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PR00811

Identifier
BCTERIALGSPD  [View Relations]  [View Alignment]  
Accession
PR00811
No. of Motifs
5
Creation Date
10-MAR-1998  (UPDATE 23-JUN-1999)
Title
Bacterial general secretion pathway protein D signature
Database References
PRINTS; PR01032 PHAGEIV
PROSITE; PS00875 T2SP_D
BLOCKS; BL00875
PFAM; PF00263 Bac_GSPproteins
INTERPRO; IPR001775
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. D'ENFERT, C., REYSS, I., WANDERSMAN, C. AND PUGSLEY, A.P.
Protein secretion by Gram-negative bacteria. Characterization of two membrane
proteins required for pullanase secretion by Escherichia coli K-12.
J.BIOL.CHEM. 264(29) 17462-17468 (1989).

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. 
 
A number of proteins are involved in the GSP; one of these is known as 
protein D (GSPD protein), the most probable location of which is the outer
membrane [4]. This suggests that protein D constitutes the apparatus of the 
accessory mechanism, and is thus involved in transporting exoproteins from
the periplasm, across the outer membrane, to the extracellular environment.
 
BCTERIALGSPD is a 5-element fingerprint that provides a signature for 
general secretion pathway protein D. The fingerprint was derived from
an initial alignment of 9 sequences: the motifs were drawn from conserved
regions within the C-terminal portion of the alignment - motif 4 includes
part of the region encoded by PROSITE pattern T2SP_D (PS00875), which
includes two conserved proline residues. Two iterations on OWL30.0 were
required to reach convergence, at which point a true set comprising 14
sequences was identified. Several partial matches were also found: those
matching 3 motifs are related gene IV and fimbrial assembly proteins, most
of which match motifs 1, 2 and 4; those matching 2 motifs are related
secretion proteins. 
 
An update on SPTR37_9f identified a true set of 19 sequences, and 18
partial matches.
Summary Information
  19 codes involving  5 elements
1 codes involving 4 elements
3 codes involving 3 elements
14 codes involving 2 elements
Composite Feature Index
51919191919
411011
322131
23101113
12345
True Positives
GSPD_AERHY    GSPD_AERSA    GSPD_ECOLI    GSPD_ERWCA    
GSPD_ERWCH GSPD_KLEPN GSPD_PSEAE GSPD_VIBCH
GSQD_ERWCH O32566 O52657 O80300
O84681 Q47423 Q52291 Q96223
VG4_BPF1 VG4_BPFD VG4_BPM13
True Positive Partials
Codes involving 4 elements
GSPD_XANCP
Codes involving 3 elements
O80264 PILQ_PSEAE VG4_BPI22
Codes involving 2 elements
COME_HAEIN HOFQ_ECOLI O52135 O67320
O85636 OMC_NEIGO P74864 P94652
P94767 Q46625 Q47631 Q50972
Q56673 VG4_BPIKE
Sequence Titles
GSPD_AERHY  GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR - AEROMONAS HYDROPHILA. 
GSPD_AERSA GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR - AEROMONAS SALMONICIDA.
GSPD_ECOLI PROBABLE GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR - ESCHERICHIA COLI.
GSPD_ERWCA GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR (PECTIC ENZYMES SECRETION PROTEIN OUTD) - ERWINIA CAROTOVORA.
GSPD_ERWCH GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR (PECTIC ENZYMES SECRETION PROTEIN OUTD) - ERWINIA CHRYSANTHEMI.
GSPD_KLEPN GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR (PULLULANASE SECRETION ENVELOPE PULD) - KLEBSIELLA PNEUMONIAE.
GSPD_PSEAE GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR - PSEUDOMONAS AERUGINOSA.
GSPD_VIBCH GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR (CHOLERA TOXIN SECRETION PROTEIN EPSD) - VIBRIO CHOLERAE.
GSQD_ERWCH GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR (PECTIC ENZYMES SECRETION PROTEIN OUTD) - ERWINIA CHRYSANTHEMI.
O32566 ETPD PROTEIN - ESCHERICHIA COLI.
O52657 XQHA - PSEUDOMONAS AERUGINOSA.
O80300 GENE IV PROTEIN (GPIV) - BACTERIOPHAGE IF1.
O84681 YOP C/GEN SECRETION PROTEIN D - CHLAMYDIA TRACHOMATIS.
Q47423 PLASMID PO157 DNA, PULD GENE - ESCHERICHIA COLI.
Q52291 UXPB, UXPA, XCPP, XCPQ, XCPR, XCPS AND XCPT GENES - PSEUDOMONAS PUTIDA.
Q96223 GENE IV PROTEIN (GPIV) - BACTERIOPHAGE F1.
VG4_BPF1 GENE IV PROTEIN (GPIV) - BACTERIOPHAGE F1.
VG4_BPFD GENE IV PROTEIN (GPIV) - BACTERIOPHAGE FD.
VG4_BPM13 GENE IV PROTEIN (GPIV) - BACTERIOPHAGE M13.

