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PR00161

Identifier
NIHGNASECYTB  [View Relations]  [View Alignment]  
Accession
PR00161
No. of Motifs
5
Creation Date
02-NOV-1994  (UPDATE 27-JUN-1999)
Title
Nickel-dependent hydrogenase/B-type cytochrome signature
Database References

PROSITE; PS00882 NI_HGENASE_CYTB_1; PS00883 NI_HGENASE_CYTB_2
BLOCKS; BL00882
PFAM; PF01292 Ni_hydr_CYTB
INTERPRO; IPR000516
Literature References
1. CAUVIN, B., COLBEAU, A. AND VIGNAIS, P.M.
The hydrogenase structural operon in Rhodobacter capsulatus contains
a third gene, HumP, necessary for the formation of a physiologically
competent hydrogenase.
MOL.MICROBIOL. 5 2519-2527 (1991).
 
2. DROSS, F., GEISLER, V., LENGER, R., THEIS, F., KRAFFT, T.,
FAHRENHOLZ, F., KOJRO, E., DUCHENE, A., TRIPIER, D., JUVENAL, K.
AND KROEGER, A.
The quinone reactive Ni/Fe-hydrogenase of Wolinella succinogenes.
EUR.J.BIOCHEMISTRY 206 93-102 (1992).
 
3. HIDALGO, E., PALACIOS, J.M., MURILLO, J. AND RUIZ-ARGUESO, T.
Nucleotide sequence and characterisation of 4 additional genes of the
hydrogenase structural operon from Rhizobium leguminosarum. 
J.BACTERIOL. 174 4130-4139 (1992).

Documentation
Bacterial membrane-bound nickel-dependent hydrogenases appear to be
associated with b-type cytochrome [1-3], which is involved in electron
transfer from hydrogen to oxygen. The cytochrome is thought to contain
4 transmembrane (TM) regions, which include several histidine residues
that may be involved in coordination of the haem iron group.
 
NIHGENASECYTB is a 5-element fingerprint that provides a signature for
nickel-dependent hydrogenase b-type cytochrome subunits. The fingerprint
was derived from an initial alignment of 7 sequences: the first 4 motifs
were drawn from the putative TM regions and the fifth includes a C-terminal
hydrophilic domain - motifs 1 and 4 span the regions encoded by PROSITE
patterns NI_HGENASE_CYTB_1 (PS00882) and NI_HGENASE_CYTB_2 (PS00883), both
of which contain conserved His residues. Two iterations on OWL24.0 were
required to reach convergence, at which point a true set comprising 10
sequences was identified. A single partial match was also found, a fragment
lacking the last 3 motifs.
 
An update on SPTR37_9f identified a true set of 14 sequences, and 1
partial match.
Summary Information
  14 codes involving  5 elements
1 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
51414141414
411110
300000
200000
12345
True Positives
CYBH_ALCEU    CYBH_AZOCH    CYBH_AZOVI    CYBH_BRAJA    
CYBH_ECOLI CYBH_RHILV CYBH_RHOCA CYBH_WOLSU
O25350 O66896 O86470 P81606
Q45248 Q56361
True Positive Partials
Codes involving 4 elements
P95495
Sequence Titles
CYBH_ALCEU  PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - ALCALIGENES EUTROPHUS. 
CYBH_AZOCH PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - AZOTOBACTER CHROOCOCCUM MCD 1.
CYBH_AZOVI PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - AZOTOBACTER VINELANDII.
CYBH_BRAJA PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - BRADYRHIZOBIUM JAPONICUM.
CYBH_ECOLI PROBABLE NI/FE-HYDROGENASE 1 B-TYPE CYTOCHROME SUBUNIT - ESCHERICHIA COLI.
CYBH_RHILV PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
CYBH_RHOCA PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
CYBH_WOLSU QUINONE-REACTIVE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - WOLINELLA SUCCINOGENES.
O25350 QUINONE-REACTIVE NI/FE HYDROGENASE, CYTOCHROME B SUBUNIT (HYDC) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O66896 NI/FE HYDROGENASE B-TYPE CYTOCHROME SUBUNIT - AQUIFEX AEOLICUS.
O86470 UPTAKE HYDROGENASE - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
P81606 PROBABLE NI/FE-HYDROGENASE B-TYPE CYTOCHROME SUBUNIT (HOXZ) - PSEUDOMONAS CARBOXYDOVORANS.
Q45248 HYDROGEN-UPTAKE HYDROGENASE GENE CLUSTER (HUPL) - BRADYRHIZOBIUM JAPONICUM.
Q56361 HYDROGENASE BIOSYNTHESIS OPERON ENCODING HUPS, HUPL, HUPC, HUPD, HUPH, GENES, COMPLETE CDS, AND HUPI - THIOCAPSA ROSEOPERSICINA.

