WORKLIST ENTRIES (1):

PREPILNPTASE View alignment     Type IV prepilin cysteine protease (C20) family signature
 Type of fingerprint: COMPOUND with 4  elements
Links:
   PRINTS; PR00705 PAPAIN; PR00704 CALPAIN; PR00966 NIAPOTYPTASE
   PRINTS; PR00703 ADVENDOPTASE; PR00797 STREPTOPAIN; PR00707 UBCTHYDRLASE
   PRINTS; PR00776 HEMOGLOBNASE; PR00706 PYROGLUPTASE; PR00916 2CENDOPTASE
   PRINTS; PR00917 SRSVCYSPTASE
   INTERPRO; IPR000045

 Creation date 26-APR-1998; UPDATE 28-JUL-1999

   1. RAWLINGS, N.D. AND BARRETT, A.J.
   Families of cysteine peptidases.
   METHODS ENZYMOL. 244 461-486 (1994).

   2. RAWLINGS, N.D. AND BARRETT, A.J.
   Evolutionary families of peptidases.
   BIOCHEM.J. 290 205-218 (1993).

   3. BAIROCH, A. AND RAWLINGS, N.
   Classification of peptidase families and index of peptidase entries in
   SWISS-PROT.
   http://expasy.hcuge.ch/cgi-bin/lists?peptidas.txt

   Cysteine protease activity is dependent on an active dyad of cysteine and
   histidine, the order and spacing of these residues varying in the 20 or so
   known families. Cysteine proteases have been grouped into two clans (CA and
   CB). Families C1, C2 and C10 are loosely termed papain-like and belong 
   to clan CA; five cysteine proteases belong to clan CB; other families have
   not been assigned to clans. Nearly half of all cysteine proteases are found 
   exclusively in viruses. The order of catalytic cysteine and histidine 
   residues within the primary structure differs between the families and is 
   an indication of convergent evolution [1-3].
   
   Bacteria produce a number of protein precursors that undergo post-
   translational methylation and proteolysis prior to secretion as active
   proteins. Type IV prepilin leader peptidases, which belong to the C20 family
   of cysteine proteases, are enzymes that mediate this type of post-
   translational modification. Type IV pilin is a protein found on the surface
   of Pseudomonas aeruginosa, Neisseria gonorrhoeae and other Gram-negative
   pathogens. Pilin subunits attach the infecting organism to the surface of 
   host epithelial cells. They are synthesised as prepilin subunits, which 
   differ from mature pilin by virtue of containing a 6-8 residue leader
   peptide consisting of charged amino acids. Mature type IV pilins also
   contain a methylated N-terminal phenylalanine residue. 
  
   Prepilin leader peptidases are found on the cytosolic membrane surface,
   where they have dual activity, involving cleavage of glycine-phenylalanine
   bonds and methylation of the newly-revealed N-terminal phenylalanine. The
   consensus sequence for the site of proteolytic cleavage is -G+F-T-L/I-, in
   which the Gly P1 residue is essential [1]. The peptidases are suseptible to 
   thiol blocking reagents. Site directed mutagenesis has indicated four highly
   conserved cysteine residues that affect both the protease and methylase 
   activity.
   
   PREPILNPTASE is a 4-element fingerprint that provides a signature for the 
   type IV leaderpeptidase (C20) family of cysteine proteases. The fingerprint
   was derived from an initial alignment of 13 sequences: the motifs were drawn
   from conserved regions spanning the central portion of the alignment. Two
   iterations on OWL30.1 were required to reach convergence, at which point a
   true set comprising 19 sequences was found. 
  
   An update on SPTR37_9f identified a true set of 23 sequences, and 5
   partial matches.

  SUMMARY INFORMATION
     23 codes involving  4 elements
      3 codes involving  3 elements
      2 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    4|  23   23   23   23  
    3|   3    1    3    2  
    2|   2    0    2    0  
   --+---------------------
     |   1    2    3    4  

True positives..
 LEP3_AERHY     O68964         Q56740         O68839         
 O54483         LEP3_PSEAE     LEP3_KLEPN     O32576         
 O53004         LEP3_ERWCH     LEP3_PSEPU     LEP3_ECOLI     
 LEP3_ERWCA     LEP3_NEIGO     Q53404         Q56763         
 Q46525         P72640         O68927         Q46836         
 O30387         LEP3_VIBCH     Q56668         
Subfamily:  Codes involving 3 elements
 Subfamily True positives..
 O68433         O68932         LEP3_BACSU     
Subfamily:  Codes involving 2 elements
 Subfamily True positives..
 P94648         Q57382         


