WORKLIST ENTRIES (1):
LEADERPTASE View alignment View Structure Bacterial leader peptidase 1 (S26A) family signature
Type of fingerprint: COMPOUND with 3 elements
Links:
PRINTS; PR00722 CHYMOTRYPSIN; PR00861 ALYTICPTASE; PR00798 TOGAVIRIN
PRINTS; PR00921 IGASERPTASE; PR00723 SUBTILISIN; PR00862 PROLIGOPTASE
PRINTS; PR00724 CRBOXYPTASEC; PR00725 DADACBPTASE1; PR00922 DADACBPTASE3
PRINTS; PR00923 LACTOPTASE; PR00830 ENDOLAPTASE; PR00726 LEXASERPTASE
PRINTS; PR00728 SIGNALPTASE; PR00729 CDVENDOPTASE; PR00793 PROAMNOPTASE
PRINTS; PR00995 CAPILLOPTASE; PR00127 CLPPROTEASEP
INTERPRO; IPR000223
PROSITE; PS00501 SPASE_I_1; PS00760 SPASE_I_2; PS00761 SPASE_I_3
PFAM; PF00461 Peptidase_S26
Creation date 10-MAY-1997; UPDATE 27-JUN-1999
1. RAWLINGS, N.D. AND BARRETT, A.J.
Families of serine peptidases.
METHODS ENZYMOL. 244 19-61 (1994).
2. RAWLINGS, N.D AND BARRETT, A.J.
Evolutionary families of peptidases.
BIOCHEM.J. 290 205-218 (1993).
Proteolytic enzymes that exploit serine in their catalytic activity are
ubiquitous, being found in viruses, bacteria and eukaryotes [1]. They
include a wide range of peptidase activity, including exopeptidase, endo-
peptidase, oligopeptidase and omega-peptidase activity. Over 20 families
(denoted S1-S26) of serine protease have been identified, these being
grouped into 6 clans (SA, SB, SC, SE, SF and SG) on the basis of structural
similarity and other functional evidence [1]. Structures are known for four
of the clans (SA, SB, SC and SE): these appear to be totally unrelated,
suggesting at least four evolutionary origins of serine peptidases and
possibly many more [1].
Notwithstanding their different evolutionary origins, there are similarities
in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin
and carboxypeptidase C clans have a catalytic triad of serine, aspartate and
histidine in common: serine acts as a nucleophile, aspartate as an
electrophile, and histidine as a base [1]. The geometric orientations of
the catalytic residues are similar between families, despite different
protein folds [1]. The linear arrangements of the catalytic residues
commonly reflect clan relationships. For example the catalytic triad in
the chymotrypsin clan (SA) is ordered HDS, but is ordered DHS in the
subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [1,2].
At least 3 eubacterial leader peptidases are known: murein prelipoprotein
peptidase, which cleaves the leader peptide from a component of the
bacterial outer membrane; type IV prepilin leader peptidase; and the serine-
dependent leader peptidase 1, which has the more general role of cleaving
the leader peptide from a variety of secreted proteins and proteins directed
to the periplasm and periplasmic membrane [1]. Leader peptidase 1 is
similar to the eukaryotic signal peptidase, although the bacterial protein
is monomeric, while the eukaryotic protein is multimeric [1].
Mitochondria contain a similar two-subunit serine protease that removes
leader peptides from nuclear- and mitochondrially-encoded proteins, which
localise in the inner mitochondrial space [1]. The catalytic residues of a
number of these peptides have been identified as a serine/lysine dyad [1].
LEADERPTASE is a 3-element fingerprint that provides a signature for the
bacterial leader peptidase 1 (S26A) family. The fingerprint was derived from
an initial alignment of 6 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motif 1 includes the
region encoded by PROSITE pattern SPASE_I_1 (PS00501), which contains the
catalytic serine; motif 2 includes the region encoded by PROSITE pattern
SPASE_I_2 (PS00760), which contains the active lysine; and motif 3 includes
the region encoded by PROSITE pattern SPASE_I_3 (PS00761), a conserved
C-terminal region of unknown function. Two iterations on OWL29.3 were
required to reach convergence, at which point a true set comprising 23
sequences was identified.
