SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR00445

Identifier
HUPFHYPC  [View Relations]  [View Alignment]  
Accession
PR00445
No. of Motifs
4
Creation Date
09-DEC-1995  (UPDATE 17-JUN-1999)
Title
HupF/HypC hydrogenase expression/synthesis family signature
Database References

PROSITE; PS01097 HUPF_HYPC
BLOCKS; BL01097
INTERPRO; IPR001109
Literature References
1. COLBEAU, A., RICHAUD, P., TOUSSAINT, B., CABALLERO, F.J., ELSTER, C., 
DELPHIN, C., SMITH, R.L., CHABERT, J. AND VIGNAIS, P.M.
Organisation of the genes necessary for hydrogenase expression in
Rhodobacter capsulatus. Sequence analysis and identification of 
two hyp regulatory mutants.
MOL.MICROBIOL. 8 15-29 (1993).

Documentation
Bacterial membrane-bound nickel-dependent hydrogenases require several
gene products for their expresssion and/or synthesis [1]. Amongst these
is a group that codes for a family of small proteins (80-110 residues),
which includes A.eutrophus and A.vinelandii hoxL and hypC, R.leguminosarum
and R.capsulatus hupF and hypC, and E.coli hypC and hybG.
 
HUPFHYPC is a 4-element fingerprint that provides a signature for the
hupF/hypC family. The fingerprint was derived from an initial alignment
of 8 sequences: the motifs were drawn from short conserved regions 
spanning the full alignment length - motif 1 spans the region encoded by
PROSITE pattern HUPF_HYPC (PS01097), which includes a conserved N-terminal
Met-Cys dipeptide. Two iterations on OWL26.3 were required to reach 
convergence, at which point a true set comprising 14 sequences was
identified. A single partial match was also found, S39402, a hupF protein
that fails to make a significant match with the final motif.
 
An update on SPTR37_9f identified a true set of 14 sequences, and 8
partial matches.
Summary Information
  14 codes involving  4 elements
5 codes involving 3 elements
3 codes involving 2 elements
Composite Feature Index
414141414
35550
23030
1234
True Positives
HOXL_ALCEU    HOXL_AZOVI    HUPF_RHILV    HUPN_AZOCH    
HYBG_ECOLI HYPC_ALCEU HYPC_AZOCH HYPC_AZOVI
HYPC_ECOLI HYPC_RHILV HYPC_RHOCA HYPC_SYNY3
P95497 YFRC_PROVU
True Positive Partials
Codes involving 3 elements
HUPF_BRAJA HUPF_RHOCA O27686 O28902
Q45250
Codes involving 2 elements
O25559 O69402 Y200_METJA
Sequence Titles
HOXL_ALCEU  HYDROGENASE EXPRESSION/FORMATION PROTEIN HOXL - ALCALIGENES EUTROPHUS. 
HOXL_AZOVI HYDROGENASE EXPRESSION/FORMATION PROTEIN HOXL - AZOTOBACTER VINELANDII.
HUPF_RHILV HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPF - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
HUPN_AZOCH HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPN - AZOTOBACTER CHROOCOCCUM MCD 1.
HYBG_ECOLI HYDROGENASE-2 OPERON PROTEIN HYBG - ESCHERICHIA COLI.
HYPC_ALCEU HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - ALCALIGENES EUTROPHUS.
HYPC_AZOCH PROBABLE HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - AZOTOBACTER CHROOCOCCUM MCD 1.
HYPC_AZOVI PROBABLE HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - AZOTOBACTER VINELANDII.
HYPC_ECOLI HYDROGENASE ISOENZYMES FORMATION PROTEIN HYPC - ESCHERICHIA COLI.
HYPC_RHILV HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
HYPC_RHOCA HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
HYPC_SYNY3 HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P95497 HUPF PROTEIN - PSEUDOMONAS HYDROGENOVORA.
YFRC_PROVU FRD OPERON HYPOTHETICAL PROTEIN C - PROTEUS VULGARIS.

