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PR00812

Identifier
BCTERIALGSPF  [View Relations]  [View Alignment]  
Accession
PR00812
No. of Motifs
4
Creation Date
18-MAR-1998  (UPDATE 13-JUN-1999)
Title
Bacterial general secretion pathway protein F signature
Database References

PROSITE; PS00874 T2SP_F
BLOCKS; BL00874
PFAM; PF00482 GSPII_F
INTERPRO; IPR003004
Literature References
1. SALMOND, G.P.C. AND REEVES, P.J.
Membrane traffic wardens and protein secretion in Gram-negative bacteria.
TRENDS BIOCHEM.SCI. 18 7-12 (1993).
 
2. WANDERSMAN, C.
Secretion across the bacterial outer membrane.
TRENDS GENET. 8(9) 317-321 (1992).
 
3. LORY, S.
Determinants of extracellular protein secretion in Gram-negative bacteria.
J.BACTERIOL. 174(11) 3423-3428 (1992). 
 
4. BALY, M., FILLOUX, A., AKRIM, M., BALL, G., LAZDUNSKI, A. AND TOMMASSEN, J.
Protein secretion in Pseudomonas aeruginosa: Characterization of the seven xcp
genes and processing of secretory apparatus components by prepilin peptidase.
MOL.MICROBIOL. 6(9) 1121-1131 (1992)

Documentation
The general (type II) secretion pathway (GSP) within Gram-negative bacteria
is a signal sequence-dependent process repsonsible for protein export [1-3].
The process has two stages: exoproteins are first translocated across the
inner membrane by the general signal-dependent export pathway (GEP), and 
then across the outer membrane by a species-specific accessory mechanism. 
 
The GSP is a composite of several proteins, one of which is termed general
secretion pathway protein F (GSPF), which is thought to be located within
the inner membrane [4]. This suggests that protein F is part of the GEP
apparatus, which aids translocation of exoproteins from the cytoplasm to the
periplasm, prior to transport across the outer membrane. GSPF is a highly
hyrdophobic protein containing ~400 amino acids.
 
BCTERIALGSPF is a 4-element fingerprint that provides a signature for 
general secretion pathway protein F. The fingerprint was derived from an
initial alignment of 8 sequences: the motifs were drawn from conserved 
regions spanning virtually the full alignment length - motif 2 includes the
region encoded by PROSITE pattern T2SP_F (PS00874), which contains 2
conserved proline residues. Two iterations on OWL30.0 were required to
reach convergence, at which point a true set comprising 12 sequences was
identified. Several partial matches were also found: PILC_PSEPU is a related
fimbrial assembly protein that matches motifs 1-3; those matching 2 motifs
are fimbrial assembly proteins that match motifs 1 and 2.
 
An update on SPTR37_9f identified a true set of 10 sequences, and 4
partial matches.
Summary Information
  10 codes involving  4 elements
1 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
410101010
31110
23300
1234
True Positives
GSPF_AERHY    GSPF_ECOLI    GSPF_ERWCA    GSPF_ERWCH    
GSPF_KLEPN GSPF_PSEAE GSPF_VIBCH GSPF_XANCP
O32568 Q52293
True Positive Partials
Codes involving 3 elements
PILC_PSEPU
Codes involving 2 elements
O85599 PILC_PSEAE Q56739
Sequence Titles
GSPF_AERHY  GENERAL SECRETION PATHWAY PROTEIN F - AEROMONAS HYDROPHILA. 
GSPF_ECOLI PUTATIVE GENERAL SECRETION PATHWAY PROTEIN F (PROTEIN TRANSPORT PROTEIN HOFF) - ESCHERICHIA COLI.
GSPF_ERWCA GENERAL SECRETION PATHWAY PROTEIN F (PECTIC ENZYMES SECRETION PROTEIN OUTF) - ERWINIA CAROTOVORA.
GSPF_ERWCH GENERAL SECRETION PATHWAY PROTEIN F (PECTIC ENZYMES SECRETION PROTEIN OUTF) - ERWINIA CHRYSANTHEMI.
GSPF_KLEPN GENERAL SECRETION PATHWAY PROTEIN F (PULLULANASE SECRETION PROTEIN PULF) - KLEBSIELLA PNEUMONIAE.
GSPF_PSEAE GENERAL SECRETION PATHWAY PROTEIN F - PSEUDOMONAS AERUGINOSA.
GSPF_VIBCH GENERAL SECRETION PATHWAY PROTEIN F (CHOLERA TOXIN SECRETION PROTEIN EPSF) - VIBRIO CHOLERAE.
GSPF_XANCP GENERAL SECRETION PATHWAY PROTEIN F - XANTHOMONAS CAMPESTRIS (PV. CAMPESTRIS).
O32568 ETPF PROTEIN - ESCHERICHIA COLI.
Q52293 UXPB, UXPA, XCPP, XCPQ, XCPR, XCPS AND XCPT GENES - PSEUDOMONAS PUTIDA.

