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0  structures 34  species 0  interactions 54  sequences 3  architectures

Family: 5HT_transporter (PF03491)

Summary: Serotonin (5-HT) neurotransmitter transporter, N-terminus

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Serotonin (5-HT) neurotransmitter transporter, N-terminus Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013086

Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions [PUBMED:15336049]. Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl-, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl- [PUBMED:8811182]. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters [PUBMED:8103691, PUBMED:7823024].

Sequence analysis of the Na+/Cl- neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters [PUBMED:9779464].

The serotonin (5-HT) neurotransmitter transporter is known to be expressed in the brain and also in the periphery: on platelet, placental and pulmonary cell membranes. The brain 5-HT transporter is thought to be the principal site of action of therapeutic anti-depressants (which inhibit this transporter), and it may also mediate the behavioural effects of cocaine and amphetamines [PUBMED:7681602]. The human form (630 amino acids) is 92% identical to the rat brain 5-HT transporter, and shares the same predicted topology and conserved sites for post-translational modification.

This domain is found at the N-terminal region of some 5-HT neurotransmitters.

Gene Ontology

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Domain organisation

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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
(3)
Full
(54)
Representative proteomes NCBI
(41)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(4)
RP75
(20)
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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
(3)
Full
(54)
Representative proteomes NCBI
(41)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(4)
RP75
(20)
Alignment:
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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
(3)
Full
(54)
Representative proteomes NCBI
(41)
Meta
(0)
RP15
(1)
RP35
(2)
RP55
(4)
RP75
(20)
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.

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.

Pfam alignments:

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: PRINTS
Previous IDs: none
Type: Family
Author: Griffiths-Jones SR
Number in seed: 3
Number in full: 54
Average length of the domain: 39.10 aa
Average identity of full alignment: 70 %
Average coverage of the sequence by the domain: 7.22 %

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 20.3 20.3
Trusted cut-off 20.9 22.2
Noise cut-off 20.2 19.9
Model length: 42
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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