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PR00446

Identifier
HYDRGNUPTAKE  [View Relations]  [View Alignment]  
Accession
PR00446
No. of Motifs
5
Creation Date
09-DEC-1995  (UPDATE 28-JUL-1999)
Title
Hydrogen uptake protein signature
Database References

INTERPRO; IPR000671
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).
 
2. MENON, N.K., ROBBINS, J., PECK, H.D., CHATELUS, C.Y., CHOI, E.S. AND
PRZYBYLA, A.E.
Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1
operon containing six open reading frames.
J.BACTERIOL. 172 1969-1977 (1990).
 
3. HIDALGO, E., LEYVA, A. AND RUIZ-ARGUESO, T.
Nucleotide sequence of the hydrogenase structural genes from Rhizobium
leguminosarum.
PLANT MOL.BIOL. 15 367-370 (1990).
 
4. MENON, A.L., MORTENSON, L.E. AND ROBSON, R.L.
Nucleotide sequences and genetic analysis of hydrogen oxidation (hox)
genes in Azotobacter vinelandii.
J.BACTERIOL. 174 4549-4557 (1992).
 
5. KORTLUKE, C., HORSTMANN, K., SCHWARTZ, E., ROHDE, M., BINSACK, R. 
AND FRIEDRICH, B.
A gene complex coding for the membrane-bound hydrogenase of Alcaligenes
eutrophus H16.
J.BACTERIOL. 174 6277-6289 (1992).

Documentation
The hydrogenase-specific gene (hup and hyp) products of R.capsulatus show
[1] a high degree of similarity to hydrogenase gene products from E.coli 
(hyaD) [2], R.leguminosarum (hupD) [3], A.vinlandii (hoxM) [4] and
A.eutrophus (hoxM) [5], which together are designated the hupD/hyaD family.
The hup and hox gene products are absolutely required for hydrogenase
activity, hoxM mediating the attachment of hydrogenase to the bacterial
membrane, which is essential for enzymatic activity. The function of hyaD
is unknown, but with hyaE could form a complex involved in processing of
the hydrogenase 1 structural operon. 
 
HYDRGNUPTAKE is a 5-element fingerprint that provides a signature for the
hupD/hyaD family. The fingerprint was derived from an initial alignment of
6 sequences: the motifs were drawn from short conserved regions spanning
the full alignment length. Two iterations on OWL26.3 were required to reach
convergence, at which point a true set comprising 14 sequences was
identified. Two partial matches were also found, both of which are
hypothetical proteins: S24796 fails to make a significant match with 
motif 3, and PQ0128 is a fragment lacking the portion of sequence bearing
the final 3 motifs.
 
