WORKLIST ENTRIES (1):

ECOLIPORIN View alignment View Structure      E.coli/Salmonella-type porin signature
 Type of fingerprint: COMPOUND with 6  elements
Links:
   PRINTS; PR00182 ECOLNEIPORIN; PR00184 NEISSPPORIN; PR00185 EUKARYTPORIN
   INTERPRO; IPR001897
   PDB; 1OMF 3Dinfo
   SCOP; 1OMF
   CATH; 1OMF

 Creation date 19-MAR-1993; UPDATE 07-JUN-1999

   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).

   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 FINGERPRINT INDEX
  
    6|  26   26   26   26   26   26  
    5|   0    0    0    0    0    0  
    4|   0    0    0    0    0    0  
    3|   0    0    0    0    0    0  
    2|   1    1    0    0    0    0  
   --+-------------------------------
     |   1    2    3    4    5    6  

True positives..
 OMS2_SALTI     O85030         OMPN_ECOLI     O87754         
 NMPC_ECOLI     PHOE_ECOLI     OMPC_KLEPN     OMPC_SALTI     
 PORI_BPPA2     OMS1_SALTI     OMPF_SERMA     PHOE_KLEOX     
 OMPC_ECOLI     OMPC_SALTY     PHOE_ENTCL     PHOE_SALTY     
 PHOE_CITFR     YEDS_ECOLI     PHOE_KLEPN     PHOE_SALTI     
 OMPF_ECOLI     OMPF_SALTI     OMPF_SALTY     O87753         
 OMPC_SERMA     OMPF_XENNE     
Subfamily:  Codes involving 2 elements
 Subfamily True positives..
 P77519         


  PROTEIN TITLES
   OMS2_SALTI       OUTER MEMBRANE PROTEIN S2 PRECURSOR - SALMONELLA TYPHI.
   O85030           PORIN OMPN - ESCHERICHIA COLI.
   OMPN_ECOLI       OUTER MEMBRANE PROTEIN N PRECURSOR (PORIN OMPN) - ESCHERICHI
   O87754           OMPK37 PORIN PRECURSOR - KLEBSIELLA PNEUMONIAE.
   NMPC_ECOLI       OUTER MEMBRANE PORIN PROTEIN NMPC PRECURSOR - ESCHERICHIA CO
   PHOE_ECOLI       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - ESCHERICHIA COLI.
   OMPC_KLEPN       OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) (PORIN OMPK3
   OMPC_SALTI       OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SALMONELLA
   PORI_BPPA2       OUTER MEMBRANE PORIN PROTEIN LC PRECURSOR - BACTERIOPHAGE PA
   OMS1_SALTI       OUTER MEMBRANE PROTEIN S1 PRECURSOR - SALMONELLA TYPHI.
   OMPF_SERMA       OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) - SERRATIA M
   PHOE_KLEOX       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - KLEBSIELLA OXYTOCA
   OMPC_ECOLI       OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) (OUTER MEMBR
   OMPC_SALTY       OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SALMONELLA
   PHOE_ENTCL       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - ENTEROBACTER CLOAC
   PHOE_SALTY       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - SALMONELLA TYPHIMU
   PHOE_CITFR       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - CITROBACTER FREUND
   YEDS_ECOLI       POTENTIAL OUTER MEMBRANE PROTEIN YEDS PRECURSOR - ESCHERICHI
   PHOE_KLEPN       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - KLEBSIELLA PNEUMON
   PHOE_SALTI       OUTER MEMBRANE PORE PROTEIN E PRECURSOR - SALMONELLA TYPHI.
   OMPF_ECOLI       OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBR
   OMPF_SALTI       OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBR
   OMPF_SALTY       OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBR
   O87753           OMPK35 PORIN PRECURSOR - KLEBSIELLA PNEUMONIAE.
   OMPC_SERMA       OUTER MEMBRANE PROTEIN C PRECURSOR (PORIN OMPC) - SERRATIA M
   OMPF_XENNE       OUTER MEMBRANE PROTEIN F PRECURSOR (PORIN OMPF) (OUTER MEMBR
 