HUPF_BRAJA HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPF - BRADYRHIZOBIUM JAPONICUM.
HUPF_RHOCA HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPF - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
O27686 HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPC - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O28902 HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPC) - ARCHAEOGLOBUS FULGIDUS.
Q45250 HYDROGEN-UPTAKE HYDROGENASE GENE CLUSTER (HUPL) - BRADYRHIZOBIUM JAPONICUM.

O25559 HYDROGENASE EXPRESSION/FORMATION PROTEIN (HYPC) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O69402 HYND PROTEIN - DESULFOVIBRIO GIGAS.
Y200_METJA PUTATIVE HYDROGENASE EXPRESSION/FORMATION PROTEIN MJ0200 - METHANOCOCCUS JANNASCHII.
Scan History
OWL26_3    2  500  NSINGLE    
SPTR37_9f 3 140 NSINGLE
Initial Motifs
Motif 1  width=8
Element Seqn Id St Int Rpt
CIGIPMQV HOXL_ALCEU 2 2 -
CLAIPARL HYPC_ALCEU 2 2 -
CVGIPVQL HUPF_RHOCA 2 2 -
CIGIPMRV HUPF_RHILV 2 2 -
CLGIPGQV YFRC_PROVU 2 2 -
CIGVPGQI HYPC_ECOLI 2 2 -
CLAIPVRI HYPC_AZOVI 2 2 -
CIGVPGQV HYBG_ECOLI 2 2 -

Motif 2 width=17
Element Seqn Id St Int Rpt
GVVDLSGVRKTISLALM HYPC_ALCEU 18 8 -
GDVIEDGRPGLVDLSLV HUPF_RHOCA 17 7 -
ALVDVCGVKREVNIALV YFRC_PROVU 20 10 -
AKVDVCGIQRDVDLTLV HYPC_ECOLI 17 7 -
AVACIGGLRKTINVALL HYPC_AZOVI 18 8 -
AQVEVCGIKRDVNIALI HYBG_ECOLI 20 10 -
AVCAGRGERRRVSSALV HOXL_ALCEU 17 7 -
AQCERHGAISSISLMLV HUPF_RHILV 17 7 -

Motif 3 width=17
Element Seqn Id St Int Rpt
PGDWVLAFLGAAREVLT HUPF_RHOCA 38 4 -
IGKWVLVHVGFAMSIVN YFRC_PROVU 45 8 -
VGQWVLVHVGFAMSVIN HYPC_ECOLI 44 10 -
VGDYVILHVGFALQKLD HYPC_AZOVI 39 4 -
LGQWVLVHVGFAMSIID HYBG_ECOLI 45 8 -
QGDWLLVFLDSARERID HOXL_ALCEU 38 4 -
VGDYVIVHVGYAIGKID HYPC_ALCEU 39 4 -
PGTHLLTHLGSAIRVLD HUPF_RHILV 38 4 -

Motif 4 width=13
Element Seqn Id St Int Rpt
EEAERTLRLFAEL HYPC_ALCEU 57 1 -
DEARAIDDALAGL HUPF_RHILV 56 1 -
QEAQETLNALMAM YFRC_PROVU 63 1 -
PEAAAQISAALGG HUPF_RHOCA 55 0 -
AEARDTLDALQNM HYPC_ECOLI 62 1 -
AEAQRTLALLAEL HYPC_AZOVI 57 1 -
DEAKATLDALRQM HYBG_ECOLI 63 1 -
HEIDATLDMLQAA HOXL_ALCEU 59 4 -
Final Motifs
Motif 1  width=8
Element Seqn Id St Int Rpt
CLGIPGQV YFRC_PROVU 2 2 -
CIGVPGQI HYPC_ECOLI 2 2 -
CLAIPVRI HYPC_AZOCH 2 2 -
CLAIPVRI HYPC_AZOVI 2 2 -
CLGIPGQI HYPC_RHOCA 2 2 -
CIGVPGQV HYBG_ECOLI 2 2 -
CIGIPMQV HOXL_ALCEU 2 2 -
CIGIPMRV P95497 2 2 -
CLAIPVQV HYPC_RHILV 2 2 -
CLAIPARL HYPC_ALCEU 2 2 -
CLALPGQV HYPC_SYNY3 2 2 -
CIGIPMRV HUPF_RHILV 2 2 -
CIGIPLQV HUPN_AZOCH 2 2 -
CIGIPLRV HOXL_AZOVI 2 2 -