An update on SPTR37_9f identified a true set of 42 sequences, and 2
partial matches.
SUMMARY INFORMATION
42 codes involving 3 elements
2 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
3| 42 42 42
2| 2 0 2
--+----------------
| 1 2 3
True positives..
LEP_BACLI LEP_PSEFL LEPA_BACAM LEPP_BACNA
LEP_ECOLI O69160 LEP_BACAM LEPT_BACSU
LEPQ_BACNA LEPS_BACSU LEP_SALTY Q45225
LEP_HAEIN P72660 O69886 O54237
P73157 LEP_MYCTU O33021 O67088
LEP_STAAU LEPC_BACCL LEP_PHOLA LEPU_BACSU
Q52697 O69885 O86869 O69884
O07560 O84023 O04348 LEP_STRPN
O69887 O86870 O83896 IMP1_YEAST
O25300 O83215 O74800 IMP2_YEAST
LEPH_STAAU O51061
Subfamily: Codes involving 2 elements
Subfamily True positives..
O51062 O51278
PROTEIN TITLES
LEP_BACLI SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEP_PSEFL SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEPA_BACAM SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEPP_BACNA SIGNAL PEPTIDASE I P (EC 3.4.21.89) (SPASE I) (LEADER PEPTID
LEP_ECOLI SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
O69160 PROKARYOTIC TYPE I SIGNAL PEPTIDASE SIPF - BRADYRHIZOBIUM JA
LEP_BACAM SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEPT_BACSU SIGNAL PEPTIDASE I T (EC 3.4.21.89) (SPASE I) (LEADER PEPTID
LEPQ_BACNA SIGNAL PEPTIDASE I P (EC 3.4.21.89) (SPASE I) (LEADER PEPTID
LEPS_BACSU SIGNAL PEPTIDASE I S (EC 3.4.21.89) (SPASE I) (LEADER PEPTID
LEP_SALTY SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
Q45225 SIPS - BRADYRHIZOBIUM JAPONICUM.
LEP_HAEIN SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
P72660 LEADER PEPTIDASE I - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
O69886 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR, AND S
O54237 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
P73157 LEADER PEPTIDASE I - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
LEP_MYCTU PROBABLE SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER
O33021 SIGNAL PEPTIDASE I - MYCOBACTERIUM LEPRAE.
O67088 TYPE-I SIGNAL PEPTIDASE - AQUIFEX AEOLICUS.
LEP_STAAU SIGNAL PEPTIDASE IB (EC 3.4.21.89) (SPASE IB) (LEADER PEPTID
LEPC_BACCL SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEP_PHOLA SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
LEPU_BACSU SIGNAL PEPTIDASE I U (EC 3.4.21.89) (SPASE I) (LEADER PEPTID
Q52697 LEADER PEPTIDASE - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS
O69885 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR.
O86869 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
O69884 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR, AND S
O07560 HYPOTHETICAL 19.0 KD PROTEIN - BACILLUS SUBTILIS.
O84023 SIGNAL PEPTIDASE I - CHLAMYDIA TRACHOMATIS.
O04348 CHLOROPLAST THYLAKOIDAL PROCESSING PEPTIDASE (LEADER PEPTIDA
LEP_STRPN SIGNAL PEPTIDASE I (EC 3.4.21.89) (SPASE I) (LEADER PEPTIDAS
O69887 PUTATIVE SIGNAL PEPTIDASE I - STREPTOMYCES COELICOLOR.
O86870 SIGNAL PEPTIDASE I - STREPTOMYCES LIVIDANS.
O83896 SIGNAL PEPTIDASE I, PUTATIVE - TREPONEMA PALLIDUM.
