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53  structures 1098  species 0  interactions 3532  sequences 58  architectures

Family: Alba (PF01918)

Summary: Alba

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Alba Provide feedback

Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.

Literature references

  1. Aravind L, Iyer LM, Anantharaman V; , Genome Biol 2003;4:R64.: The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism. PUBMED:14519199 EPMC:14519199

  2. Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF; , Science 2002;296:148-151.: The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. PUBMED:11935028 EPMC:11935028

  3. Xue H, Guo R, Wen Y, Liu D, Huang L; , J Bacteriol 2000;182:3929-3933.: An abundant DNA binding protein from the hyperthermophilic archaeon Sulfolobus shibatae affects DNA supercoiling in a temperature-dependent fashion. PUBMED:10869069 EPMC:10869069

  4. Forterre P, Confalonieri F, Knapp S; , Mol Microbiol 1999;32:669-670.: Identification of the gene encoding archeal-specific DNA-binding proteins of the Sac10b family. PUBMED:10320587 EPMC:10320587


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002775

Members of this group include the archaeal protein Alba and eukaryotic Ribonuclease P subunits Pop7/Rpp20 and Rpp25. The Alba domain is closely related to the RNA-binding versions of the IF3-C fold such as YhbY and IF3-C. The eukaryotic lineages of the Alba family are principally involved in RNA metabolism, suggesting that the ancestral function of the IF3-C fold was related to RNA interaction [ PUBMED:14519199 ].

Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner [ PUBMED:10869069 ]. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [ PUBMED:16256418 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 AlbA (CL0441), which has the following description:

This is a family of DNA and RNA binding proteins found from archaea to humans.

The clan contains the following 4 members:

Alba AlbA_2 Rpp20 SpoVS

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(81)
Full
(3532)
Representative proteomes UniProt
(8173)
RP15
(697)
RP35
(1798)
RP55
(2961)
RP75
(3901)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(81)
Full
(3532)
Representative proteomes UniProt
(8173)
RP15
(697)
RP35
(1798)
RP55
(2961)
RP75
(3901)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(81)
Full
(3532)
Representative proteomes UniProt
(8173)
RP15
(697)
RP35
(1798)
RP55
(2961)
RP75
(3901)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Enright A
Previous IDs: DUF78;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 81
Number in full: 3532
Average length of the domain: 66.00 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 31.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 67
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Alba domain has been found. There are 53 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2KNZ3 View 3D Structure Click here
A0A0R0IXP9 View 3D Structure Click here
A0A0R0IYN3 View 3D Structure Click here
A0A0R0KBI5 View 3D Structure Click here
A0A1D6EAY3 View 3D Structure Click here
A0A1D6EU65 View 3D Structure Click here
A0A1D6GGF8 View 3D Structure Click here
A0A1D6I3A5 View 3D Structure Click here
A0A1D6IUH8 View 3D Structure Click here
A0A1D6IYT9 View 3D Structure Click here
A0A1D6J367 View 3D Structure Click here
A0A1D6JQZ2 View 3D Structure Click here
A0A1D6KKX6 View 3D Structure Click here
A0A1D6KM75 View 3D Structure Click here
A0A1D6PKL9 View 3D Structure Click here
A0A1D8PQD1 View 3D Structure Click here
A0A1I9LSC0 View 3D Structure Click here
A0A1Q0ZFB6 View 3D Structure Click here
A0A2R8QR57 View 3D Structure Click here
A4HVG8 View 3D Structure Click here
A4IA34 View 3D Structure Click here
B0BMX6 View 3D Structure Click here
B4FSE0 View 3D Structure Click here
B6T175 View 3D Structure Click here
B8A2G7 View 3D Structure Click here
C6SVJ8 View 3D Structure Click here
C6SW53 View 3D Structure Click here
C6SXI4 View 3D Structure Click here
C6T4F4 View 3D Structure Click here
C6TE19 View 3D Structure Click here
I1JAQ0 View 3D Structure Click here
I1JRN9 View 3D Structure Click here
I1KBE3 View 3D Structure Click here
I1LBN1 View 3D Structure Click here
I1M5S6 View 3D Structure Click here
I1NIR8 View 3D Structure Click here
K7MSX8 View 3D Structure Click here
K7UR36 View 3D Structure Click here
O22969 View 3D Structure Click here
O96240 View 3D Structure Click here