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8  structures 6890  species 0  interactions 35362  sequences 200  architectures

Family: SSF (PF00474)

Summary: Sodium:solute symporter 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 "Sodium-solute symporter". More...

Sodium-solute symporter Edit Wikipedia article

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.

Sodium:solute symporter family Provide feedback

This family includes P33413 which is not in the Prosite entry. Membership of this family is supported by a significant blast score.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001734

Sodium/substrate symport (or co-transport) is a widespread mechanism of solute transport across cytoplasmic membranes of pro- and eukaryotic cells. Thereby the energy stored in an inwardly directed electrochemical sodium gradient (sodium motive force, SMF) is used to drive solute accumulation against a concentration gradient. The SMF is generated by primary sodium pumps (e.g. sodium/potassium ATPases, sodium translocating respiratory chain complexes) or via the action of sodium/proton antiporters. Sodium/substrate transporters are grouped in different families based on sequence similarities [ PUBMED:1965458 , PUBMED:8031825 ].

One of these families, known as the sodium:solute symporter family (SSSF), contains over a hundred members of pro- and eukaryotic origin [ PUBMED:12354616 ]. The average hydropathy plot for SSSF proteins predicts 11 to 15 putative transmembrane domains (TMs) in alpha-helical conformation. A secondary structure model of PutP from Escherichia coli suggests the protein contains 13 TMs with the N terminus located on the periplasmic side of the membrane and the C terminus facing the cytoplasm. The results support the idea of a common topological motif for members of the SSSF. Transporters with a C-terminal extension are proposed to have an additional 14th TM.

An ordered binding model of sodium/substrate transport suggests that sodium binds to the empty transporter first, thereby inducing a conformational alteration which increases the affinity of the transporter for the solute. The formation of the ternary complex induces another structural change that exposes sodium and substrate to the other site of the membrane. Substrate and sodium are released and the empty transporter re-orientates in the membrane allowing the cycle to start again.

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 20 members:

AA_permease AA_permease_2 AA_permease_C Aa_trans BCCT BenE Branch_AA_trans CstA HCO3_cotransp K_trans MFS_MOT1 Na_Ala_symp Nramp SNF Spore_permease SSF 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 (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
(10)
Full
(35362)
Representative proteomes UniProt
(135319)
RP15
(5354)
RP35
(16220)
RP55
(34646)
RP75
(56365)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(10)
Full
(35362)
Representative proteomes UniProt
(135319)
RP15
(5354)
RP35
(16220)
RP55
(34646)
RP75
(56365)
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
(10)
Full
(35362)
Representative proteomes UniProt
(135319)
RP15
(5354)
RP35
(16220)
RP55
(34646)
RP75
(56365)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 10
Number in full: 35362
Average length of the domain: 344.70 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 70.88 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 406
Family (HMM) version: 19
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 SSF domain has been found. There are 8 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
A0A0A0US36 View 3D Structure Click here
A0A0G2JY02 View 3D Structure Click here
A0A0G2K630 View 3D Structure Click here
A0A0G2K669 View 3D Structure Click here
A0A0G2KH46 View 3D Structure Click here
A0A0G2KQP1 View 3D Structure Click here
A0A0H2UJX9 View 3D Structure Click here
A0A0R4IUP3 View 3D Structure Click here
A0A1D8PDB5 View 3D Structure Click here
A0A1D8PFU4 View 3D Structure Click here
A0A1D8PJY8 View 3D Structure Click here
A0A1D8PNR5 View 3D Structure Click here
A0PJK1 View 3D Structure Click here
A4IG60 View 3D Structure Click here
A8WHP3 View 3D Structure Click here
B1WBT6 View 3D Structure Click here
B7ZVD9 View 3D Structure Click here
B8JHU7 View 3D Structure Click here
D3Z9E5 View 3D Structure Click here
D3ZIS0 View 3D Structure Click here
E9QAB5 View 3D Structure Click here
E9QDC2 View 3D Structure Click here
F1LQV2 View 3D Structure Click here
F1LWL8 View 3D Structure Click here
F1Q620 View 3D Structure Click here
F1Q7N5 View 3D Structure Click here
F1QBX6 View 3D Structure Click here
F4KD71 View 3D Structure Click here
G3V8X5 View 3D Structure Click here
I1JVV4 View 3D Structure Click here
O02228 View 3D Structure Click here
O17394 View 3D Structure Click here
O70247 View 3D Structure Click here
O94469 View 3D Structure Click here
P07117 View 3D Structure Click here
P13866 View 3D Structure Click here
P16256 View 3D Structure Click here
P31448 View 3D Structure Click here
P31639 View 3D Structure Click here
P32705 View 3D Structure Click here
P33413 View 3D Structure Click here
P53790 View 3D Structure Click here
P53792 View 3D Structure Click here
P53794 View 3D Structure Click here
P83740 View 3D Structure Click here
P91659 View 3D Structure Click here
Q1EHB4 View 3D Structure Click here
Q23616 View 3D Structure Click here
Q2FWY7 View 3D Structure Click here
Q2G161 View 3D Structure Click here
Q2M3M2 View 3D Structure Click here
Q3ZMH1 View 3D Structure Click here
Q49B93 View 3D Structure Click here
Q59UP3 View 3D Structure Click here
Q5AKW0 View 3D Structure Click here
Q5RIG1 View 3D Structure Click here
Q5SWY8 View 3D Structure Click here
Q5U3A9 View 3D Structure Click here
Q5U4D8 View 3D Structure Click here
Q63008 View 3D Structure Click here
Q7K3Q2 View 3D Structure Click here
Q7T384 View 3D Structure Click here
Q7XBS0 View 3D Structure Click here
Q8BGY9 View 3D Structure Click here
Q8BYF6 View 3D Structure Click here
Q8C3K6 View 3D Structure Click here
Q8IN99 View 3D Structure Click here
Q8IPY0 View 3D Structure Click here
Q8K0E3 View 3D Structure Click here
Q8N695 View 3D Structure Click here
Q8SWV5 View 3D Structure Click here
Q8TFG0 View 3D Structure Click here
Q8VDT1 View 3D Structure Click here
Q8WWX8 View 3D Structure Click here
Q91ZP4 View 3D Structure Click here
Q923I7 View 3D Structure Click here
Q92911 View 3D Structure Click here
Q961Q9 View 3D Structure Click here
Q99PN0 View 3D Structure Click here
Q9ET37 View 3D Structure Click here
Q9GZV3 View 3D Structure Click here
Q9JKZ2 View 3D Structure Click here
Q9JMD7 View 3D Structure Click here
Q9NY91 View 3D Structure Click here
Q9URY6 View 3D Structure Click here
Q9V9U1 View 3D Structure Click here
Q9V9U2 View 3D Structure Click here
Q9VBK1 View 3D Structure Click here
Q9VE46 View 3D Structure Click here
Q9VGP3 View 3D Structure Click here
Q9VLR8 View 3D Structure Click here
Q9VQ85 View 3D Structure Click here
Q9W3R0 View 3D Structure Click here
Q9Y289 View 3D Structure Click here
Q9Z1F2 View 3D Structure Click here