P95495 CYTOCHROME B - PSEUDOMONAS HYDROGENOVORA.
Scan History
OWL24_0    2  25   NSINGLE    
SPTR37_9f 2 15 NSINGLE
Initial Motifs
Motif 1  width=24
Element Seqn Id St Int Rpt
APLRLWHWVTALSIVVLGVTGYFI CYBH_AZOVI 27 27 -
APVRLWHWVNALAIVVLAVTGFFI CYBH_ALCEU 35 35 -
APVRVWHWVNALAITILVVTGYFI CYBH_RHOCA 48 48 -
APVRIWHWINAFSILTLALTGYFI CYBH_RHILV 27 27 -
APVRIWHWLTVLCMAVLMVTGYFI CYBH_ECOLI 16 16 -
ALTRWFHWIRAIAIFVLIVTGFYI CYBH_WOLSU 19 19 -

Motif 2 width=25
Element Seqn Id St Int Rpt
YLMGYIRFAHFAAGYVLAIGFLGRV CYBH_AZOVI 65 14 -
FLMGYIRFAHFVAAYIFAIGMLGRI CYBH_ALCEU 73 14 -
FVMGYIRFAHFAAGVVMSVAFFGRI CYBH_RHOCA 87 15 -
FLMGYIRFIHFAAGQLLAVFLILRV CYBH_RHILV 65 14 -
FYMGYIRLIHFSAGMVFTVVLLMRI CYBH_ECOLI 54 14 -
FMYALARSWHQIFGFALIAVTIFRV CYBH_WOLSU 58 15 -

Motif 3 width=20
Element Seqn Id St Int Rpt
MFCFFVVGAVFMSVTGFALY CYBH_AZOVI 144 54 -
MFFIFFLSSVFMILTGFAMY CYBH_ALCEU 152 54 -
MFTFITLGITFMMITGWALY CYBH_RHOCA 166 54 -
MFLMFTLPLLFMAITGFALY CYBH_RHILV 144 54 -
AMFGYFLMSVFMIITGFALY CYBH_ECOLI 132 53 -
AYMGLMVLILLISVTGIILY CYBH_WOLSU 134 51 -

Motif 4 width=23
Element Seqn Id St Int Rpt
HTWHHLGMWYLVVFVMVHVYLAV CYBH_AZOVI 191 27 -
HTWHHLGMWFIVVFVIVHVYAAI CYBH_ALCEU 199 27 -
HTLHHLGMWAIVIFAIIHIYAAV CYBH_RHOCA 213 27 -
HTYHHLGMWVILVFVMVHIYVAV CYBH_RHILV 191 27 -
HSWHRLGMWLIGAFVIGHVYMAL CYBH_ECOLI 181 29 -
RAIHHITTWAFVIFIPVHIYMAT CYBH_WOLSU 183 29 -

Motif 5 width=14
Element Seqn Id St Int Rpt
SLISTMVGGWRMFK CYBH_AZOVI 222 8 -
SVVSTMVSGYRTFK CYBH_ALCEU 230 8 -
SMVSTMISGHRTFK CYBH_RHOCA 244 8 -
SIISSMISGERLFK CYBH_RHILV 222 8 -
TVISTMVNGYRSHK CYBH_ECOLI 212 8 -
GGIDSIFSGFRYHK CYBH_WOLSU 214 8 -
Final Motifs
Motif 1  width=24
Element Seqn Id St Int Rpt
APVRICHWVNAFSIIVLMVTGYLI CYBH_BRAJA 36 36 -
APVRICHWVNAFSIIVLMVTGYLI Q45248 38 38 -
APLRLWHWVTALSIVVLGVTGYFI CYBH_AZOVI 27 27 -
APLRLWHWVTALSIVVLGVTGYFI CYBH_AZOCH 27 27 -
APVRLWHWVNALAIVVLAVTGFFI CYBH_ALCEU 35 35 -
APVRVWHWVNALAITILVVTGYFI CYBH_RHOCA 48 48 -
APVRIWHWINAFSILTLALTGYFI CYBH_RHILV 27 27 -
VPVRLWHWLNAAMIFLLIGTGYLI O86470 47 47 -
APVRLWHWINAIAILVLALTGFFI P81606 34 34 -
APLRAWHWINALSITILAITGYLI Q56361 44 44 -
APVRIWHWLTVLCMAVLMVTGYFI CYBH_ECOLI 16 16 -
ASLRIWHWINFLTIMVLFFTGLYI O66896 10 10 -
ALTRWFHWIRAIAIFVLIVTGFYI CYBH_WOLSU 19 19 -
GFVRFFHWVRALSIFALIATGFYI O25350 15 15 -