PILC_PSEPU FIMBRIAL ASSEMBLY PROTEIN PILC - PSEUDOMONAS PUTIDA.

O85599 TYPE IV PILIN BIOGENESIS PROTEIN - VIBRIO VULNIFICUS.
PILC_PSEAE FIMBRIAL ASSEMBLY PROTEIN PILC - PSEUDOMONAS AERUGINOSA.
Q56739 VVPC - VIBRIO VULNIFICUS.
Scan History
OWL30_0    2  300  NSINGLE    
SPTR37_9f 2 100 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
DLALLTRQLATLV GSPF_ERWCA 69 69 -
DLALLTRQLATLV GSPF_ERWCH 68 68 -
DLALVTRQLATLV GSPF_KLEPN 62 62 -
ELALITRQLATLV GSPF_AERHY 49 49 -
DLALITRQLATLV GSPF_VIBCH 67 67 -
ELTLFTRQLATLS GSPF_ECOLI 60 60 -
DLALVTRQLATLV GSPF_PSEAE 67 67 -
ALVQFTQQLATLI GSPF_XANCP 53 53 -

Motif 2 width=29
Element Seqn Id St Int Rpt
RIQQAMIYPCVLTVVAIAVVSILLSVVVP GSPF_ERWCA 168 86 -
RIQQAMIYPCVLTLVAISVVSILLSAVVP GSPF_ERWCH 166 85 -
RLLQAMIYPIVLTLVAVSVIVILLSTVVP GSPF_KLEPN 141 66 -
KLLQAMIYPIVLTLVAVGVISILLTAVVP GSPF_AERHY 148 86 -
KLQQAMIYPVVLVVFAVGIVAFLLAAVVP GSPF_VIBCH 166 86 -
KLIQSLIYPCMLTTVAIGVVIILLTAVVP GSPF_ECOLI 159 86 -
KIQLALLYPVILMVASLAIVGFLLGYVVP GSPF_PSEAE 166 86 -
KVINALIYPAILLAVVGCALLFLLGYVVP GSPF_XANCP 151 85 -

Motif 3 width=15
Element Seqn Id St Int Rpt
LALGLFEPLLVVSMA GSPF_ERWCA 371 174 -
LVLGLFEPLLVVSMA GSPF_ERWCH 367 172 -
LALSLFEPLLVVAMA GSPF_KLEPN 344 174 -
IALGVFEPLLVVSMA GSPF_AERHY 351 174 -
IALGIFTPALIALMA GSPF_VIBCH 369 174 -
LTLSIFEPALIITMA GSPF_ECOLI 362 174 -
LMVGLFEPFMLIFMG GSPF_PSEAE 369 174 -
RALAALVPLITLVLA GSPF_XANCP 354 174 -