GSPD_XANCP GENERAL SECRETION PATHWAY PROTEIN D PRECURSOR - XANTHOMONAS CAMPESTRIS (PV. CAMPESTRIS).

O80264 SIMILAR TO GENE IV PROTEIN :ACC# A04268 - VIBRIO CHOLERAE FILAMENTOUS BACTERIOPHAGE FS-2.
PILQ_PSEAE FIMBRIAL ASSEMBLY PROTEIN PILQ PRECURSOR - PSEUDOMONAS AERUGINOSA.
VG4_BPI22 GENE IV PROTEIN (GPIV) - BACTERIOPHAGE I2-2.

COME_HAEIN COMPETENCE PROTEIN E PRECURSOR (DNA TRANSFORMATION PROTEIN COME) - HAEMOPHILUS INFLUENZAE.
HOFQ_ECOLI PROTEIN TRANSPORT PROTEIN HOFQ PRECURSOR - ESCHERICHIA COLI.
O52135 ESCC - ESCHERICHIA COLI.
O67320 GENERAL SECRETION PATHWAY PROTEIN D - AQUIFEX AEOLICUS.
O85636 L0041 - ESCHERICHIA COLI.
OMC_NEIGO OUTER MEMBRANE PROTEIN OMC PRECURSOR - NEISSERIA GONORRHOEAE.
P74864 SPIA - SALMONELLA TYPHIMURIUM.
P94652 EXPORTER PROTEIN - CHLOROBIUM LIMICOLA.
P94767 HRCC PRECURSOR - ERWINIA CHRYSANTHEMI.
Q46625 HRCC PRECURSOR - ERWINIA AMYLOVORA.
Q47631 SEPC - ESCHERICHIA COLI.
Q50972 PILQ - NEISSERIA GONORRHOEAE.
Q56673 MANNOSE-SENSITIVE HEMAGGLUTININ D - VIBRIO CHOLERAE.
VG4_BPIKE GENE IV PROTEIN (GPIV) - BACTERIOPHAGE IKE.
Scan History
OWL30_0    2  300  NSINGLE    
SPTR37_9f 3 40 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
QVLVEAIIVEI GSPD_AERHY 353 353 -
QVLVEAIIVEI GSPD_AERSA 352 352 -
QVLVEAAIVEI GSPD_PSEAE 360 360 -
QVLIEALIVEM GSPD_VIBCH 343 343 -
QVHIEAQIAEV GSPD_XANCP 479 479 -
QVLVEAIIAEV GSPD_KLEPN 346 346 -
QVLVEAIIAEV GSPD_ERWCA 335 335 -
QVLVEAIIVEV GSPD_ECOLI 351 351 -
QVLVEAIIAEI GSPD_ERWCH 399 399 -

Motif 2 width=25
Element Seqn Id St Int Rpt
MLVTALSTNTKSDILSTPSIVTMDN GSPD_AERHY 432 68 -
ALVTALSANTKSNLLSTPSLLTLDN GSPD_PSEAE 434 63 -
AIISALDQVTNLRLLQTPSVFVRNN GSPD_XANCP 553 63 -
ALINAVSNDSSSNILSSPSITVMDN GSPD_VIBCH 445 91 -
MLLTALSSSTKNDILATPSIVTLDN GSPD_KLEPN 426 69 -
MLMTALSSNSKNDILATPSIVTLDN GSPD_ERWCA 415 69 -
VLLTALASNNKNDILATPSIVTLDN GSPD_ECOLI 433 71 -
MLLTALSSDGKNDVLATPSIVTLDN GSPD_ERWCH 479 69 -
ALVTALSTSTKSDILSTPSIVTMDN GSPD_AERSA 431 68 -

Motif 3 width=11
Element Seqn Id St Int Rpt
VPFQTGSYTTN GSPD_PSEAE 469 10 -
IPINSTSINTG GSPD_XANCP 588 10 -
VPVLTGSQTTS GSPD_KLEPN 461 10 -
VPVLAGSQTTS GSPD_ERWCA 450 10 -
VPVLSGSQTTS GSPD_ECOLI 468 10 -
VPVLTGSQTTV GSPD_ERWCH 514 10 -
VPVQTGTQNST GSPD_AERHY 467 10 -
VPVQSGSQSST GSPD_AERSA 466 10 -
VPVITGSTAGS GSPD_VIBCH 480 10 -