Motif 2 width=25
Element Seqn Id St Int Rpt
FVMGYIRFAHFAAGQVLAVFFLTRI CYBH_BRAJA 74 14 -
FVMGYIRFAHFAAGQVLAVFFLTRI Q45248 76 14 -
YLMGYIRFAHFAAGYVLAIGFLGRV CYBH_AZOVI 65 14 -
YLMGYIRFAHFAAGYVLAIGFLGRV CYBH_AZOCH 65 14 -
FLMGYIRFAHFVAAYIFAIGMLGRI CYBH_ALCEU 73 14 -
FVMGYIRFAHFAAGVVMSVAFFGRI CYBH_RHOCA 87 15 -
FLMGYIRFIHFAAGQLLAVFLILRV CYBH_RHILV 65 14 -
FVFGYIRFAHFAAGQVLTVAFAARI O86470 86 15 -
FLMGYIRFTHFTAGYILAIGFLFRF P81606 72 14 -
YVMGYIRFAHFAAAYVFVIAFIFRI Q56361 82 14 -
FYMGYIRLIHFSAGMVFTVVLLMRI CYBH_ECOLI 54 14 -
ITMGFIRFLHFSAGYVLLFSFLFRI O66896 54 20 -
FMYALARSWHQIFGFALIAVTIFRV CYBH_WOLSU 58 15 -
LLQAYVRSFHVMFGFLLISALIFRT O25350 55 16 -

Motif 3 width=20
Element Seqn Id St Int Rpt
MFTGFTLFVAFMIVTGFALY CYBH_BRAJA 153 54 -
MFTGFTLFVAFMIVTGFALY Q45248 155 54 -
MFCFFVVGAVFMSVTGFALY CYBH_AZOVI 144 54 -
MFCFFVIGAVFMSVTGFALY CYBH_AZOCH 144 54 -
MFFIFFLSSVFMILTGFAMY CYBH_ALCEU 152 54 -
MFTFITLGITFMMITGWALY CYBH_RHOCA 166 54 -
MFLMFTLPLLFMAITGFALY CYBH_RHILV 144 54 -
MFFFITLGMSFMIVTGFALY O86470 165 54 -
MFLFITIGTMFMILTGFALY P81606 151 54 -
MVVIITVGGLVMIVTGFALY Q56361 161 54 -
AMFGYFLMSVFMIITGFALY CYBH_ECOLI 132 53 -
AYFFVYLMIFFMIATGFGMY O66896 128 49 -
AYMGLMVLILLISVTGIILY CYBH_WOLSU 134 51 -
AYSTLIVLIVLMSLSGMVLY O25350 130 50 -

Motif 4 width=23
Element Seqn Id St Int Rpt
HTWHHLGMWALVVFVMVHIYAAV CYBH_BRAJA 199 26 -
HTWHHLGMWALVVFVMVHIYAAV Q45248 202 27 -
HTWHHLGMWYLVVFVMVHVYLAV CYBH_AZOVI 191 27 -
HTWHHLGMWYLVVFVMIHVYLAA CYBH_AZOCH 191 27 -
HTWHHLGMWFIVVFVIVHVYAAI CYBH_ALCEU 199 27 -
HTLHHLGMWAIVIFAIIHIYAAV CYBH_RHOCA 213 27 -
HTYHHLGMWVILVFVMVHIYVAV CYBH_RHILV 191 27 -
HTLHHLGMWSIVIFTIIHIYAAV O86470 212 27 -
HTLHRLGMWWILTFVIIHIYVAI P81606 198 27 -
RMWHHWGMWVIVIFVMLHVYTAI Q56361 208 27 -
HSWHRLGMWLIGAFVIGHVYMAL CYBH_ECOLI 181 29 -
HYWHHIVAWLIILFFIVHVYFVS O66896 174 26 -
RAIHHITTWAFVIFIPVHIYMAT CYBH_WOLSU 183 29 -
RFIHHLATWGFILFVPVHVYMVF O25350 179 29 -

Motif 5 width=14
Element Seqn Id St Int Rpt
SIISSMISGERQFR CYBH_BRAJA 230 8 -
SIISSMISGERQFR Q45248 233 8 -
SLISTMVGGWRMFK CYBH_AZOVI 222 8 -
SLISTMVGGWRMFK CYBH_AZOCH 222 8 -
SVVSTMVSGYRTFK CYBH_ALCEU 230 8 -
SMVSTMISGHRTFK CYBH_RHOCA 244 8 -
SIISSMISGERLFK CYBH_RHILV 222 8 -
SMISTIVSGWRTFK O86470 243 8 -
SIVSTMISGHRTFK P81606 229 8 -
SLISTMVSGWRMFK Q56361 239 8 -
TVISTMVNGYRSHK CYBH_ECOLI 212 8 -
GEVSSMFNGSKFFK O66896 205 8 -
GGIDSIFSGFRYHK CYBH_WOLSU 214 8 -
SGADSMINGYGYTK O25350 210 8 -