_SALTY OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBRANE PROTEIN 1A, IA, OR B) - SALMONELLA TYPHIMURIUM.
OMPF_SERMA OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) - SERRATIA MARCESCENS.
OMPF_XENNE OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBRANE PROTEIN OPNP) - XENORHABDUS NEMATOPHILUS.
OMPN_ECOLI OUTER MEMBRANE PROTEIN N PRECURSOR (PORIN OMPN) - ESCHERICHIA COLI.
OMS1_SALTI OUTER MEMBRANE PROTEIN S1 PRECURSOR - SALMONELLA TYPHI.
OMS2_SALTI OUTER MEMBRANE PROTEIN S2 PRECURSOR - SALMONELLA TYPHI.
PHOE_CITFR OUTER MEMBRANE PORE PROTEIN E PRECURSOR - CITROBACTER FREUNDII.
PHOE_ECOLI OUTER MEMBRANE PORE PROTEIN E PRECURSOR - ESCHERICHIA COLI.
PHOE_ENTCL OUTER MEMBRANE PORE PROTEIN E PRECURSOR - ENTEROBACTER CLOACAE.
PHOE_KLEOX OUTER MEMBRANE PORE PROTEIN E PRECURSOR - KLEBSIELLA OXYTOCA.
PHOE_KLEPN OUTER MEMBRANE PORE PROTEIN E PRECURSOR - KLEBSIELLA PNEUMONIAE.
PHOE_SALTI OUTER MEMBRANE PORE PROTEIN E PRECURSOR - SALMONELLA TYPHI.
PHOE_SALTY OUTER MEMBRANE PORE PROTEIN E PRECURSOR - SALMONELLA TYPHIMURIUM.
PORI_BPPA2 OUTER MEMBRANE PORIN PROTEIN LC PRECURSOR - BACTERIOPHAGE PA-2.
YEDS_ECOLI POTENTIAL OUTER MEMBRANE PROTEIN YEDS PRECURSOR - ESCHERICHIA COLI.

P77519 FROM BASES 1540626 TO 1550846 (SECTION 134 OF 400) OF THE COMPLETE GENOME (SECTION 134 OF 400) - ESCHERICHIA COLI.
Scan History
OWL19_1    2  100  NSINGLE    
OWL25_3 1 100 NSINGLE
SPTR37_9f 2 27 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
AEIYNKDGNKLDVYGKV PHOE_ECOLI 22 22 -
AEIYNKDGNKLDLFGKV OMPC_SALTI 22 22 -
AEIYNKDSNKLDLYGKV PORI_BPPA2 24 24 -
AEVYNKDGNKLDLYGKV OMPC_ECOLI 22 22 -

Motif 2 width=19
Element Seqn Id St Int Rpt
DGDQSYIRFGFKGETQIND PHOE_ECOLI 51 12 -
DGDQTYMRIGFKGETQVND OMPC_SALTI 51 12 -
DGDTTYARLGFKGETQIND PORI_BPPA2 53 12 -
DGDQTYMRLGFKGETQVTD OMPC_ECOLI 51 12 -

Motif 3 width=23
Element Seqn Id St Int Rpt
TRLAFAGLKYKDLGSFDYGRNLG PHOE_ECOLI 95 25 -
TRVAFAGLKFADAGSFDYGRNYG OMPC_SALTI 94 24 -
THLAFAGLKFGDYGSIDYGRNYG PORI_BPPA2 98 26 -
TRVAFAGLKFQDVGSFDYGRNYG OMPC_ECOLI 94 24 -

Motif 4 width=23
Element Seqn Id St Int Rpt
GLATYRNTDFFGVIDGLNLTLQY PHOE_ECOLI 150 32 -
GYATYRNTDFFGLVDGLDFALQY OMPC_SALTI 148 31 -
GFATYRNNDFFGLVDGLNFAAQY PORI_BPPA2 153 32 -
GFATYRNTDFFGLVDGLNFAVQY OMPC_ECOLI 148 31 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GLKYDANNIYLATFYSET PHOE_ECOLI 234 61 -
GLKYDANNIYLAAQYSQT OMPC_SALTI 243 72 -
GLKYDANNIYLATTYSET PORI_BPPA2 244 68 -
GLKYDANNIYLAAQYTQT OMPC_ECOLI 245 74 -

