Summary: Membrane transport protein
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Membrane transport protein Provide feedback
This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life.
Internal database links
SCOOP: | SBF SBF_like |
External database links
Transporter classification: | 2.A.69 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004776
This entry represents a mostly uncharacterised family of membrane transport proteins found in eukaryotes, bacteria and archaea. Most characterised members of this family are the PIN components of auxin efflux systems from plants. These carriers are saturable, auxin-specific, and localized to the basal ends of auxin transport-competent cells [ PUBMED:16054428 , PUBMED:15564124 ]. Plants typically posses several of these proteins, each displaying a unique tissue-specific expression pattern. They are expressed in almost all plant tissues including vascular tissues and roots, and influence many processes including the establishment of embryonic polarity, plant growth, apical hook formation in seedlings and the photo- and gravitrophic responses. These plant proteins are typically 600-700 amino acyl residues long and exhibit 8-12 transmembrane segments.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | integral component of membrane (GO:0016021) |
Biological process | transmembrane transport (GO:0055085) |
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 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 15 members:
Asp-Al_Ex Cons_hypoth698 DUF3100 DUF819 Glt_symporter KdgT LrgB 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 (18) |
Full (24951) |
Representative proteomes | UniProt (87582) |
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RP15 (3219) |
RP35 (12136) |
RP55 (24104) |
RP75 (39873) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (18) |
Full (24951) |
Representative proteomes | UniProt (87582) |
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RP15 (3219) |
RP35 (12136) |
RP55 (24104) |
RP75 (39873) |
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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: | TIGRFAMs & Pfam-B_5261 (Release 7.5) |
Previous IDs: | Auxin_eff; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
TIGRFAMs, Griffiths-Jones SR |
Number in seed: | 18 |
Number in full: | 24951 |
Average length of the domain: | 211.9 aa |
Average identity of full alignment: | 11 % |
Average coverage of the sequence by the domain: | 81.8 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 387 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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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.
trRosetta Structure
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.
- View the contact map and structural model in InterPro
- Download the model in PDB format
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