Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 910  species 0  interactions 5209  sequences 55  architectures

Family: AA_permease_C (PF13906)

Summary: C-terminus of AA_permease

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.

C-terminus of AA_permease Provide feedback

This is the C-terminus of AA-permease enzymes that is not captured by the models PF00324 and PF13520.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR029485

This entry represents the C-terminal of the cationic amino acid transporters (CATs) from bacteria, plants and animals. CATs are permeases involved in the transport of the cationic amino acids.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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
(40)
Full
(5209)
Representative proteomes UniProt
(9423)
RP15
(729)
RP35
(2323)
RP55
(4625)
RP75
(6212)
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
(5209)
Representative proteomes UniProt
(9423)
RP15
(729)
RP35
(2323)
RP55
(4625)
RP75
(6212)
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
(5209)
Representative proteomes UniProt
(9423)
RP15
(729)
RP35
(2323)
RP55
(4625)
RP75
(6212)
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: Jackhmmer:Q7Z475
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 40
Number in full: 5209
Average length of the domain: 49.90 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 8.30 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 51
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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
A0A096TLT9 View 3D Structure Click here
A0A0G2K1G8 View 3D Structure Click here
A0A0G2KSE4 View 3D Structure Click here
A0A0N7KHQ0 View 3D Structure Click here
A0A0P0XZ15 View 3D Structure Click here
A0A0P0Y735 View 3D Structure Click here
A0A0P0YD22 View 3D Structure Click here
A0A0R0I7B0 View 3D Structure Click here
A0A0R0IAD8 View 3D Structure Click here
A0A0R4INA7 View 3D Structure Click here
A0A1D6GQB5 View 3D Structure Click here
A0A1D6ITD3 View 3D Structure Click here
A0A1D6KGL2 View 3D Structure Click here
A0A1D6KX53 View 3D Structure Click here
A0A1D6KZ93 View 3D Structure Click here
A0A1D6MG65 View 3D Structure Click here
A0A1D6MG66 View 3D Structure Click here
A0A1D6QHX3 View 3D Structure Click here
A4IG22 View 3D Structure Click here
B0UYF2 View 3D Structure Click here
B5D5N9 View 3D Structure Click here
B5DFJ0 View 3D Structure Click here
C0HEZ5 View 3D Structure Click here
C0P3V4 View 3D Structure Click here
E7F8S7 View 3D Structure Click here
E9PWS4 View 3D Structure Click here
E9QF99 View 3D Structure Click here
F1QNI7 View 3D Structure Click here
F1R9X0 View 3D Structure Click here
I1K1U1 View 3D Structure Click here
I1K4C9 View 3D Structure Click here
I1KZY5 View 3D Structure Click here
I1L147 View 3D Structure Click here
I1L151 View 3D Structure Click here
I1L225 View 3D Structure Click here
I1L617 View 3D Structure Click here
I1MKW7 View 3D Structure Click here
I1N8D3 View 3D Structure Click here
I1N8D4 View 3D Structure Click here
I1NFE8 View 3D Structure Click here
K7KN88 View 3D Structure Click here
K7L6C1 View 3D Structure Click here
K7L6C2 View 3D Structure Click here
K7LMX4 View 3D Structure Click here
K7MLQ3 View 3D Structure Click here
K7MUP1 View 3D Structure Click here
K7TR83 View 3D Structure Click here
O08812 View 3D Structure Click here
O17069 View 3D Structure Click here
O17167 View 3D Structure Click here
O43246 View 3D Structure Click here
O44798 View 3D Structure Click here
O64759 View 3D Structure Click here
P18581 View 3D Structure Click here
P30823 View 3D Structure Click here
P30825 View 3D Structure Click here
P52569 View 3D Structure Click here
P70423 View 3D Structure Click here
Q09143 View 3D Structure Click here
Q0JBB8 View 3D Structure Click here
Q2FYJ4 View 3D Structure Click here
Q2PDY3 View 3D Structure Click here
Q2QLZ1 View 3D Structure Click here
Q337V1 View 3D Structure Click here
Q54EJ9 View 3D Structure Click here
Q54F04 View 3D Structure Click here
Q54W03 View 3D Structure Click here
Q5PR34 View 3D Structure Click here
Q5Z6S8 View 3D Structure Click here
Q6H6H8 View 3D Structure Click here
Q84MA5 View 3D Structure Click here
Q84ST3 View 3D Structure Click here
Q8BLQ7 View 3D Structure Click here
Q8BXR1 View 3D Structure Click here
Q8GYB4 View 3D Structure Click here
Q8TBB6 View 3D Structure Click here
Q8W4K3 View 3D Structure Click here
Q8WY07 View 3D Structure Click here
Q9ASS7 View 3D Structure Click here
Q9C5D6 View 3D Structure Click here
Q9LD96 View 3D Structure Click here
Q9LZ20 View 3D Structure Click here
Q9SHH0 View 3D Structure Click here
Q9SQZ0 View 3D Structure Click here
Q9VNP7 View 3D Structure Click here
Q9VPG2 View 3D Structure Click here
Q9VVM0 View 3D Structure Click here
Q9VWD3 View 3D Structure Click here

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.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;