Motif 6 width=20
Element Seqn Id St Int Rpt
ANKTQNFEAVAQYQFDFGLR PHOE_ECOLI 262 10 -
ANKAQNFEVVAQYQFDFGLR OMPC_SALTI 281 20 -
ANKAQNFEAVAQYQFDFGLR PORI_BPPA2 273 11 -
ANKAQNFEAVAQYQFDFGLR OMPC_ECOLI 274 11 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
AEIYNKDGNKLDLYGKV OMS2_SALTI 22 22 -
AEVYNKDGNKLDLYGKV O85030 22 22 -
AEVYNKDGNKLDLYGKV OMPN_ECOLI 22 22 -
AEIYNKDGNKLDLYGKV O87754 22 22 -
AEIYNKDSNKLDLYGKV NMPC_ECOLI 24 24 -
AEIYNKDGNKLDVYGKV PHOE_ECOLI 22 22 -
AEIYNKDGNKLDLYGKI OMPC_KLEPN 22 22 -
AEIYNKDGNKLDLFGKV OMPC_SALTI 22 22 -
AEIYNKDSNKLDLYGKV PORI_BPPA2 24 24 -
AEIYNKNGNKLDLYGKV OMS1_SALTI 22 22 -
AEIYNKDGNKLDLYGKV OMPF_SERMA 23 23 -
AEVYNKNGNKLDVYGKV PHOE_KLEOX 22 22 -
AEVYNKDGNKLDLYGKV OMPC_ECOLI 22 22 -
AEIYNKDGNKLDLFGKV OMPC_SALTY 22 22 -
AEVYNKNGNKLDVYGKV PHOE_ENTCL 22 22 -
AEVYNKNGNKLDVYGKV PHOE_SALTY 21 21 -
AEVYNKNGNKLDLYGKV PHOE_CITFR 22 22 -
AEVYNKDGNKLDLYGKV YEDS_ECOLI 22 22 -
AEVYNKNANKLDVYGKI PHOE_KLEPN 22 22 -
AEVYNKNGNKLDVYGKV PHOE_SALTI 21 21 -
AEIYNKDGNKVDLYGKA OMPF_ECOLI 23 23 -
AEIYNKDGNKLDLYGKA OMPF_SALTI 23 23 -
AEIYNKDGNKLDLYGKA OMPF_SALTY 23 23 -
AEIYNKNGNKLDFYGKM O87753 23 23 -
AEIYNKDGNKLDLYGKV OMPC_SERMA 22 22 -
AEIFNKDGNKLDLYGKV OMPF_XENNE 22 22 -

Motif 2 width=19
Element Seqn Id St Int Rpt
DGDQTYMRVGFKGETQIND OMS2_SALTI 51 12 -
DGDQSYARLGFKGETQIND O85030 51 12 -
DGDQSYARLGFKGETQIND OMPN_ECOLI 51 12 -
DGDQTYLRFGFKGETQIND O87754 51 12 -
DGDTTYARLGFKGETQIND NMPC_ECOLI 53 12 -
DGDQSYIRFGFKGETQIND PHOE_ECOLI 51 12 -
DGDQTYMRLGVKGETQIND OMPC_KLEPN 51 12 -
DGDQTYMRIGFKGETQVND OMPC_SALTI 51 12 -
DGDTTYARLGFKGETQIND PORI_BPPA2 53 12 -
DGDQSYARIGFKGETQIND OMS1_SALTI 51 12 -
DGDQTYVRFGFKGETQITD OMPF_SERMA 52 12 -
DGDQTYVRFGIKGETQIND PHOE_KLEOX 51 12 -
DGDQTYMRLGFKGETQVTD OMPC_ECOLI 51 12 -
DGDQTYMRIGFKGETQVND OMPC_SALTY 51 12 -
DGDQTYVRFGFKGETQIND PHOE_ENTCL 51 12 -
DGDQSYVRFGFKGETQIND PHOE_SALTY 50 12 -
DGDQSYIRLGFKGETQIND PHOE_CITFR 51 12 -
DGDMSYARIGFKGETQIAD YEDS_ECOLI 51 12 -
DGDQTYVRFGIKGETQINE PHOE_KLEPN 51 12 -
DGDQSYVRFGFKGKTQIND PHOE_SALTI 50 12 -
NGDMTYARLGFKGETQINS OMPF_ECOLI 57 17 -
NADQTYAQIGFKGETQINT OMPF_SALTI 53 13 -
NADQTYAQIGFKGETQINT OMPF_SALTY 53 13 -
SDDTTYARIGLKGETQIND O87753 53 13 -
DGDQSYMRFGLRGETQISD OMPC_SERMA 51 12 -
DGDDSYARIGIKGETQISD OMPF_XENNE 52 13 -

