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PR01180

Identifier
ARGDCRBXLASE  [View Relations]  [View Alignment]  
Accession
PR01180
No. of Motifs
9
Creation Date
18-SEP-1999
Title
Arginine decarboxylase signature
Database References
PRINTS; PR01179 ODADCRBXLASE
INTERPRO; IPR002985
Literature References
1. MARTIN, C., CAMI, B., YEH, P., STRAGIER, P., PARSOT, C. AND PATTE, J.-C.
Pseudomonas aeruginosa diaminopimelate decarboxylase: evolutionary 
relationship with other amino acid decarboxylases.
MOL.BIOL.EVOL. 5 549-559 (1988).
 
2. SANDMEIER, E., HALE, T.I. AND CHRISTEN, P.
Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid
decarboxylases. 
EUR.J.BIOCHEMISTRY 221 997-1002 (1994).
 
3. RASTOGI, R., DULSON, J. AND ROTHSTEIN, S.J.
Cloning of tomato (Lycopersicon esculentum Mill.) arginine decarboxylase
gene and its expression during fruit ripening.
PLANT PHYSIOL. 103 829-834 (1993). 
 
4. POULIN, R., LU, L., ACKERMANN, B., BEY, P. AND PEGG, A.E.
Mechanism of the irreversible inactivation of mouse ornithine decarboxylase
by alpha-difluoromethylornithine. Characterization of sequences at the
inhibitor and coenzyme binding sites.
J.BIOL.CHEM. 267 150-158 (1992).

Documentation
Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-, 
arginine- and related substrates can be classified into different families
on the basis of sequence similarity [1,2]. One of these families includes:
eukaryotic ornithine decarboxylase (ODC), which catalyses the transformation
of ornithine into putrescine; prokaryotic diaminopimelic acid decarboxylase
(DAPDC), which catalyses the conversion of diaminopimelic acid into lysine,
the final step of lysine biosynthesis; Pseudomonas syringae pv. tabaci
protein, tabA, which is probably involved in tabtoxin biosynthesis and
is similar to DAPDC; and bacterial and plant biosynthetic arginine
decarboxylase (ADC), which catalyses the transformation of arginine 
into agmatine, the first step in putrescine synthesis from arginine.
 
Although these proteins, which are known collectively as group IV
decarboxylases [2], probably share a common evolutionary origin, their
levels of sequence similarity are low, being confined to a few short
conserved regions.
 
The tomato ADC gene contains an open reading frame encoding a polypeptide
of 502 amino acids and a predicted molecular mass of ~55 kD [3]. The 
predicted amino acid sequence shares 47 and 38% identify with oat and 
E.coli ADCs, respectively. Gel blot hybridisation experiments show that,
in tomato, ADC is encoded by a single gene and is expressed as a transcript
of ~2.2kb in the fruit pericarp and leaf tissues [3]. 
 
ARGDCRBXLASE is a 9-element fingerprint that provides a signature for
arginine decarboxylases. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those sections
that characterise the arginine decarboxylases but distinguish them from
the rest of the ODA family. Four iterations on SPTR37_10f were required to
reach convergence, at which point a true set comprising 13 sequences was
identified. Several partial matches were also found: Q9ZKH4 and O25176 are
arginine carboxylases that match only 5 motifs; and O69203 is a closely
related diaminopimelate decarboxylase that matches 2 motifs.
Summary Information
  13 codes involving  9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
2 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
9131313131313131313
8000000000
7000000000
6000000000
5022000222
4000000000
3000000000
2000001001
123456789
True Positives
O04429        O23141        O64453        O82475        
P72587 P74576 Q38938 SPE1_AVESA
SPE1_DIACA SPE1_LYCES SPE1_PEA SPE1_SOYBN
SPEA_ECOLI
True Positive Partials
Codes involving 5 elements
O25176 Q9ZKH4
Codes involving 2 elements
O69203
Sequence Titles
O04429      ARGININE DECARBOXYLASE - DIANTHUS CARYOPHYLLUS (CARNATION) (CLOVE PINK). 
O23141 ARGININE DECARBOXYLASE (EC 4.1.1.19) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O64453 ARGININE DECARBOXYLASE - NICOTIANA SYLVESTRIS (WOOD TOBACCO).
O82475 ARGININE DECARBOXYLASE - BRASSICA JUNCEA (LEAF MUSTARD) (INDIAN MUSTARD).
P72587 ARGININE DECARBOXYLASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P74576 ARGININE DECARBOXYLASE - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q38938 ARGININE DECARBOXYLASE - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SPE1_AVESA ARGININE DECARBOXYLASE (EC 4.1.1.19) (ARGDC) (ADC) - AVENA SATIVA (OAT).
SPE1_DIACA ARGININE DECARBOXYLASE (EC 4.1.1.19) (ARGDC) (ADC) - DIANTHUS CARYOPHYLLUS (CARN
SPE1_LYCES ARGININE DECARBOXYLASE (EC 4.1.1.19) (ARGDC) (ADC) - LYCOPERSICON ESCULENTUM (TO
SPE1_PEA ARGININE DECARBOXYLASE (EC 4.1.1.19) (ARGDC) (ADC) - PISUM SATIVUM (GARDEN PEA).
SPE1_SOYBN ARGININE DECARBOXYLASE (EC 4.1.1.19) (ARGDC) (ADC) - GLYCINE MAX (SOYBEAN).
SPEA_ECOLI BIOSYNTHETIC ARGININE DECARBOXYLASE (EC 4.1.1.19) (ADC) - ESCHERICHIA COLI.