IMP1_YEAST MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 1 (EC 3.4.99.-
O25300 SIGNAL PEPTIDASE I (LEPB) - HELICOBACTER PYLORI (CAMPYLOBACT
O83215 SIGNAL PEPTIDASE I (SIP) - TREPONEMA PALLIDUM.
O74800 PUTATIVE MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2 - S
IMP2_YEAST MITOCHONDRIAL INNER MEMBRANE PROTEASE SUBUNIT 2 (EC 3.4.99.-
LEPH_STAAU INACTIVE SIGNAL PEPTIDASE IA - STAPHYLOCOCCUS AUREUS.
O51061 SIGNAL PEPTIDASE I (LEPB-1) - BORRELIA BURGDORFERI (LYME DIS
O51062 SIGNAL PEPTIDASE I (LEPB-2) - BORRELIA BURGDORFERI (LYME DIS
O51278 SIGNAL PEPTIDASE I (LEPB-3) - BORRELIA BURGDORFERI (LYME DIS
SCAN HISTORY
OWL29_3 2 100 NSINGLE
SPTR37_9f 2 100 NSINGLE
INITIAL MOTIF SETS
LEADERPTASE1 Length of motif = 17 Motif number = 1
Bacterial leader peptidase 1 motif I - 1
PCODE ST INT
FLFEPYVVEGKSMDPTL LEPP_BACSU 33 33
FLFEPYLVEGTSMDPTL LEP_BACLI 33 33
FLFAPYVVDGESMEPTL LEPA_BACAM 34 34
FLVEPFQIPSGSMKPTL LEP_PSEFL 79 79
FLYEPFQIPSGSMMPTL LEP_SALTY 80 80
FVARPYLIPSESMEPTL LEP_MYCTU 85 85
LEADERPTASE2 Length of motif = 13 Motif number = 2
Bacterial leader peptidase 1 motif II - 1
PCODE ST INT
YVKRLIGLPGDTV LEPP_BACSU 84 34
YVKRLIGLPGDTV LEP_BACLI 84 34
YVKRIIGLPGDTV LEPA_BACAM 83 32
YIKRVVGLPGDVV LEP_PSEFL 143 47
YIKRAVGLPGDKI LEP_SALTY 144 47
LVKRVIAVGGQTV LEP_MYCTU 172 70
LEADERPTASE3 Length of motif = 20 Motif number = 3
Bacterial leader peptidase 1 motif III - 1
PCODE ST INT
VPKDKYFVMGDNRQESMDSR LEPP_BACSU 138 41
VPEGKYFVMGDNRQRSMDSR LEP_BACLI 138 41
VPDDKYFVMGDNRRNSMDSR LEPA_BACAM 137 41
VPAGHYFMMGDNRDNSNDSR LEP_PSEFL 216 60
VPPGQYFMMGDNRDNSADSR LEP_SALTY 264 107
VPPGRVWVMGDNRTHSADSR LEP_MYCTU 228 43
FINAL MOTIF SETS
LEADERPTASE1 Length of motif = 17 Motif number = 1
Bacterial leader peptidase 1 motif I - 2
PCODE ST INT
FLFEPYLVEGTSMDPTL LEP_BACLI 33 33
FLVEPFQIPSGSMKPTL LEP_PSEFL 79 79
FLFAPYVVDGESMEPTL LEPA_BACAM 34 34
FLFEPYVVEGKSMDPTL LEPP_BACNA 33 33
FIYEPFQIPSGSMMPTL LEP_ECOLI 80 80
FLFQPFNIPSGSMKATL O69160 33 33
FLFEPYLVEGSSMYPTL LEP_BACAM 40 40
FLFEPYLVEGSSMYPTL LEPT_BACSU 40 40
FLFEPYIVQGESMKPTL LEPQ_BACNA 32 32