  PROTEIN TITLES
   LEP3_AERHY       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   O68964           TYPE IV PREPILIN PEPTIDASE TAPD - AEROMONAS SALMONICIDA.
   Q56740           VVPD - VIBRIO VULNIFICUS.
   O68839           TYPE 4 PREPILIN PEPTIDASE VCPD - VIBRIO CHOLERAE.
   O54483           PILD - AEROMONAS SALMONICIDA.
   LEP3_PSEAE       TYPE 4 PREPILIN PEPTIDASE (EC 3.4.99.-) (PROTEIN SECRETION P
   LEP3_KLEPN       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   O32576           ETPN PROTEIN - ESCHERICHIA COLI.
   O53004           ORF2 PROTEIN - ESCHERICHIA COLI.
   LEP3_ERWCH       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   LEP3_PSEPU       TYPE 4 PREPILIN PEPTIDASE (EC 3.4.99.-) (PROTEIN SECRETION P
   LEP3_ECOLI       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   LEP3_ERWCA       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   LEP3_NEIGO       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   Q53404           TYPE IV PREPILIN PEPTIDASE - NEISSERIA GONORRHOEAE.
   Q56763           XPSO - XANTHOMONAS CAMPESTRIS.
   Q46525           FIMP - BACTEROIDES NODOSUS (DICHELOBACTER NODOSUS).
   P72640           TYPE 4 PREPILIN PEPTIDASE - SYNECHOCYSTIS SP. (STRAIN PCC 68
   O68927           LEADER PEPTIDASE HOPD - SALMONELLA TYPHIMURIUM.
   Q46836           ORF_F310 - ESCHERICHIA COLI.
   O30387           PILD - MYXOCOCCUS XANTHUS.
   LEP3_VIBCH       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
   Q56668           TOXIN CO-REGULATED PILUS - VIBRIO CHOLERAE.
 
   O68433           TYPE IV PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE PILD
   O68932           LEADER PEPTIDASE HOPD - ESCHERICHIA COLI.
   LEP3_BACSU       TYPE 4 PREPILIN-LIKE PROTEIN SPECIFIC LEADER PEPTIDASE (EC 3
 
   P94648           PREPILIN PEPTIDASE HOMOLOG - CHLOROBIUM LIMICOLA.
   Q57382           BFPP - ESCHERICHIA COLI.