An update on SPTR37_9f identified a true set of 22 sequences, and 2
partial matches.
Summary Information
  22 codes involving  5 elements
0 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
52222222222
400000
322101
200000
12345
True Positives
FRHD_METJA    FRHD_METTH    HOXM_ALCEU    HOXM_AZOVI    
HUPD_BRAJA HUPD_RHILV HUPD_RHOCA HUPM_AZOCH
HYAD_ECOLI HYBD_ECOLI HYCI_ECOLI O28893
O33166 O66898 O69401 P95496
Q00392 Q00396 Q45249 Q52829
Q56362 Y253_METJA
True Positive Partials
Codes involving 3 elements
O25351 O58707
Sequence Titles
FRHD_METJA  COENZYME F420 HYDROGENASE DELTA SUBUNIT (PUTATIVE COENZYME F420 HYDROGENASE PROCESSING SUBUNIT) - METHANOCOCCUS JANNASCHII. 
FRHD_METTH COENZYME F420 HYDROGENASE DELTA SUBUNIT (PUTATIVE COENZYME F420 HYDROGENASE PROCESSING SUBUNIT) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
HOXM_ALCEU HYDROGENASE EXPRESSION/FORMATION PROTEIN HOXM - ALCALIGENES EUTROPHUS.
HOXM_AZOVI HYDROGENASE EXPRESSION/FORMATION PROTEIN HOXM - AZOTOBACTER VINELANDII.
HUPD_BRAJA HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPD - BRADYRHIZOBIUM JAPONICUM.
HUPD_RHILV HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPD - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
HUPD_RHOCA HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPD - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
HUPM_AZOCH HYDROGENASE EXPRESSION/FORMATION PROTEIN HUPM - AZOTOBACTER CHROOCOCCUM MCD 1.
HYAD_ECOLI HYDROGENASE 1 MATURATION PROTEASE (EC 3.4.-.-) - ESCHERICHIA COLI.
HYBD_ECOLI HYDROGENASE 2 MATURATION PROTEASE (EC 3.4.-.-) - ESCHERICHIA COLI.
HYCI_ECOLI HYDROGENASE 3 MATURATION PROTEASE (EC 3.4.-.-) - ESCHERICHIA COLI.
O28893 F420-NONREDUCING HYDROGENASE (VHTD-2) - ARCHAEOGLOBUS FULGIDUS.
O33166 F420-REDUCING HYDROGENASE ISOENZYME II DELTA SUBUNIT - METHANOSARCINA BARKERI.
O66898 HUPD HYDROGENASE RELATED FUNCTION - AQUIFEX AEOLICUS.
O69401 HYNC PROTEIN - DESULFOVIBRIO GIGAS.
P95496 HUPD PROTEIN - PSEUDOMONAS HYDROGENOVORA.
Q00392 18.5 KD PROTEIN IN FRCA-FRCG INTERGENIC REGION - METHANOCOCCUS VOLTAE.
Q00396 19.1 KD PROTEIN IN FRUA-FRUG INTERGENIC REGION - METHANOCOCCUS VOLTAE.
Q45249 HYDROGEN-UPTAKE HYDROGENASE GENE CLUSTER (HUPL) - BRADYRHIZOBIUM JAPONICUM.
Q52829 HUPD - RHIZOBIUM LEGUMINOSARUM.
Q56362 HYDROGENASE BIOSYNTHESIS OPERON ENCODING HUPS, HUPL, HUPC, HUPD, HUPH, GENES, COMPLETE CDS, AND HUPI - THIOCAPSA ROSEOPERSICINA.
Y253_METJA PUTATIVE HYDROGENASE MATURATION PROTEASE MJ0253 (EC 3.-.-.-) - METHANOCOCCUS JANNASCHII.

O25351 QUINONE-REACTIVE NI/FE HYDROGENASE (HYDD) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O58707 147AA LONG HYPOTHETICAL HYDROGENASE - PYROCOCCUS HORIKOSHII.
Scan History
OWL26_3    2  300  NSINGLE    
SPTR37_9f 3 120 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
ILVLGIGNILWAD HUPD_RHILV 15 15 -
VLVLGIGNVLWAD HUPD_RHOCA 9 9 -
VVAMGIGNVLWAD HOXM_ALCEU 2 2 -
VVVMGLGNLLWAD HYAD_ECOLI 6 6 -
ILVLGVGNILLTD HYBD_ECOLI 3 3 -
ILVVGCGNILFKD FRHD_METTH 7 7 -

Motif 2 width=12
Element Seqn Id St Int Rpt
DEGFGVRAVEAF HUPD_RHILV 27 -1 -
DEGFGVRCVERM HUPD_RHOCA 21 -1 -
DEGFGVRCIETL HOXM_ALCEU 14 -1 -
DEGFGVRVAERL HYAD_ECOLI 18 -1 -
DEAIGVRIVEAL HYBD_ECOLI 15 -1 -
DDGFGPEVIKAL FRHD_METTH 19 -1 -

Motif 3 width=18
Element Seqn Id St Int Rpt
NVTILDGGTQGLYLVQFV HUPD_RHILV 47 8 -
NVRLLDGGTQGLYLLPFL HUPD_RHOCA 41 8 -
QVCLVDGGTQGLYLIHHV HOXM_ALCEU 34 8 -
YVEIVDGGTQGLNLLGYV HYAD_ECOLI 38 8 -
YVEILDGGTAGMELLGDM HYBD_ECOLI 35 8 -
NVMFIDAGTGGPHFVFSL FRHD_METTH 42 11 -