Motif 4 width=19
Element Seqn Id St Int Rpt
GIPFLSKLPVVGALFGRKT GSPD_XANCP 697 98 -
KVPLLGDIPVIGALFRSTS GSPD_KLEPN 559 87 -
KVPLLGDIPVLGYLFRSNS GSPD_ERWCA 548 87 -
KVPLLGDIPLVGQLFRYTS GSPD_ECOLI 563 84 -
KVPLLGDIPWLGSLFRSKT GSPD_ERWCH 614 89 -
KVPLLGDIPVLGYLFRSTS GSPD_AERHY 565 87 -
KVPLLGDIPVLGYLFRSTN GSPD_AERSA 565 88 -
KVPLLGDIPLLGRLFRSTK GSPD_PSEAE 569 89 -
KVPLLGDIPLLGQLFRSTS GSPD_VIBCH 575 84 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KRNLMVFLRPTVVRD GSPD_PSEAE 592 4 -
KKNLMVFIKPTIIRD GSPD_VIBCH 598 4 -
KRNLMLFIRPTVIRD GSPD_KLEPN 582 4 -
RREVIVLITPSIVRN GSPD_XANCP 720 4 -
KRNLMLFIRPSIIRD GSPD_ERWCA 571 4 -
KRNLMVFIRPTIIRD GSPD_ECOLI 586 4 -
KRNLMLFLRPTIIRD GSPD_ERWCH 637 4 -
KRNLMVFIRPTILRD GSPD_AERHY 588 4 -
KRNLMVFIRPTILRD GSPD_AERSA 588 4 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
QVLVEAIIAEV GSPD_KLEPN 346 346 -
QVLVEAIIAEI GSQD_ERWCH 399 399 -
QVLVEAIIAEI O32566 276 276 -
QVLVEAIIAEI Q47423 287 287 -
QVLVEAIIAEV GSPD_ERWCA 335 335 -
QVLVEAIIVEV GSPD_ECOLI 351 351 -
QVLVEAIIAEI GSPD_ERWCH 399 399 -
QVLVEAIIVEI GSPD_AERHY 353 353 -
QVLVEAIIVEI GSPD_AERSA 352 352 -
QVLVEAAIVEI GSPD_PSEAE 360 360 -
QLLVEAAIVEL O52657 352 352 -
QVLIEALIVEM GSPD_VIBCH 343 343 -
QVVVEAIIAEV Q52291 291 291 -
QILIEGLIFEV Q96223 197 197 -
QILIEGLIFEV VG4_BPF1 197 197 -
QILIEGLIFEV VG4_BPFD 197 197 -
QILIEGLIFEV VG4_BPM13 197 197 -
QVLVESVIFET O80300 199 199 -
QVYIEVLILET O84681 596 596 -

Motif 2 width=25
Element Seqn Id St Int Rpt
MLLTALSSSTKNDILATPSIVTLDN GSPD_KLEPN 426 69 -
MLLTALSSDSKNDVLATPSIVTLDN GSQD_ERWCH 479 69 -
MLLTALSTSSKNDILATPSIVTLDN O32566 352 65 -
MLLTALSTSSKNDILATPSIVTLDN Q47423 363 65 -
MLMTALSSNSKNDILATPSIVTLDN GSPD_ERWCA 415 69 -
VLLTALASNNKNDILATPSIVTLDN GSPD_ECOLI 433 71 -
MLLTALSSDGKNDVLATPSIVTLDN GSPD_ERWCH 479 69 -
MLVTALSTNTKSDILSTPSIVTMDN GSPD_AERHY 432 68 -
ALVTALSTSTKSDILSTPSIVTMDN GSPD_AERSA 431 68 -
ALVTALSANTKSNLLSTPSLLTLDN GSPD_PSEAE 434 63 -
ALVTALSRNSRSNLLSTPSLLTLDN O52657 425 62 -
ALINAVSNDSSSNILSSPSITVMDN GSPD_VIBCH 445 91 -
MLVNALKGKSGFNLLSTPTLLTLDN Q52291 374 72 -
LSVRALKTNSHSKILSVPRILTLSG Q96223 256 48 -
LSVRALKTNSHSKILSVPRILTLSG VG4_BPF1 256 48 -
LSVRALKTNSHSKILSVPRILTLSG VG4_BPFD 256 48 -
LSVRALKTNSHSKILSVPRILTLSG VG4_BPM13 256 48 -
LSLKALETSSKSTLLSMPRILTMSG O80300 259 49 -
GLLSALDQDGDTTVVLNPRIMAQDT O84681 700 93 -

