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2  structures 2361  species 0  interactions 15351  sequences 207  architectures

Family: OPT (PF03169)

Summary: OPT oligopeptide transporter protein

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.

OPT oligopeptide transporter protein Provide feedback

The OPT family of oligopeptide transporters is distinct from the ABC PF00005 and PTR PF00854 transporter families. OPT transporters were first recognised in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP [1].

Literature references

  1. Lubkowitz MA, Barnes D, Breslav M, Burchfield A, Naider F, Becker JM; , Mol Microbiol 1998;28:729-741.: Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters. PUBMED:9643541 EPMC:9643541


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004813

The transporter OPT family are transporters of small oligopeptides, demonstrated experimentally in three different species of yeast. OPT1 is not a member of the ABC or PTR membrane transport families [ PUBMED:9043116 ].

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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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
(40)
Full
(15351)
Representative proteomes UniProt
(32876)
RP15
(2255)
RP35
(7443)
RP55
(12463)
RP75
(17757)
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
(40)
Full
(15351)
Representative proteomes UniProt
(32876)
RP15
(2255)
RP35
(7443)
RP55
(12463)
RP75
(17757)
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
(40)
Full
(15351)
Representative proteomes UniProt
(32876)
RP15
(2255)
RP35
(7443)
RP55
(12463)
RP75
(17757)
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: Pfam-B_3048 (release 6.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 40
Number in full: 15351
Average length of the domain: 527.5 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 84.14 %

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 25.8 25.8
Trusted cut-off 25.8 25.8
Noise cut-off 25.7 25.7
Model length: 616
Family (HMM) version: 18
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 OPT domain has been found. There are 2 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
A0A0D2GS56 View 3D Structure Click here
A0A0D2GX87 View 3D Structure Click here
A0A0P0VN85 View 3D Structure Click here
A0A0R0E8P2 View 3D Structure Click here
A0A0R0EMA8 View 3D Structure Click here
A0A0R0EWN0 View 3D Structure Click here
A0A0R0FWY1 View 3D Structure Click here
A0A0R0FWZ0 View 3D Structure Click here
A0A0R0IHE9 View 3D Structure Click here
A0A0R0IKF9 View 3D Structure Click here
A0A0R0KBQ9 View 3D Structure Click here
A0A175VQW7 View 3D Structure Click here
A0A175VQW8 View 3D Structure Click here
A0A175VS45 View 3D Structure Click here
A0A175VTJ1 View 3D Structure Click here
A0A175VTZ8 View 3D Structure Click here
A0A175VZ94 View 3D Structure Click here
A0A175VZM1 View 3D Structure Click here
A0A175VZY1 View 3D Structure Click here
A0A1C1CKG9 View 3D Structure Click here
A0A1C1CTE4 View 3D Structure Click here
A0A1D6DZY7 View 3D Structure Click here
A0A1D6E0F0 View 3D Structure Click here
A0A1D6E4E1 View 3D Structure Click here
A0A1D6E5T4 View 3D Structure Click here
A0A1D6E5T6 View 3D Structure Click here
A0A1D6ECH4 View 3D Structure Click here
A0A1D6ECI1 View 3D Structure Click here
A0A1D6FHB2 View 3D Structure Click here
A0A1D6FNU8 View 3D Structure Click here
A0A1D6FNU9 View 3D Structure Click here
A0A1D6G8Y8 View 3D Structure Click here
A0A1D6H144 View 3D Structure Click here
A0A1D6H3S5 View 3D Structure Click here
A0A1D6HE34 View 3D Structure Click here
A0A1D6HET2 View 3D Structure Click here
A0A1D6HET4 View 3D Structure Click here
A0A1D6HGM2 View 3D Structure Click here
A0A1D6JBB9 View 3D Structure Click here
A0A1D6KI03 View 3D Structure Click here