   P77519           FROM BASES 1540626 TO 1550846 (SECTION 134 OF 400) OF THE CO

SCAN HISTORY OWL19_1 2 100 NSINGLE OWL25_3 1 100 NSINGLE SPTR37_9f 2 27 NSINGLE INITIAL MOTIF SETS ECOLIPORIN1 Length of motif = 17 Motif number = 1 E.coli porin motif I - 1 PCODE ST INT AEIYNKDGNKLDVYGKV PHOE_ECOLI 22 22 AEVYNKDGNKLDLYGKV OMPC_ECOLI 22 22 AEIYNKDGNKLDLFGKV OMPC_SALTI 22 22 AEIYNKDSNKLDLYGKV PORI_BPPA2 24 24 ECOLIPORIN2 Length of motif = 19 Motif number = 2 E.coli porin motif II - 1 PCODE ST INT DGDQSYIRFGFKGETQIND PHOE_ECOLI 51 12 DGDQTYMRLGFKGETQVTD OMPC_ECOLI 51 12 DGDQTYMRIGFKGETQVND OMPC_SALTI 51 12 DGDTTYARLGFKGETQIND PORI_BPPA2 53 12 ECOLIPORIN3 Length of motif = 23 Motif number = 3 E.coli porin motif III - 1 PCODE ST INT TRLAFAGLKYKDLGSFDYGRNLG PHOE_ECOLI 95 25 TRVAFAGLKFQDVGSFDYGRNYG OMPC_ECOLI 94 24 TRVAFAGLKFADAGSFDYGRNYG OMPC_SALTI 94 24 THLAFAGLKFGDYGSIDYGRNYG PORI_BPPA2 98 26 ECOLIPORIN4 Length of motif = 23 Motif number = 4 E.coli porin motif IV - 1 PCODE ST INT GLATYRNTDFFGVIDGLNLTLQY PHOE_ECOLI 150 32 GFATYRNTDFFGLVDGLNFAVQY OMPC_ECOLI 148 31 GYATYRNTDFFGLVDGLDFALQY OMPC_SALTI 148 31 GFATYRNNDFFGLVDGLNFAAQY PORI_BPPA2 153 32 ECOLIPORIN5 Length of motif = 18 Motif number = 5 E.coli porin motif V - 1 PCODE ST INT GLKYDANNIYLATFYSET PHOE_ECOLI 234 61 GLKYDANNIYLAAQYTQT OMPC_ECOLI 245 74 GLKYDANNIYLAAQYSQT OMPC_SALTI 243 72 GLKYDANNIYLATTYSET PORI_BPPA2 244 68 ECOLIPORIN6 Length of motif = 20 Motif number = 6 E.coli porin motif VI - 1 PCODE ST INT ANKTQNFEAVAQYQFDFGLR PHOE_ECOLI 262 10 ANKAQNFEAVAQYQFDFGLR OMPC_ECOLI 274 11 ANKAQNFEVVAQYQFDFGLR OMPC_SALTI 281 20 ANKAQNFEAVAQYQFDFGLR PORI_BPPA2 273 11 FINAL MOTIF SETS ECOLIPORIN1 Length of motif = 17 Motif number = 1 E.coli porin motif I - 2 PCODE ST INT 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 ECOLIPORIN2 Length of motif = 19 Motif number = 2 E.coli porin motif II - 2 PCODE ST INT 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 ECOLIPORIN3 Length of motif = 23 Motif number = 3 E.coli porin motif III - 2 PCODE ST INT 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 ECOLIPORIN4 Length of motif = 23 Motif number = 4 E.coli porin motif IV - 2 PCODE ST INT 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 ECOLIPORIN5 Length of motif = 18 Motif number = 5 E.coli porin motif V - 2 PCODE ST INT 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 ECOLIPORIN6 Length of motif = 20 Motif number = 6 E.coli porin motif VI - 2 PCODE ST INT 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

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