Motif 3 width=11
Element Seqn Id St Int Rpt
VPVLTGSQTTS GSPD_KLEPN 461 10 -
VPVLTGSQTTS GSQD_ERWCH 514 10 -
VPVLSGSQTTS O32566 387 10 -
VPVLSGSQTTS Q47423 398 10 -
VPVLAGSQTTS GSPD_ERWCA 450 10 -
VPVLSGSQTTS GSPD_ECOLI 468 10 -
VPVLTGSQTTV GSPD_ERWCH 514 10 -
VPVQTGTQNST GSPD_AERHY 467 10 -
VPVQSGSQSST GSPD_AERSA 466 10 -
VPFQTGSYTTN GSPD_PSEAE 469 10 -
VPFQTGSYTTS O52657 460 10 -
VPVITGSTAGS GSPD_VIBCH 480 10 -
VPFVTGSVTQN Q52291 409 10 -
VPFITGRVTGE Q96223 291 10 -
VPFITGRVTGE VG4_BPF1 291 10 -
VPFITGRVTGE VG4_BPFD 291 10 -
VPFITGRVTGE VG4_BPM13 291 10 -
VPFVTGRVTGE O80300 294 10 -
VIQETGSVTQN O84681 743 18 -

Motif 4 width=19
Element Seqn Id St Int Rpt
KVPLLGDIPVIGALFRSTS GSPD_KLEPN 559 87 -
KVPLLGDIPWLGSLFRSKS GSQD_ERWCH 612 87 -
KVPLLGDIPVLGHLFRAKS O32566 485 87 -
KVPLLGDIPVLGHLFRAKS Q47423 496 87 -
KVPLLGDIPVLGYLFRSNS GSPD_ERWCA 548 87 -
KVPLLGDIPLVGQLFRYTS GSPD_ECOLI 563 84 -
KVPLLGDIPWLGSLFRSKT GSPD_ERWCH 614 89 -
KVPLLGDIPVLGYLFRSTS GSPD_AERHY 565 87 -
KVPLLGDIPVLGYLFRSTN GSPD_AERSA 565 88 -
KVPLLGDIPLLGRLFRSTK GSPD_PSEAE 569 89 -
RVPLLGDIPGVGRLFRSSR O52657 561 90 -
KVPLLGDIPLLGQLFRSTS GSPD_VIBCH 575 84 -
RVPLLGDIPYLGRLFRSDA Q52291 503 83 -
GVPFLSKIPLIGLLFSSRS Q96223 388 86 -
GVPFLSKIPLIGLLFSSRS VG4_BPF1 388 86 -
GVPFLSKIPLIGLLFSSRS VG4_BPFD 388 86 -
GVPFLSKIPLIGLLFSSRS VG4_BPM13 388 86 -
SVPWVSKIPLIGALFTSKS O80300 391 86 -
GVPLLSSLPLIKGLFSRSI O84681 830 76 -

Motif 5 width=15
Element Seqn Id St Int Rpt
KRNLMLFIRPTVIRD GSPD_KLEPN 582 4 -
KRNLMLFLRPTIIRD GSQD_ERWCH 635 4 -
KRNLMLFIRPTIIRE O32566 508 4 -
KRNLMLFIRPTIIRE Q47423 519 4 -
KRNLMLFIRPSIIRD GSPD_ERWCA 571 4 -
KRNLMVFIRPTIIRD GSPD_ECOLI 586 4 -
KRNLMLFLRPTIIRD GSPD_ERWCH 637 4 -
KRNLMVFIRPTILRD GSPD_AERHY 588 4 -
KRNLMVFIRPTILRD GSPD_AERSA 588 4 -
KRNLMVFLRPTVVRD GSPD_PSEAE 592 4 -
KRNLMVFLRPSIVRD O52657 584 4 -
KKNLMVFIKPTIIRD GSPD_VIBCH 598 4 -
KQNLMVFIRPRILRD Q52291 526 4 -
ESTLYVLVKATIVRA Q96223 411 4 -
ESTLYVLVKATIVRA VG4_BPF1 411 4 -
ESTLYVLVKATIVRA VG4_BPFD 411 4 -
ESTLYVLVKATIVRA VG4_BPM13 411 4 -
KRTLYILIRARVVNL O80300 414 4 -
KRNIMIFIKPKVISS O84681 853 4 -