Motif 2 width=17
Element Seqn Id St Int Rpt
ALVDVCGVKREVNIALV YFRC_PROVU 20 10 -
AKVDVCGIQRDVDLTLV HYPC_ECOLI 17 7 -
AVACIGGLRKTINVALL HYPC_AZOCH 18 8 -
AVACIGGLRKTINVALL HYPC_AZOVI 18 8 -
ALADVSGVKRAVNVACV HYPC_RHOCA 20 10 -
AQVEVCGIKRDVNIALI HYBG_ECOLI 20 10 -
AVCAGRGERRRVSSALV HOXL_ALCEU 17 7 -
ALCLGRGGQRRISTILV P95497 17 7 -
AKVTLDGVSKIVSTALV HYPC_RHILV 18 8 -
GVVDLSGVRKTISLALM HYPC_ALCEU 18 8 -
GKVSFGGIIKTISLAYV HYPC_SYNY3 23 13 -
AQCERHGAISSISLMLV HUPF_RHILV 17 7 -
ALCGDDREARWIDTRLI HUPN_AZOCH 17 7 -
ALCGDENGVRWIDTRLV HOXL_AZOVI 17 7 -

Motif 3 width=17
Element Seqn Id St Int Rpt
IGKWVLVHVGFAMSIVN YFRC_PROVU 45 8 -
VGQWVLVHVGFAMSVIN HYPC_ECOLI 44 10 -
VGDYVILHVGFALQKLD HYPC_AZOCH 39 4 -
VGDYVILHVGFALQKLD HYPC_AZOVI 39 4 -
LGHWALIHVGFAMSLID HYPC_RHOCA 45 8 -
LGQWVLVHVGFAMSIID HYBG_ECOLI 45 8 -
QGDWLLVFLDSARERID HOXL_ALCEU 38 4 -
AGDWLLVFLDSARERID P95497 38 4 -
VGDYVVLHVGYALAKID HYPC_RHILV 39 4 -
VGDYVIVHVGYAIGKID HYPC_ALCEU 39 4 -
VGDYVIVHVGFAISIVD HYPC_SYNY3 44 4 -
PGTHLLTHLGSAIRVLD HUPF_RHILV 38 4 -
PGDWLLVFLGAAREALD HUPN_AZOCH 38 4 -
PGDWLLVFLDAAREILD HOXL_AZOVI 38 4 -

Motif 4 width=13
Element Seqn Id St Int Rpt
QEAQETLNALMAM YFRC_PROVU 63 1 -
AEARDTLDALQNM HYPC_ECOLI 62 1 -
AEARRTLALLAEL HYPC_AZOCH 57 1 -
AEAQRTLALLAEL HYPC_AZOVI 57 1 -
AEAARTLEALRDL HYPC_RHOCA 63 1 -
DEAKATLDALRQM HYBG_ECOLI 63 1 -
HEIDATLDMLQAA HOXL_ALCEU 59 4 -
AEIDATLDLLQAA P95497 59 4 -
EEAERTLALIRER HYPC_RHILV 57 1 -
EEAERTLRLFAEL HYPC_ALCEU 57 1 -
EAAQETLIDLAEM HYPC_SYNY3 62 1 -
DEARAIDDALAGL HUPF_RHILV 56 1 -
AQIRDALCALQAV HUPN_AZOCH 59 4 -
GRAARIREALRAL HOXL_AZOVI 56 1 -