Motif 4 width=11
Element Seqn Id St Int Rpt
DRLIGFDAIDY HUPD_RHILV 68 3 -
EALIVFDAVDF HUPD_RHOCA 62 3 -
SRLLIFDAIDY HOXM_ALCEU 55 3 -
SHLLILDAIDY HYAD_ECOLI 59 3 -
DHLIIADAIVS HYBD_ECOLI 56 3 -
KKMIVVDVVEF FRHD_METTH 65 5 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GLEPGTMKVVEDDEVPK HUPD_RHILV 79 0 -
GFTPGTLVTMRDDDVPA HUPD_RHOCA 73 0 -
GLPPGTLRIIEDEAVPK HOXM_ALCEU 66 0 -
GLEPGTLRTYAGERIPA HYAD_ECOLI 70 0 -
KNAPGTMMILRDEEVPA HYBD_ECOLI 68 1 -
NAEPGTLRKFDVTEIPK FRHD_METTH 76 0 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
ILVLGIGNILWAD Q52829 15 15 -
ILVLGIGNILWAD HUPD_BRAJA 10 10 -
ILVLGIGNILWAD Q45249 10 10 -
ILVLGIGNILWAD HUPD_RHILV 15 15 -
ILILGIGNLLWAD HOXM_AZOVI 6 6 -
ILVLGIGNLLWAD Q56362 7 7 -
ILILGIGNLLWAD HUPM_AZOCH 8 8 -
IIVLGIGNVLWAD P95496 20 20 -
VLVLGIGNVLWAD HUPD_RHOCA 9 9 -
VVAMGIGNVLWAD HOXM_ALCEU 2 2 -
VVVMGLGNLLWAD HYAD_ECOLI 6 6 -
ILVLGVGNILLTD HYBD_ECOLI 3 3 -
ILVMGVGNILYTD O69401 8 8 -
ILIVGCGNLLFGD Y253_METJA 6 6 -
ITVLGIGNILLSD O66898 2 2 -
IVVAGCGNPLFAD O33166 8 8 -
ILVLGCGNILFGD Q00392 9 9 -
IMVLACGNILFAD FRHD_METJA 28 28 -
TLILACGNILFAD Q00396 18 18 -
ILVVGVGNPLMGD O28893 4 4 -
ILVVGCGNILFKD FRHD_METTH 7 7 -
DVLLCVGNSMMGD HYCI_ECOLI 2 2 -

Motif 2 width=12
Element Seqn Id St Int Rpt
DEGFGVRAVEAF Q52829 27 -1 -
DEGFGVRAVEEF HUPD_BRAJA 22 -1 -
DEGFGVRAVEEF Q45249 22 -1 -
DEGFGVRAVEAF HUPD_RHILV 27 -1 -
DEGFGVRCVELL HOXM_AZOVI 18 -1 -
DEGFGVRAVEAL Q56362 19 -1 -
DEGFGVRCVELL HUPM_AZOCH 20 -1 -
DEGLGVRCVELL P95496 32 -1 -
DEGFGVRCVERM HUPD_RHOCA 21 -1 -
DEGFGVRCIETL HOXM_ALCEU 14 -1 -
DEGFGVRVAERL HYAD_ECOLI 18 -1 -
DEAIGVRIVEAL HYBD_ECOLI 15 -1 -
DEGLGVRLVEHL O69401 20 -1 -
DDGFGCEVVSKL Y253_METJA 18 -1 -
DEGLGVRTVEEL O66898 14 -1 -
DDGFGPAVVEKL O33166 20 -1 -
DDGFGYHMIKRL Q00392 21 -1 -
DDGFSVHVIEKL FRHD_METJA 40 -1 -
DDGFSVHVIEKL Q00396 30 -1 -
DDGLGIRVVEEL O28893 16 -1 -
DDGFGPEVIKAL FRHD_METTH 19 -1 -
DDGAGPLLAEKC HYCI_ECOLI 14 -1 -