Motif 3 width=23
Element Seqn Id St Int Rpt
TRLAFAGLKFGDYGSFDYGRNYG OMS2_SALTI 95 25 -
TRLAFAGLKFADYGSFDYGRNYG O85030 95 25 -
TRLAFAGLKFADYGSFDYGRNYG OMPN_ECOLI 95 25 -
TRLAFAGIKVGDYGSFDYGRNYG O87754 95 25 -
TRLAFAGLKFGDYGSIDYGRNYG NMPC_ECOLI 98 26 -
TRLAFAGLKYKDLGSFDYGRNLG PHOE_ECOLI 95 25 -
TRLAFAGLKFGDAGSFDYGRNYG OMPC_KLEPN 95 25 -
TRVAFAGLKFADAGSFDYGRNYG OMPC_SALTI 94 24 -
THLAFAGLKFGDYGSIDYGRNYG PORI_BPPA2 98 26 -
TRLGFAGLKFGEYGSFDYGRNYG OMS1_SALTI 95 25 -
TRLGFAGLKFADYGSFDYGRNYG OMPF_SERMA 97 26 -
TRLAFAGVKVKNYGSFDYGRNLG PHOE_KLEOX 94 24 -
TRVAFAGLKFQDVGSFDYGRNYG OMPC_ECOLI 94 24 -
TRVAFAGLKFADAGSFDYGRNYG OMPC_SALTY 94 24 -
TRLAFAGLKLKDFGSLDYGRNLG PHOE_ENTCL 94 24 -
TRLAFAGLKLKDIGSFDYGRNLG PHOE_SALTY 94 25 -
TRLAFAGSKLKNLGSFDYGRNLG PHOE_CITFR 95 25 -
TRLAFAGLGFGQNGTFDYGRNYG YEDS_ECOLI 95 25 -
TRLAFAGVKLKNYGSFDYGRNLG PHOE_KLEPN 95 25 -
TRLAFAGLKLKDIGSFDYGRNLG PHOE_SALTI 94 25 -
TRLAFAGLKYADVGSFDYGRNYG OMPF_ECOLI 103 27 -
VRLAFAGLKYAEVGSIDYGRNYG OMPF_SALTI 98 26 -
VRLAFAGLKYAEVGSIDYGRNYG OMPF_SALTY 98 26 -
TRLAFAGLKAGEYGSFDYGRNYG O87753 96 24 -
TRYGFAGLKFGDYGSFDYGRNTG OMPC_SERMA 95 25 -
TRLAFAGLKFANYGSLDYGRNYR OMPF_XENNE 96 25 -

Motif 4 width=23
Element Seqn Id St Int Rpt
GVATYRNTDFFGLVDGLNFALQY OMS2_SALTI 150 32 -
GVATYRNTDFFGLVNGLNFAVQY O85030 150 32 -
GVATYRNTDFFGLVNGLNFAVQY OMPN_ECOLI 150 32 -
GVATYRNSDFFGLVEGLNFALQY O87754 150 32 -
GVATYRNNDFFGLVDGLNFAAQY NMPC_ECOLI 153 32 -
GLATYRNTDFFGVIDGLNLTLQY PHOE_ECOLI 150 32 -
GVATYRNSDFFGLVDGLNFALQY OMPC_KLEPN 149 31 -
GYATYRNTDFFGLVDGLDFALQY OMPC_SALTI 148 31 -
GFATYRNNDFFGLVDGLNFAAQY PORI_BPPA2 153 32 -
GVATYRNTDFFGLVEGLNFALQY OMS1_SALTI 150 32 -
GVATYRNNNFFGLVDGLNFALQY OMPF_SERMA 152 32 -
GLATYRNTDFFGVVDGLDLTLQY PHOE_KLEOX 149 32 -
GFATYRNTDFFGLVDGLNFAVQY OMPC_ECOLI 148 31 -
GYATYRNTDFFGLVDGLDFALQY OMPC_SALTY 148 31 -
GLATYRNTDFFGAIDGLDMTLQY PHOE_ENTCL 149 32 -
GLATYRNTDFFGIVDGLDLTLQY PHOE_SALTY 149 32 -
GLATYRNTDFFGVVDGLDLTLQY PHOE_CITFR 150 32 -
GVATYRNNGFFGXVDGLNFALQY YEDS_ECOLI 150 32 -
GLATYRNTDFFGLVDGLDLTLQY PHOE_KLEPN 150 32 -
GLATYRNTDFFGIVDGLDLTLQY PHOE_SALTI 149 32 -
GVATYRNSNFFGLVDGLNFAVQY OMPF_ECOLI 157 31 -
GLLTYRNSDFFGLVDGLSFGIQY OMPF_SALTI 155 34 -
GLLTYRNSDFFGLVDGLSFGIQY OMPF_SALTY 155 34 -
GVATYRNSDFFGLVDGLSFALQY O87753 151 32 -
GLATYRNNDFFGLVDGLNFALQY OMPC_SERMA 149 31 -
GLLTYRNTDFFGLVDGLNFRLQY OMPF_XENNE 151 32 -