O25176 ARGININE DECARBOXYLASE (SPEA) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
Q9ZKH4 ARGININE DECARBOXYLASE - HELICOBACTER PYLORI J99.

O69203 DIAMINOPIMELATE DECARBOXYLASE - ACTINOSYNNEMA PRETIOSUM AURANTICUM.
Scan History
SPTR37_10f 4  50   NSINGLE    
Initial Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
FPDVLKNRLETLQSAF SPE1_LYCES 7 7 -
FPDVLRHRINSLHTAF SPE1_AVESA 69 69 -
FPQILQHRLRSINAAF SPEA_ECOLI 92 92 -

Motif 2 width=15
Element Seqn Id St Int Rpt
YEAHYQGVYPVKCNQ SPE1_LYCES 31 8 -
YGSVYQGVFPVKVNQ SPE1_AVESA 93 8 -
YNGDYFLVYPIKVNQ SPEA_ECOLI 116 8 -

Motif 3 width=16
Element Seqn Id St Int Rpt
VCNGFKDTEYISLALV SPE1_LYCES 89 43 -
VCNGYKDSAYVALALA SPE1_AVESA 151 43 -
VCNGYKDREYIRLALI SPEA_ECOLI 170 39 -

Motif 4 width=22
Element Seqn Id St Int Rpt
VLEQEEELDLVIDISRKMSVRP SPE1_LYCES 115 10 -
VLEMEEELDIVIEESSKLGVEP SPE1_AVESA 177 10 -
VIEKMSEIAIVLDEAERLNVVP SPEA_ECOLI 196 10 -

Motif 5 width=23
Element Seqn Id St Int Rpt
GLRAKLRTKHSGHFGSTSGEKGK SPE1_LYCES 139 2 -
GVRAKLLTKIPGHFGSTAGKHGK SPE1_AVESA 201 2 -
GVRARLRSQGSGKWQSSGGEKSK SPEA_ECOLI 220 2 -

Motif 6 width=18
Element Seqn Id St Int Rpt
CDRKGGKHPVICSESGRA SPE1_LYCES 267 105 -
CDYHGVPHPVLCTESGRA SPE1_AVESA 331 107 -
CEENGLPHPTVITESGRA SPEA_ECOLI 347 104 -

Motif 7 width=22
Element Seqn Id St Int Rpt
NLSVFTSIPDFWGFSQLFPIVP SPE1_LYCES 394 109 -
NLSVFSLMPDYWGIQHLFPMMP SPE1_AVESA 435 86 -
NFSLFQSMPDAWGIDQLFPVLP SPEA_ECOLI 488 123 -

Motif 8 width=26
Element Seqn Id St Int Rpt
LDEKPTMRGILSDLTCDSDGKVDKFI SPE1_LYCES 419 3 -
LDEKPTHKATLVDVTCDSDGKVDKFI SPE1_AVESA 460 3 -
LDQVPERRAVLLDITCDSDGAIDHYI SPEA_ECOLI 513 3 -

Motif 9 width=22
Element Seqn Id St Int Rpt
GAYEEALGGLHNLFGGPSVVRV SPE1_LYCES 471 26 -
GAYQEALSNKHNLFGGPSLVRV SPE1_AVESA 511 25 -
GAYQEILGNMHNLFGDTEAVDV SPEA_ECOLI 566 27 -
Final Motifs
Motif 1  width=16
Element Seqn Id St Int Rpt
FPDVLKNRLECLQSAF O23141 112 112 -
FPDVLKNRLECLQSAF Q38938 101 101 -
FPDVLKNRLESLQSAF O82475 106 106 -
FPDVLKHRLESLQSAF O04429 121 121 -
FPDVLKHRLESLQSAF SPE1_DIACA 121 121 -
FPDVLKNRLETLQSAF SPE1_LYCES 7 7 -
FPDILKNRLESLQSVF O64453 122 122 -
FPDVLKDRLESIHAAF SPE1_PEA 126 126 -
FPDVLKNRLESLQSAF SPE1_SOYBN 118 118 -
FPDVLRHRINSLHTAF SPE1_AVESA 69 69 -
FSDILADRINRLNAAF P74576 106 106 -
FSDILADRLERLNSCF P72587 84 84 -
FPQILQHRLRSINAAF SPEA_ECOLI 92 92 -

