Summary: Sodium Bile acid symporter family
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.
Sodium Bile acid symporter family Provide feedback
This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+ [2]. Also in the family is ARC3 from S. cerevisiae Q06598 this is a putative transmembrane protein involved in resistance to arsenic compounds [1].
Literature references
-
Bobrowicz P, Wysocki R, Owsianik G, Goffeau A, Ulaszewski S; , Yeast 1997;13:819-828.: Isolation of three contiguous genes, ACR1, ACR2 and ACR3, involved in resistance to arsenic compounds in the yeast Saccharomyces cerevisiae. PUBMED:9234670 EPMC:9234670
-
Hagenbuch B, Stieger B, Foguet M, Lubbert H, Meier PJ; , Proc Natl Acad Sci U S A 1991;88:10629-10633.: Functional expression cloning and characterization of the hepatocyte Na+/bile acid cotransport system. PUBMED:1961729 EPMC:1961729
Internal database links
SCOOP: | DUF6338 Mem_trans Na_H_Exchanger OAD_beta SBF_like |
Similarity to PfamA using HHSearch: | SBF_like |
External database links
Transporter classification: | 2.A.28 2.A.59 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002657
This family of proteins are found both in prokaryotes and eukaryotes. They are related to the human bile acid:sodium symporters (TC 2.A.28), which are transmembrane proteins functioning in the liver in the uptake of bile acids from portal blood plasma, a process mediated by the co-transport of Na + [ PUBMED:1961729 ].
This entry also includes members of the ACR3 family of arsenite (As(III)) permeases, which confer resistance to arsenic by extrusion from cells [ PUBMED:19494117 ]. They exist in prokaryotes and eukaryotes (lower plants and fungi) [ PUBMED:20530755 , PUBMED:24291645 ]. The ACR3 permeases have ten-transmembrane span topology [ PUBMED:18088595 ]. Corynebacterium glutamicum has three Acr3 proteins, CgAcr3-1, CgAcr3-2, and CgAcr3-3. CgAcr3-1 is thought to be an antiporter that catalyses arsenite-proton exchange [ PUBMED:22102279 ].
The Shewanella oneidensis Acr3 is not able to transport As(III) and confers resistance only to arsenate (As(V)) [ PUBMED:19039703 ], whereas the Acr3 orthologue from Synechocystis mediates tolerance to As(III), As(V) and antimonite (Sb(III)) [ PUBMED:12949088 ].
In budding yeast, overexpression of the Acr3 gene confers an arsenite- but not an arsenate-resistance phenotype [ PUBMED:9234670 ]. Saccharomyces cerevisiae Acr3 is a plasma membrane metalloid/H+ antiporter that transports arsenite and antimonite [ PUBMED:21447319 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | membrane (GO:0016020) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Pfam Clan
This family is a member of clan CPA_AT (CL0064), which has the following description:
This Clan contains transporter proteins that belong to the CPA superfamily and AT superfamily according to TCDB [1].
The clan contains the following 13 members:
Asp-Al_Ex Cons_hypoth698 DUF819 Glt_symporter KdgT Lys_export Mem_trans Na_H_antiport_1 Na_H_Exchanger OAD_beta SBF SBF_like Sbt_1Alignments
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 (17) |
Full (12096) |
Representative proteomes | UniProt (47305) |
||||
---|---|---|---|---|---|---|---|
RP15 (1667) |
RP35 (5693) |
RP55 (11667) |
RP75 (19349) |
||||
Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (17) |
Full (12096) |
Representative proteomes | UniProt (47305) |
||||
---|---|---|---|---|---|---|---|
RP15 (1667) |
RP35 (5693) |
RP55 (11667) |
RP75 (19349) |
||||
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: | Pfam-B_697 (release 4.2) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 17 |
Number in full: | 12096 |
Average length of the domain: | 184.70 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 52.63 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 195 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
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 SBF domain has been found. There are 7 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.
Loading structure mapping...