Motif 5 width=18
Element Seqn Id St Int Rpt
GLKYDANNIYLATMYSET OMS2_SALTI 251 78 -
GLKYDANNIYLATMYSET O85030 244 71 -
GLKYDANNIYLATMYSET OMPN_ECOLI 244 71 -
GLKYDANDIYLATMYSET O87754 249 76 -
GLKYDANNIYLATTYSET NMPC_ECOLI 244 68 -
GLKYDANNIYLATFYSET PHOE_ECOLI 234 61 -
GLKYDANNIYLATQYTQT OMPC_KLEPN 242 70 -
GLKYDANNIYLAAQYSQT OMPC_SALTI 243 72 -
GLKYDANNIYLATTYSET PORI_BPPA2 244 68 -
GAKYDAYNVYLAAMYAET OMS1_SALTI 257 84 -
GAKYDANNVYLAAMYAET OMPF_SERMA 237 62 -
GLKYDANNIYLATMYSET PHOE_KLEOX 232 60 -
GLKYDANNIYLAAQYTQT OMPC_ECOLI 245 74 -
GLKYDANNIYVAAQYFQT OMPC_SALTY 243 72 -
GLKYDANDIYLAAMYSET PHOE_ENTCL 233 61 -
GVKYDANDIYIATFYSET PHOE_SALTY 233 61 -
GLKYDANDIYIATFYSET PHOE_CITFR 234 61 -
GAKYDANNVYLAAMYAET YEDS_ECOLI 256 83 -
GLKYDANNIYLATMYSET PHOE_KLEPN 234 61 -
GVKYDANDIYIATFYSET PHOE_SALTI 233 61 -
GLKYDANNIYLAANYGET OMPF_ECOLI 239 59 -
GAKYDANNVYLAAVYAET OMPF_SALTI 237 59 -
GAKYDANNVYLAAVYAET OMPF_SALTY 237 59 -
SAKYDANNIYAAVMYSQT O87753 233 59 -
GLKYDANDVYLAVMFTQS OMPC_SERMA 244 72 -
GAKYDANNVYLAAMYGET OMPF_XENNE 241 67 -

Motif 6 width=20
Element Seqn Id St Int Rpt
ANKTQNFEVTAQYQFDFGLR OMS2_SALTI 286 17 -
ANKTQNFEVTAQYQFDFGLR O85030 275 13 -
ANKTQNFEVTAQYQFDFGLR OMPN_ECOLI 275 13 -
ANKTQNFEVTAQYQFDFGLR O87754 278 11 -
ANKAQNFEAVAQYQFDFGLR NMPC_ECOLI 273 11 -
ANKTQNFEAVAQYQFDFGLR PHOE_ECOLI 262 10 -
ANKAQNFEVAAQYQFDFGLR OMPC_KLEPN 271 11 -
ANKAQNFEVVAQYQFDFGLR OMPC_SALTI 281 20 -
ANKAQNFEAVAQYQFDFGLR PORI_BPPA2 273 11 -
ANKTQNFEVVAQYQFDFGLR OMS1_SALTI 292 17 -
ASKTQNFEVTAQYQFDFGLR OMPF_SERMA 279 24 -
ANKAQNFEAVAQYQFDFGLR PHOE_KLEOX 260 10 -
ANKAQNFEAVAQYQFDFGLR OMPC_ECOLI 274 11 -
ANKAQNFEVVAQYQFDFGLR OMPC_SALTY 281 20 -
ANKAQNFEVVAQYQFDFGLR PHOE_ENTCL 261 10 -
ANKTQNFEAVIQYQFDFGLR PHOE_SALTY 261 10 -
ANKTQNFEAVVQYQFDFGLR PHOE_CITFR 262 10 -
ANKTQNFEVVAQYQFDFGLR YEDS_ECOLI 294 20 -
ANKAQNFEAVAQYQFDFGLR PHOE_KLEPN 262 10 -
ANKTQNFEAVIQYQFDFGLR PHOE_SALTI 261 10 -
ANKTQDVLLVAQYQFDFGLR OMPF_ECOLI 273 16 -
ANKTQNLEVVAQYQFDFGLR OMPF_SALTI 271 16 -
ANKTQNLEVVAQYQFDFGLR OMPF_SALTY 271 16 -
AGKTQNFEAVVQYQFDFGLR O87753 262 11 -
ANKAQSFEAYAHYQFDFGLR OMPC_SERMA 278 16 -
ANKTQNIELTAQYLFSDLGL OMPF_XENNE 277 18 -