Motif 2 width=15
Element Seqn Id St Int Rpt
YDSHYQGVYPVKCNQ O23141 136 8 -
YDSHYQGVYPVKCNQ Q38938 125 8 -
YESRYQGVYPVKCNQ O82475 130 8 -
YGSHYQGVYPVKCNQ O04429 145 8 -
YGSHYQGVYPVKCNQ SPE1_DIACA 145 8 -
YEAHYQGVYPVKCNQ SPE1_LYCES 31 8 -
YEAHYQGVYPVKCNQ O64453 146 8 -
YESHYQGVYPVKCNQ SPE1_PEA 150 8 -
YESHYQGVYPVKCNQ SPE1_SOYBN 142 8 -
YGSVYQGVFPVKVNQ SPE1_AVESA 93 8 -
YPNTYRGVYPIKCNQ P74576 130 8 -
YPNTYQAVYPVKCNQ P72587 108 8 -
YNGDYFLVYPIKVNQ SPEA_ECOLI 116 8 -

Motif 3 width=16
Element Seqn Id St Int Rpt
VCNGFKDAEYISLALL O23141 194 43 -
VCNGFKDSEYISLALF Q38938 183 43 -
VCNGFKDAEYVSLALL O82475 188 43 -
VCNGFKDAEYISLAII O04429 203 43 -
VCNGFKDAEYISLAII SPE1_DIACA 203 43 -
VCNGFKDTEYISLALV SPE1_LYCES 89 43 -
VCNGFKDAEYISLALV O64453 204 43 -
VCNGFKDSEYISLALI SPE1_PEA 208 43 -
ICNGFKDAEYISLALV SPE1_SOYBN 200 43 -
VCNGYKDSAYVALALA SPE1_AVESA 151 43 -
ICNGYKDREYIETALL P74576 195 50 -
ICNGYKDQDYLETALL P72587 172 49 -
VCNGYKDREYIRLALI SPEA_ECOLI 170 39 -

Motif 4 width=22
Element Seqn Id St Int Rpt
VLEQEEELDLVIELSQKMNVRP O23141 220 10 -
VLEQEEELDLVIDLSQKMNVRP Q38938 209 10 -
VLEQEEELDLVIALSKKVNVRP O82475 214 10 -
VIEQEEEVDMAIELSRKMGIRP O04429 229 10 -
VIEQEEEVDMAIELSRKMGIRP SPE1_DIACA 229 10 -
VLEQEEELDLVIDISRKMSVRP SPE1_LYCES 115 10 -
VLEQEEELDLVIDISKKMAVRP O64453 230 10 -
VLEQEEELDMVVEISNKLCIRP SPE1_PEA 234 10 -
VVEQEEEVDLIVELSKKLCIKP SPE1_SOYBN 226 10 -
VLEMEEELDIVIEESSKLGVEP SPE1_AVESA 177 10 -
VVEQVAEVALAIEISSNLGIKP P74576 221 10 -
IIEQLRELEWVLHISQQLNIKP P72587 198 10 -
VIEKMSEIAIVLDEAERLNVVP SPEA_ECOLI 196 10 -

Motif 5 width=23
Element Seqn Id St Int Rpt
GLRAKLRTKHSGHFGSTSGEKGK O23141 244 2 -
GLRAKLRTKHSGHFGSTSGEKGK Q38938 233 2 -
GLRAKLRTKHSGHFGSTSGEKGK O82475 238 2 -
GVRAKLRTKHSGHFGSTSGEKGK O04429 253 2 -
GVRAKLRTKHSGHFGSTSGEKGK SPE1_DIACA 253 2 -
GLRAKLRTKHSGHFGSTSGEKGK SPE1_LYCES 139 2 -
GLRAKLRTKHSGHFGSTSGEKGK O64453 254 2 -
GVRAKLKTKHSGHFGATSGDKGK SPE1_PEA 258 2 -
GLRAKLRTKHSGHFGGIFRRRGK SPE1_SOYBN 250 2 -
GVRAKLLTKIPGHFGSTAGKHGK SPE1_AVESA 201 2 -
GVRAKLSTQGMGRWGISTGDRAK P74576 245 2 -
GVRARLSCQSLKSSEISSGNGDR P72587 222 2 -
GVRARLRSQGSGKWQSSGGEKSK SPEA_ECOLI 220 2 -