Motif 3 width=18
Element Seqn Id St Int Rpt
NVTILDGGTQGLYLVQFV Q52829 47 8 -
NVTILDGGTQGLYLVNYL HUPD_BRAJA 42 8 -
NVTILDGGTQGLYLVNYL Q45249 42 8 -
NVTILDGGTQGLYLVQFV HUPD_RHILV 47 8 -
GVRLMDGGTQGIYLVQHV HOXM_AZOVI 38 8 -
NVQLLDGGTQGIYLVDRV Q56362 39 8 -
GVRLMDGGTQGIYLVQHV HUPM_AZOCH 40 8 -
HVQLVDGGTQGLYLISYV P95496 52 8 -
NVRLLDGGTQGLYLLPFL HUPD_RHOCA 41 8 -
QVCLVDGGTQGLYLIHHV HOXM_ALCEU 34 8 -
YVEIVDGGTQGLNLLGYV HYAD_ECOLI 38 8 -
YVEILDGGTAGMELLGDM HYBD_ECOLI 35 8 -
QVTLFDGGTLGMRLMGPI O69401 40 8 -
NVEVIDAGASGAYYLMTL Y253_METJA 37 7 -
NVKVLDGGTLGIDLLYHI O66898 34 8 -
NVTVVDAGLGGPHFVFTL O33166 39 7 -
KIQLIDAGTGAFSLYFII Q00392 46 13 -
KIALVDAGAGAPQQVLTL FRHD_METJA 62 10 -
HVALVDAGAGAPQQVLTL Q00396 52 10 -
NVTVMDGGTGSFDLVNYF O28893 35 7 -
NVMFIDAGTGGPHFVFSL FRHD_METTH 42 11 -
NWVVIDGGSAPENDIVAI HYCI_ECOLI 32 6 -

Motif 4 width=11
Element Seqn Id St Int Rpt
DRLIVFDAIDY Q52829 68 3 -
DRLIVFDAIDY HUPD_BRAJA 63 3 -
DRLIVFDAIDY Q45249 63 3 -
DRLIGFDAIDY HUPD_RHILV 68 3 -
DCLIVFDAVDY HOXM_AZOVI 59 3 -
DVLVVFDAVDY Q56362 60 3 -
DCLIVFDAVDY HUPM_AZOCH 61 3 -
ERLLILDAIDY P95496 73 3 -
EALIVFDAVDF HUPD_RHOCA 62 3 -
SRLLIFDAIDY HOXM_ALCEU 55 3 -
SHLLILDAIDY HYAD_ECOLI 59 3 -
DHLIIADAIVS HYBD_ECOLI 56 3 -
DLLIVLDAVLG O69401 61 3 -
KKIIVVDAIDF Y253_METJA 60 5 -
EKLLIIDAVLG O66898 55 3 -
KTLIIVDIADF O33166 63 6 -
KKIVIADIIDY Q00392 71 7 -
KKIIVVDVIDW FRHD_METJA 87 7 -
KNITVVDVIDY Q00396 77 7 -
DVVVIVDAVNF O28893 56 3 -
KKMIVVDVVEF FRHD_METTH 65 5 -
TRLLIVDATDM HYCI_ECOLI 55 5 -

Motif 5 width=17
Element Seqn Id St Int Rpt
GLEPGTMKVVEDDEVPK Q52829 79 0 -
GLEPGRLKLVRDDEVPR HUPD_BRAJA 74 0 -
GLEPGRLKLVRDDEVPR Q45249 74 0 -
GLEPGTMKVVEDDEVPK HUPD_RHILV 79 0 -
GLAPGTLKIVRDDEVPR HOXM_AZOVI 70 0 -
GLPPGTMKRVEDDEVPR Q56362 71 0 -
GLAPGTLKVVRDDEVPR HUPM_AZOCH 72 0 -
GLAPGTLRIIEDEEVPK P95496 84 0 -
GFTPGTLVTMRDDDVPA HUPD_RHOCA 73 0 -
GLPPGTLRIIEDEAVPK HOXM_ALCEU 66 0 -
GLEPGTLRTYAGERIPA HYAD_ECOLI 70 0 -
KNAPGTMMILRDEEVPA HYBD_ECOLI 68 1 -
GDEPGAMYRLTGDDLRK O69401 72 0 -
DLEPGTIKKIDVDELPN Y253_METJA 71 0 -
GKKPGTFYKIKNENVKK O66898 66 0 -
GGEPGELRWLSVDELPV O33166 74 0 -
GLEPGTLKKLCVEDIPN Q00392 82 0 -
GIKPGEIKIIEKDELPN FRHD_METJA 98 0 -
GLEPGTIEILTKENLPN Q00396 88 0 -
GGKPGRVYRLPVERVLK O28893 67 0 -
NAEPGTLRKFDVTEIPK FRHD_METTH 76 0 -
GLNPGEIRIIDPDDIAE HYCI_ECOLI 66 0 -