SCAN HISTORY OWL30_0 2 550 NSINGLE SPTR37_9f 2 100 NSINGLE INITIAL MOTIF SETS PREPILNPTASE1 Length of motif = 18 Motif number = 1 Type IV prepilin protease motif I - 1 PCODE ST INT LSVIDFRTQLLPDKLTLP LEP3_ECOLI 90 90 LTFIDLDKMLLPDQLTLP LEP3_AERHY 147 147 LAVIDCHTALLPDVLTLP ECPO15711 107 107 LAAIDARTQLLPDVMTLP LEP3_ERWCH 145 145 LAAIDAQTQLLPDGLTLP LEP3_KLEPN 133 133 LTFIDADTQYLPDSMTLP LEP3_NEIGO 143 143 LTVIDIKTLLLPDELTLS LEP3_ERWCA 144 144 MSLIDADHQLLPDVLVLP LEP3_PSEAE 145 145 LFVIDFKSMLLPNLLTYP LEP3_VIBCH 121 121 LSLIDHDQQLLPDAIVLP LEP3_PSEPU 144 144 LTLIDWDTMTLPNSLTKP S74490 117 117 LAFIDLDHWILPLSMTVP AF0036323 122 122 VAVTDIHFMLIPNRILIF LEP3_BACSU 109 109 PREPILNPTASE2 Length of motif = 11 Motif number = 2 Type IV prepilin protease motif II - 1 PCODE ST INT LVCHKEGLGYG LEP3_ECOLI 147 39 LLTGKEGMGYG LEP3_AERHY 204 39 FATGREGLGYG ECPO15711 164 39 LLSGREALGHG LEP3_ERWCH 202 39 LLSGKEALGYG LEP3_KLEPN 190 39 LLTGKTGMGNG LEP3_NEIGO 200 39 YATGKEALGYG LEP3_ERWCA 201 39 LVTGKEGMGYG LEP3_PSEAE 202 39 LFKRIDVMGGG LEP3_VIBCH 178 39 LVTGKEGMGYG LEP3_PSEPU 201 39 LLLGREGMGDG S74490 180 45 KVFQREALGAG AF0036323 179 39 AAITHGGVGGG LEP3_BACSU 161 34 PREPILNPTASE3 Length of motif = 12 Motif number = 3 Type IV prepilin protease motif III - 1 PCODE ST INT DFKLLAAAGAWC LEP3_ECOLI 158 0 DFKLLAALGAWL LEP3_AERHY 215 0 DFKLAAALGAWM ECPO15711 175 0 DFKLLAALGAWL LEP3_ERWCH 213 0 DFKLLAALGAWL LEP3_KLEPN 201 0 DFKLIAALGAWL LEP3_NEIGO 211 0 DFKLLAALGAWL LEP3_ERWCA 212 0 DFKLLAMLGAWG LEP3_PSEAE 213 0 DIKLYTAIGTLI LEP3_VIBCH 189 0 DFKLLALLGAWG LEP3_PSEPU 212 0 DPKLASMVGAWL S74490 191 0 DKYLVAMLGAFL AF0036323 190 0 DIKLFAVIGFVL LEP3_BACSU 172 0 PREPILNPTASE4 Length of motif = 16 Motif number = 4 Type IV prepilin protease motif IV - 1 PCODE ST INT GWQTLPMILLIASLGG LEP3_ECOLI 170 0 GWQALPIVLLLSSLVG LEP3_AERHY 227 0 GWQALPSILLFASVSG ECPO15711 187 0 GWQALPNLVLIASLTG LEP3_ERWCH 225 0 GWQALPQTLLLASPAA LEP3_KLEPN 213 0 GISALPVLIFVSSLIG LEP3_NEIGO 223 0 GWQALPNLVLVAALSG LEP3_ERWCA 224 0 GWQILPLTILLSSLVG LEP3_PSEAE 225 0 GVEFVPYLFLLSSIIA LEP3_VIBCH 201 0 GWQVLPLTLLLSSVLG LEP3_PSEPU 224 0 GWPSLLLTTFIACFIG S74490 203 0 TWRALLGVLLFASMQG AF0036323 202 0 GVKMLAAAFFFSVLIG LEP3_BACSU 184 0 FINAL MOTIF SETS PREPILNPTASE1 Length of motif = 18 Motif number = 1 Type IV prepilin protease motif I - 2 PCODE ST INT LTFIDLDKMLLPDQLTLP LEP3_AERHY 147 147 LTFIDLDKMLLPDQLTLP O68964 148 148 ATFIDLDTMLLPDQLTLP Q56740 143 143 ATFIDFDTLLLPDQLTLP O68839 143 143 LTFIDLDKMLLXDQLNLX O54483 148 148 MSLIDADHQLLPDVLVLP LEP3_PSEAE 145 145 LAAIDAQTQLLPDGLTLP LEP3_KLEPN 133 133 LAVIDCHTALLPDVLTLP O32576 107 107 LAVIDCHTALLPDVLTLP O53004 107 107 LAAIDARTQLLPDVMTLP LEP3_ERWCH 145 145 LSLIDHDQQLLPDAIVLP LEP3_PSEPU 144 144 LSVIDFRTQLLPDKLTLP LEP3_ECOLI 90 90 