Identifier | BCTERIALGSPD  [View Relations]  [View Alignment]  
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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).
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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.
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Summary Information | 19 codes involving 5 elements 1 codes involving 4 elements 3 codes involving 3 elements 14 codes involving 2 elements
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Composite Feature Index | 5 | 19 | 19 | 19 | 19 | 19 | 4 | 1 | 1 | 0 | 1 | 1 | 3 | 2 | 2 | 1 | 3 | 1 | 2 | 3 | 10 | 1 | 11 | 3 | | 1 | 2 | 3 | 4 | 5 |
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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 | |
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.
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Scan History | OWL30_0 2 300 NSINGLE SPTR37_9f 3 40 NSINGLE
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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 -
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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 -
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