Summary: N-ATPase, AtpR subunit
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N-ATPase, AtpR subunit Provide feedback
Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits ( PFAM:PF00137).
Literature references
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Dibrova DV, Galperin MY, Mulkidjanian AY;, Bioinformatics. 2010; [Epub ahead of print]: Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase. PUBMED:20472544 EPMC:20472544
Internal database links
SCOOP: | ATP-synt_I |
This tab holds annotation information from the InterPro database.
InterPro entry IPR017581
Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits [ PUBMED:20472544 ].
This entry also includes AtpR like proteins found in bacteria. Some of them have been annotated as ATP synthase protein I (atpI). However, their function still need to be verified.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan ATPase_I_AtpR (CL0478), which has the following description:
These two subunits from the F-type and N-type ATPases have been demonstrated to from functionally distinct components of these two different ATPases[1].
The clan contains the following 2 members:
ATP-synt_I AtpRAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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 (19) |
Full (360) |
Representative proteomes | UniProt (1219) |
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RP15 (42) |
RP35 (182) |
RP55 (369) |
RP75 (567) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (19) |
Full (360) |
Representative proteomes | UniProt (1219) |
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RP15 (42) |
RP35 (182) |
RP55 (369) |
RP75 (567) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | [1] |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Dibrova DV, Galperin MY |
Number in seed: | 19 |
Number in full: | 360 |
Average length of the domain: | 85.8 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 85.46 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 86 | ||||||||||||
Family (HMM) version: | 10 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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