LTVIDIKTLLLPDELTLS LEP3_ERWCA 144 144 LTFIDADTQYLPDSMTLP LEP3_NEIGO 143 143 LTFIDEDTQYLPDSMTLP Q53404 143 143 MSGIDLRHKLLPDQLTLP Q56763 142 142 LCFIDAEHQLLPDRLTLP Q46525 147 147 LTLIDWDTMTLPNSLTKP P72640 117 117 LGIYDARTGLLPDRFTCP O68927 18 18 ASVIDLDHQWLPDVFTQG Q46836 180 180 LAFIDLDHWILPLSMTVP O30387 122 122 LFVIDFKSMLLPNLLTYP LEP3_VIBCH 121 121 LFVIDFKSMLLPNLLTYP Q56668 121 121 PREPILNPTASE2 Length of motif = 11 Motif number = 2 Type IV prepilin protease motif II - 2 PCODE ST INT LLTGKEGMGYG LEP3_AERHY 204 39 LLTGKEGMGYG O68964 205 39 LLTGKEGMGYG Q56740 201 40 LLTGKEGMGYG O68839 201 40 LLTGKEGMGYG O54483 205 39 LVTGKEGMGYG LEP3_PSEAE 202 39 LLSGKEALGYG LEP3_KLEPN 190 39 FATGREGLGYG O32576 164 39 FATGREGLGYG O53004 164 39 LLSGREALGHG LEP3_ERWCH 202 39 LVTGKEGMGYG LEP3_PSEPU 201 39 LVCHKEGLGYG LEP3_ECOLI 147 39 YATGKEALGYG LEP3_ERWCA 201 39 LLTGKTGMGNG LEP3_NEIGO 200 39 LLTGKTGMGNG Q53404 200 39 QLTGKEGMGHG Q56763 199 39 LITGREGMGYG Q46525 204 39 LLLGREGMGDG P72640 180 45 LRYQKEGLGYG O68927 75 39 IVLRKEALGMG Q46836 238 40 KVFQREALGAG O30387 179 39 LFKRIDVMGGG LEP3_VIBCH 178 39 LFKRIDVMGGG Q56668 178 39 PREPILNPTASE3 Length of motif = 12 Motif number = 3 Type IV prepilin protease motif III - 2 PCODE ST INT DFKLLAALGAWL LEP3_AERHY 215 0 DFKLLAALGAWL O68964 216 0 DFKLLAALGAWL Q56740 212 0 DFKLLAALGAWL O68839 212 0 DFKLLAALGAWL O54483 216 0 DFKLLAMLGAWG LEP3_PSEAE 213 0 DFKLLAALGAWL LEP3_KLEPN 201 0 DFKLAAALGAWM O32576 175 0 DFKLAAALGAWM O53004 175 0 DFKLLAALGAWL LEP3_ERWCH 213 0 DFKLLALLGAWG LEP3_PSEPU 212 0 DFKLLAAAGAWC LEP3_ECOLI 158 0 DFKLLAALGAWL LEP3_ERWCA 212 0 DFKLIAALGAWL LEP3_NEIGO 211 0 DFKLIAALGAWL Q53404 211 0 DFKLLAALGAWC Q56763 210 0 DFKLLACLCAWQ Q46525 215 0 DPKLASMVGAWL P72640 191 0 DVKYLAALGAWH O68927 86 0 DVLLFAALGGWV Q46836 249 0 DKYLVAMLGAFL O30387 190 0 DIKLYTAIGTLI LEP3_VIBCH 189 0 DIKLYTAIGTLI Q56668 189 0 PREPILNPTASE4 Length of motif = 16 Motif number = 4 Type IV prepilin protease motif IV - 2 PCODE ST INT GWQALPIVLLLSSLVG LEP3_AERHY 227 0 GWQALPIVLLLSSLVG O68964 228 0 GWQYLPMIILLSSVVG Q56740 224 0 GWQQLPVIVLLSSVVG O68839 224 0 GWQALPIVLLLSSLVG O54483 228 0 GWQILPLTILLSSLVG LEP3_PSEAE 225 0 GWQALPQTLLLASPAA LEP3_KLEPN 213 0 GWQALPSILLFASVSG O32576 187 0 GWQALPSILLFASVSG O53004 187 0 GWQALPNLVLIASLTG LEP3_ERWCH 225 0 GWQVLPLTLLLSSVLG LEP3_PSEPU 224 0 GWQTLPMILLIASLGG LEP3_ECOLI 170 0 GWQALPNLVLVAALSG LEP3_ERWCA 224 0 GISALPVLIFVSSLIG LEP3_NEIGO 223 0 GISALPVLIFVSSLIG Q53404 223 0 GLKGILPIILISSLVG Q56763 222 0 GAWMLPIILFSAAILG Q46525 227 0 GWPSLLLTTFIACFIG P72640 203 0 CWETLPLLVFLAAMLA O68927 98 0 GALSLPNVALIASCCG Q46836 261 0 TWRALLGVLLFASMQG O30387 202 0 GVEFVPYLFLLSSIIA LEP3_VIBCH 201 0 GVEFVPYLFLLSSIIA Q56668 201 0

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