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7  structures 295  species 0  interactions 2233  sequences 22  architectures

Family: HCO3_cotransp (PF00955)

Summary: HCO3- transporter family

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

This is the Wikipedia entry entitled "Bicarbonate transporter proteins". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

HCO3- transporter family Provide feedback

This family contains Band 3 anion exchange proteins that exchange CL-/HCO3- such as P48751. This family also includes cotransporters of Na+/HCO3- such as O15153.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011531

Bicarbonate (HCO3 -) transport mechanisms are the principal regulators of pH in animal cells. Such transport also plays a vital role in acid-base movements in the stomach, pancreas, intestine, kidney, reproductive organs and the central nervous system. Functional studies have suggested four different HCO3 - transport modes. Anion exchanger proteins exchange HCO3 - for Cl- in a reversible, electroneutral manner [PUBMED:2289848]. Na+/HCO3 - co-transport proteins mediate the coupled movement of Na+ and HCO3 - across plasma membranes, often in an electrogenic manner [PUBMED:9261985]. Na- driven Cl-/HCO3 - exchange and K+/HCO3 - exchange activities have also been detected in certain cell types, although the molecular identities of the proteins responsible remain to be determined.

Sequence analysis of the two families of HCO3 - transporters that have been cloned to date (the anion exchangers and Na+/HCO3 - co-transporters) reveals that they are homologous. This is not entirely unexpected, given that they both transport HCO3 - and are inhibited by a class of pharmacological agents called disulphonic stilbenes [PUBMED:9235899]. They share around ~25-30% sequence identity, which is distributed along their entire sequence length, and have similar predicted membrane topologies, suggesting they have ~10 transmembrane (TM) domains.

This domain is found at the C terminus of many bicarbonate transport proteins. It is also found in some plant proteins responsible for boron transport [PUBMED:12447444]. In these proteins it covers almost the entire length of the sequence.

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 APC (CL0062), which has the following description:

This large superfamily contains a variety of transporters including amino acid permeases that according to TCDB belong to the APC (Amino acid-Polyamine-organoCation) superfamily.

The clan contains the following 18 members:

AA_permease AA_permease_2 AA_permease_C Aa_trans BenE Branch_AA_trans CstA HCO3_cotransp K_trans Na_Ala_symp Nramp Spore_permease SSF Sulfate_tra_GLY Sulfate_transp Transp_cyt_pur Trp_Tyr_perm Xan_ur_permease

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...

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
(18)
Full
(2233)
Representative proteomes NCBI
(1987)
Meta
(18)
RP15
(277)
RP35
(517)
RP55
(835)
RP75
(1138)
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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
(18)
Full
(2233)
Representative proteomes NCBI
(1987)
Meta
(18)
RP15
(277)
RP35
(517)
RP55
(835)
RP75
(1138)
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
(18)
Full
(2233)
Representative proteomes NCBI
(1987)
Meta
(18)
RP15
(277)
RP35
(517)
RP55
(835)
RP75
(1138)
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: Pfam-B_1004 (release 3.0)
Previous IDs: Anion_Exchanger;
Type: Family
Author: Croning MDR, Finn RD, Bateman A
Number in seed: 18
Number in full: 2233
Average length of the domain: 300.50 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 52.48 %

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 19.7 19.7
Trusted cut-off 20.0 20.1
Noise cut-off 17.8 19.2
Model length: 510
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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 HCO3_cotransp 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 seqence.

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