FIFAPYVVDGDSMYPTL LEPS_BACSU 32 32
FLYEPFQIPSGSMMPTL LEP_SALTY 80 80
ALAEPFYVPSGSMEPTL Q45225 38 38
FLFEPFQIPSGSMESTL LEP_HAEIN 104 104
FVAEPRYIPSDSMLPTL P72660 33 33
FLVQAFSIPSSSMENTL O69886 103 103
FLVQAFSIPSSSMENTL O54237 58 58
FVAEARYIPSSSMEPTL P73157 41 41
FVARPYLIPSESMEPTL LEP_MYCTU 85 85
FVARPYLIPSESMEPTL O33021 73 73
YIAQAYTIPSASMEPTL O67088 21 21
FIVTPYTIKGESMDPTL LEP_STAAU 25 25
FVFSNYVVEGKSMMPTL LEPC_BACCL 27 27
FVAEARYIPSESMLPTL LEP_PHOLA 48 48
VFYKPFLIEGSSMAPTL LEPU_BACSU 35 35
LFFQPFWIPSGSMKDTL Q52697 29 29
FLVQAFVIPSGSMEQTI O69885 74 74
FLVQAFVIPSGSMEQTI O86869 74 74
FVLQPFQIPSGSMERGL O69884 66 66
AVFIDYKVEGVSMNPTF O07560 23 23
FWFELYEVPTGSMRPTI O84023 102 102
ALAEPKSIPSTSMYPTL O04348 173 173
FFWSNVRVEGHSMDPTL LEP_STRPN 27 27
VVYRPYTVPTSSMTPTI O69887 50 50
VVYRPYTVPTSSMTPTI O86870 50 50
FAFQLYVIPSESMVPSF O83896 76 76
YAYEFTETRGESMLPTL IMP1_YEAST 28 28
FIAQAFIIPSRSMVGTL O25300 27 27
HVVAAYRIQADSMQPTL O83215 40 40
YLFQVQMTSGPSMMPTL O74800 24 24
NVVHIAQVKGTSMQPTL IMP2_YEAST 30 30
FVIVGHVIPNNDMSPTL LEPH_STAAU 24 24
FVLQIFMIKSNEMLPTI O51061 37 37
LEADERPTASE2 Length of motif = 13 Motif number = 2
Bacterial leader peptidase 1 motif II - 2
PCODE ST INT
YVKRLIGLPGDTV LEP_BACLI 84 34
YIKRVVGLPGDVV LEP_PSEFL 143 47
YVKRIIGLPGDTV LEPA_BACAM 83 32
YVKRLIGLPGDTV LEPP_BACNA 84 34
YIKRAVGLPGDKV LEP_ECOLI 144 47
YIKRVIGLPGDRV O69160 103 53
YVKRLIGKPGETV LEP_BACAM 91 34
YVKRLIGKPGETV LEPT_BACSU 91 34
YVKRLIGLPGDTI LEPQ_BACNA 83 34
YVKRIIGLPGDTV LEPS_BACSU 81 32
YIKRAVGLPGDKI LEP_SALTY 144 47
WVKRVVGLPGDRI Q45225 109 54
YIKRIVGKGGDRV LEP_HAEIN 194 73
FIKRVIALPGQTV P72660 92 42
LIKRVIGVAGDTV O69886 182 62
LIKRVIGVAGDTV O54237 137 62
FIKRIIGLPGDEV P73157 98 40
LVKRVIAVGGQTV LEP_MYCTU 172 70
LVKRVIAVGGQTV O33021 160 70
FIKRIIARGGDTV O67088 73 35
YVKRVIGVPGDKV LEP_STAAU 75 33
YVKRVIGLPGDRI LEPC_BACCL 77 33
FIKRVIGLPGETV LEP_PHOLA 107 42
FVKRLIGLPGDSI LEPU_BACSU 86 34
FIKRLIGLPGDRI Q52697 103 57
LIKRVVGVGGDHV O69885 159 68
LIKRVVGVGGDHV O86869 159 68
YIKRVVGVGGDHV O69884 120 37
LIKRVIGLPGETI O07560 73 33
YIKRCMGKPGDTV O84023 181 62
