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0  structures 32  species 0  interactions 32  sequences 1  architecture

Family: NADHdeh_related (PF10125)

Summary: NADH dehydrogenase I, subunit N related protein

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NADH dehydrogenase I, subunit N related protein Provide feedback

This family comprises a set of NADH dehydrogenase I, subunit N related proteins found in archaea. Their exact function, has not, as yet, been determined.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017059

This group contains membrane proteins that are predicted to be transmembrane subunits (EhaH) of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes.

The energy-converting hydrogenase A (eha) operon encodes a putative multisubunit membrane-bound [NiFe]-hydrogenase Eha in Methanobacterium thermoautotrophicum (strain Marburg / DSM 2133). Sequence analysis of the eha operon indicates that it encodes at least 20 proteins, including the [NiFe]-hydrogenase large subunit (INTERPRO), the [NiFe]-hydrogenase small subunit (), and two broadly conserved integral membrane proteins (this entry and ). These four proteins show high sequence similarity to subunits of the Ech hydrogenase from Methanosarcina barkeri, Escherichia coli hydrogenases 3 and 4 (Hyc and Hyf), and CO-induced hydrogenase from Rhodospirillum rubrum (Coo), all of which form a distinct group of multisubunit membrane-bound [NiFe]-hydrogenases (together called hydrogenase-3-type hydrogenases). In addition to these four subunits, the eha operon encodes a 6[4Fe-4S] polyferredoxin, a 10[4Fe-4S] polyferredoxin, ten other predicted integral membrane proteins (, , , , , , , , , ), and four hydrophilic subunits (, , , ) (the latter two hydrophilic subunits are members of well-characterised enzyme families but lack the essential amino acids assumed to form the active site [PUBMED:10491142]). All of these proteins are expressed and therefore thought to be functional subunits of the Eha hydrogenase complex [PUBMED:10491142]. Note, however, that the ten additional predicted integral membrane proteins are absent from Ech, Coo, Hyc, and Hyf complexes (and therefore from corresponding organisms), indicating that those complexes have a simpler membrane component than Eha [PUBMED:10491142].

Members of this group are homologous to the N-terminal domain of members (e.g., EhbF, HyfF of E. coli hydrogenase 4, amongst others). Therefore, this type of membrane subunit of Eha complex is conserved across the various hydrogenase-3-type hydrogenases (that is, they are not limited to the Eha subgroup). A protein with sequence similarity to the C-terminal part of EhbF () is not present in the Eha complex (not encoded by the eha operon).

Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri,Methanocaldococcus jannaschii, and M. thermoautotrophicum also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure.

Domain organisation

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Pfam Clan

This family is a member of clan ComplexI-N (CL0425), which has the following description:

This superfamily contains proteins from the families Oxidored_q1 and NADHdeh_related. The Oxidored_q1 family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. Many members of the NADHdeh_related family are archaeal and bacterial, indicating the evolutionary origins of ComplexI.

The clan contains the following 2 members:

NADHdeh_related Oxidored_q1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(8)
Full
(32)
Representative proteomes NCBI
(166)
Meta
(53)
RP15
(5)
RP35
(11)
RP55
(17)
RP75
(21)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(8)
Full
(32)
Representative proteomes NCBI
(166)
Meta
(53)
RP15
(5)
RP35
(11)
RP55
(17)
RP75
(21)
Alignment:
Format:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(8)
Full
(32)
Representative proteomes NCBI
(166)
Meta
(53)
RP15
(5)
RP35
(11)
RP55
(17)
RP75
(21)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COGs (COG4078)
Previous IDs: none
Type: Family
Author: COGs, Finn RD, Sammut SJ
Number in seed: 8
Number in full: 32
Average length of the domain: 219.20 aa
Average identity of full alignment: 57 %
Average coverage of the sequence by the domain: 99.39 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 219
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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