Motif 4 width=20
Element Seqn Id St Int Rpt
VVLFIVLAILQPILQLNTLM GSPF_ERWCA 387 1 -
IVLFIVLAILQPILQLNTLM GSPF_ERWCH 383 1 -
MVLFIVLAILQPILQLNTLM GSPF_KLEPN 360 1 -
VVLFIVMSILQPILELNNMV GSPF_AERHY 367 1 -
MVLFIVMATLMPILEMNNLM GSPF_VIBCH 385 1 -
IVLFIVVSVLQPLLQLNSMI GSPF_ECOLI 378 1 -
VVLVIVLAILLPILSLNQLV GSPF_PSEAE 385 1 -
VVGLVIISVLVPLYDLTNAI GSPF_XANCP 370 1 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
DLALLTRQLATLV GSPF_ERWCA 69 69 -
DLALLTRQLATLV GSPF_ERWCH 68 68 -
ELALLTRQLATLV O32568 68 68 -
DLALVTRQLATLV GSPF_KLEPN 62 62 -
ELALITRQLATLV GSPF_AERHY 49 49 -
DLALITRQLATLV GSPF_VIBCH 67 67 -
ELTLFTRQLATLS GSPF_ECOLI 60 60 -
DLALVTRQLATLV GSPF_PSEAE 67 67 -
QLCELTRQLATLT Q52293 61 61 -
ALVQFTQQLATLI GSPF_XANCP 53 53 -

Motif 2 width=29
Element Seqn Id St Int Rpt
RIQQAMIYPCVLTVVAIAVVSILLSVVVP GSPF_ERWCA 168 86 -
RIQQAMIYPCVLTLVAISVVSILLSAVVP GSPF_ERWCH 166 85 -
RLLQALLYPCVLTLVAVGVIAILLTAVVP O32568 167 86 -
RLLQAMIYPIVLTLVAVSVIVILLSTVVP GSPF_KLEPN 141 66 -
KLLQAMIYPIVLTLVAVGVISILLTAVVP GSPF_AERHY 148 86 -
KLQQAMIYPVVLVVFAVGIVAFLLAAVVP GSPF_VIBCH 166 86 -
KLIQSLIYPCMLTTVAIGVVIILLTAVVP GSPF_ECOLI 159 86 -
KIQLALLYPVILMVASLAIVGFLLGYVVP GSPF_PSEAE 166 86 -
KARTALIYPCVLMGVSLAVVIGLMTFVVP Q52293 160 86 -
KVINALIYPAILLAVVGCALLFLLGYVVP GSPF_XANCP 151 85 -

Motif 3 width=15
Element Seqn Id St Int Rpt
LALGLFEPLLVVSMA GSPF_ERWCA 371 174 -
LVLGLFEPLLVVSMA GSPF_ERWCH 367 172 -
LALGLFEPLLVVGMA O32568 370 174 -
LALSLFEPLLVVAMA GSPF_KLEPN 344 174 -
IALGVFEPLLVVSMA GSPF_AERHY 351 174 -
IALGIFTPALIALMA GSPF_VIBCH 369 174 -
LTLSIFEPALIITMA GSPF_ECOLI 362 174 -
LMVGLFEPFMLIFMG GSPF_PSEAE 369 174 -
TAMALFEPLMILVMG Q52293 363 174 -
RALAALVPLITLVLA GSPF_XANCP 354 174 -

Motif 4 width=20
Element Seqn Id St Int Rpt
VVLFIVLAILQPILQLNTLM GSPF_ERWCA 387 1 -
IVLFIVLAILQPILQLNTLM GSPF_ERWCH 383 1 -
VVLFIVLAILQPLLQLNNMM O32568 386 1 -
MVLFIVLAILQPILQLNTLM GSPF_KLEPN 360 1 -
VVLFIVMSILQPILELNNMV GSPF_AERHY 367 1 -
MVLFIVMATLMPILEMNNLM GSPF_VIBCH 385 1 -
IVLFIVVSVLQPLLQLNSMI GSPF_ECOLI 378 1 -
VVLVIVLAILLPILSLNQLV GSPF_PSEAE 385 1 -
VVLFIVLAVLLPIMQLNQGL Q52293 379 1 -
VVGLVIISVLVPLYDLTNAI GSPF_XANCP 370 1 -