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0  structures 2920  species 0  interactions 17705  sequences 47  architectures

Family: AA_permease (PF00324)

Summary: Amino acid permease

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This is the Wikipedia entry entitled "Amino acid permease". More...

Amino acid permease Edit Wikipedia article

Amino acid permease
Identifiers
Symbol AA_permease
Pfam PF00324
Pfam clan CL0062
InterPro IPR004841
PROSITE PDOC00191
TCDB 2.A.3
OPM superfamily 67
OPM protein 3gia

Amino acid permeases are membrane permeases involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related.[1][2][3] These proteins contain 12 transmembrane segments.

See also[edit]

Human proteins containing this domain[edit]

CIP1; SLC12A1; SLC12A2; SLC12A3; SLC12A4; SLC12A5; SLC12A6; SLC12A7; SLC12A8; SLC12A9; SLC7A1; SLC7A10; SLC7A11; SLC7A13; SLC7A14; SLC7A2; SLC7A3; SLC7A4; SLC7A5; SLC7A6; SLC7A7; SLC7A8; SLC7A9;

References[edit]

  1. ^ Weber E, Jund R, Chevallier MR (1988). "Evolutionary relationship and secondary structure predictions in four transport proteins of Saccharomyces cerevisiae". J. Mol. Evol. 27 (4): 341–350. doi:10.1007/BF02101197. PMID 3146645. 
  2. ^ Vandenbol M, Grenson M, Jauniaux JC (1989). "Nucleotide sequence of the Saccharomyces cerevisiae PUT4 proline-permease-encoding gene: similarities between CAN1, HIP1 and PUT4 permeases". Gene 83 (1): 153–159. doi:10.1016/0378-1119(89)90413-7. PMID 2687114. 
  3. ^ Reizer J, Reizer A, Finley K, Kakuda D, Saier Jr MH, MacLeod CL (1993). "Mammalian integral membrane receptors are homologous to facilitators and antiporters of yeast, fungi, and eubacteria". Protein Sci. 2 (1): 20–30. doi:10.1002/pro.5560020103. PMC 2142299. PMID 8382989. 

This article incorporates text from the public domain Pfam and InterPro IPR004841


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.

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004841

Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related [PUBMED:3146645], [PUBMED:2687114], [PUBMED:8382989]. These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment.

This domain is found in a wide variety of permeases, as well as several hypothetical proteins.

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 18 members:

AA_permease AA_permease_2 AA_permease_C Aa_trans BenE Branch_AA_trans CstA HCO3_cotransp K_trans Na_Ala_symp Nramp Spore_permease SSF Sulfate_tra_GLY 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(26)
Full
(17705)
Representative proteomes NCBI
(25995)
Meta
(1856)
RP15
(1009)
RP35
(2148)
RP55
(3513)
RP75
(4452)
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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
(26)
Full
(17705)
Representative proteomes NCBI
(25995)
Meta
(1856)
RP15
(1009)
RP35
(2148)
RP55
(3513)
RP75
(4452)
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
(26)
Full
(17705)
Representative proteomes NCBI
(25995)
Meta
(1856)
RP15
(1009)
RP35
(2148)
RP55
(3513)
RP75
(4452)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: aa_permeases;
Type: Family
Author: Finn RD, Bateman A
Number in seed: 26
Number in full: 17705
Average length of the domain: 417.10 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 85.04 %

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 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 478
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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