Motif 6 width=18
Element Seqn Id St Int Rpt
CDRSSVKHPVICSESGRA O23141 372 105 -
CDQKSVKHPVICSESGRA Q38938 361 105 -
CDQKSVKHPVICSESGRA O82475 366 105 -
CDRKGVKSPVICSESGRA O04429 381 105 -
CDRKGVKSPVICSESVRA SPE1_DIACA 381 105 -
CDRKGGKHPVICSESGRA SPE1_LYCES 267 105 -
CDRKNVKHPVICSESGRA O64453 382 105 -
CDRKNVKHPVICSESGRA SPE1_PEA 386 105 -
VCDRSVKHPVICSESGRA SPE1_SOYBN 377 104 -
CDYHGVPHPVLCTESGRA SPE1_AVESA 331 107 -
CVAAEVPCPVLISESGRA P74576 372 104 -
CELGQVSPPILVSESGRA P72587 351 106 -
CEENGLPHPTVITESGRA SPEA_ECOLI 347 104 -

Motif 7 width=22
Element Seqn Id St Int Rpt
NLSVFTSIPDLWGIDQLFPIVP O23141 497 107 -
NLSVFTSIPDFWGIDQLFPIVP Q38938 484 105 -
NLSVFHSIPDFWGIDQLFPIVP O82475 490 106 -
NLSVFTSIPDFWGIGQLFPIMP O04429 509 110 -
NLSVFTSIPDFWGIGQLFPIMP SPE1_DIACA 509 110 -
NLSVFTSIPDFWGFSQLFPIVP SPE1_LYCES 394 109 -
NLSIFTSVPDFWAIDQLFPIVP O64453 508 108 -
NLSVFTSVPDFWGINQLFPIVP SPE1_PEA 512 108 -
NLSIFTSVPDAWGIEQVFPIIP SPE1_SOYBN 500 105 -
NLSVFSLMPDYWGIQHLFPMMP SPE1_AVESA 435 86 -
NMSVFQSAPDSWAIDQLFPIMP P74576 507 117 -
NLSVFQSAPESWSLDQLFPILP P72587 487 118 -
NFSLFQSMPDAWGIDQLFPVLP SPEA_ECOLI 488 123 -

Motif 8 width=26
Element Seqn Id St Int Rpt
LDQRPGARGILSDLTCDSDGKINKFI O23141 522 3 -
LDQRPAARGILSDLTCDSDGKINKFI Q38938 509 3 -
LDQRPVARGILSDLTCDSDGKINKFI O82475 515 3 -
LDQQPKARGILSDLTCDSDGKIDKFI O04429 534 3 -
LDQQPKARGILSDLTCDSDGKIDKFI SPE1_DIACA 534 3 -
LDEKPTMRGILSDLTCDSDGKVDKFI SPE1_LYCES 419 3 -
LDERPVVRGILSDLTCDSDGKIDKFI O64453 533 3 -
LDEKPTARGILSDLTCDSDGKIDKFI SPE1_PEA 537 3 -
LDEKPSVRGILSDLTCDSDGKIDKFI SPE1_SOYBN 525 3 -
LDEKPTHKATLVDVTCDSDGKVDKFI SPE1_AVESA 460 3 -
LDEEPTQRGILADITCDSDGKIDQFI P74576 532 3 -
LNEKPSQRVILADLTCDSDGKIDRFI P72587 512 3 -
LDQVPERRAVLLDITCDSDGAIDHYI SPEA_ECOLI 513 3 -

Motif 9 width=22
Element Seqn Id St Int Rpt
GAYEEALGGVHNLFGGPSVVRV O23141 575 27 -
GAYEEALGGVHNLFGGPSVVRV Q38938 563 28 -
GAYEEALGGVHNLFGGPSVVRV O82475 564 23 -
GAYEEALGGVHNLFGGPSVVRV O04429 584 24 -
GAYEEALGGVHNLFGGPSVVRV SPE1_DIACA 584 24 -
GAYEEALGGLHNLFGGPSVVRV SPE1_LYCES 471 26 -
GAYEEALGGLHNLFGGPSVLRV O64453 590 31 -
GSYEEALGGLHNLFGGPSVVRV SPE1_PEA 588 25 -
GAYEEALGGVHNLFGGPSVVRV SPE1_SOYBN 575 24 -
GAYQEALSNKHNLFGGPSLVRV SPE1_AVESA 511 25 -
GAYQEIMGNLHNLFGDINVVHI P74576 594 36 -
GAYQEIMGNLHNLFGDINVVHI P72587 566 28 -
GAYQEILGNMHNLFGDTEAVDV SPEA_ECOLI 566 27 -