FIKRIVASEGDWV O04348 235 45
IVKRVIGMPGDTI LEP_STRPN 74 30
MVKRVVAVGGDTV O69887 100 33
MVKRVVAVGGDTV O86870 100 33
LVKRIVALPGEKV O83896 175 82
ICKRVTGMPGDLV IMP1_YEAST 81 36
YVKRNFAIGGDEV O25300 104 60
QMRRVVGLPGDTV O83215 122 65
VCKRIIGMPGDTI O74800 78 37
YCKRVKGLPFDTI IMP2_YEAST 89 42
YTSRIIAKPGQSM LEPH_STAAU 73 32
KVSRIAAVQGDSV O51061 111 57
LEADERPTASE3 Length of motif = 20 Motif number = 3
Bacterial leader peptidase 1 motif III - 2
PCODE ST INT
VPEGKYFVMGDNRQRSMDSR LEP_BACLI 138 41
VPAGHYFMMGDNRDNSNDSR LEP_PSEFL 216 60
VPDDKYFVMGDNRRNSMDSR LEPA_BACAM 137 41
VPKDKYFVMGDNRQESMDSR LEPP_BACNA 138 41
VPPGQYFMMGDNRDNSADSR LEP_ECOLI 264 107
VPAGHFFMMGDNRDNSTDSR O69160 185 69
VPKGKYFVMGDNRLNSMDSR LEP_BACAM 145 41
VPKGKYFVMGDNRLNSMDSR LEPT_BACSU 145 41
VPKDKYFVMGDNRQNSMDSR LEPQ_BACNA 137 41
VPDNKYFVMGDNRRNSMDSR LEPS_BACSU 136 42
VPPGQYFMMGDNRDNSADSR LEP_SALTY 264 107
VPAGHLFVLGDNRDNSADSR Q45225 186 64
VPEGQYFVMGDHRDHSDDSR LEP_HAEIN 288 81
VPDGQVFVMGDNRNNSNDSH P72660 136 31
VPEGKIWVMGDHRQNSRDSR O69886 234 39
VPEGKIWVMGDHRQNSRDSR O54237 189 39
VPDDQYLVLGDNRNNSYDSH P73157 142 31
VPPGRVWVMGDNRTHSADSR LEP_MYCTU 228 43
VPQGRLWVMGDNRIHSADSR O33021 216 43
VPEGYYFVMGDNRDNSQDSR O67088 178 92
IPKGKYLVLGDNREVSKDSR LEP_STAAU 137 49
VPPGCIFVLGDNRLSSWDSR LEPC_BACCL 135 45
VPADSFLVLGDNRNNSYDSH LEP_PHOLA 151 31
VPSGKYFVMGDNRLNSLDSR LEPU_BACSU 139 40
VPEGQYFFMGDNRDNSEDSR Q52697 198 82
VPEGRLWVMGDHRSNSADSR O69885 207 35
VPEGRLWVMGDHRSNSADSR O86869 207 35
VPDGTLFVLGDHRSDSSDSR O69884 169 36
VPKGKYFVVGDNRIYSFDSR O07560 131 45
IPEGHVLVLGDNCPMSADSR O84023 543 349
VPKGYVFVLGDNRNKSFDSH O04348 279 31
VPEGEYLLLGDDRLVSSDSR LEP_STRPN 158 71
VPEGRLFLLGDERRNSVDST O69887 148 35
VPEGRLFLLGDERRNSVDST O86870 148 35
LPEHNYFMMGDNRLNSTDMR O83896 441 253
VPEGHVWVTGDNLSHSLDSR IMP1_YEAST 120 26
INDDEFFMIGDNRDNSSDSR O25300 207 90
LDEHSYFVLCDNRIVSSDSR O83215 188 53
IPLGHVWLAGDNIAHSLDSR O74800 103 12
LPRGHIWVEGDNYFHSIDSN IMP2_YEAST 114 12
IPPNNFVVLNDHDNNQHDSR LEPH_STAAU 125 39
LKKNEFFLLNDNLSVLNDSR O51061 167 43
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