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
User query: Display/Full Code "ECOLIPORIN"