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0  structures 2968  species 0  interactions 13176  sequences 5  architectures

Family: LysE (PF01810)

Summary: LysE type translocator

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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.

LysE type translocator Provide feedback

This family consists of various hypothetical proteins and an l-lysine exporter LysE P94633 from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators [1]. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times [1]. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine [1].

Literature references

  1. Vrljic M, Sahm H, Eggeling L; , Mol Microbiol 1996;22:815-826.: A new type of transporter with a new type of cellular function: L- lysine export from Corynebacterium glutamicum. PUBMED:8971704 EPMC:8971704

  2. Aleshin VV, Zakataeva NP, Livshits VA; , Trends Biochem Sci 1999;24:133-135.: A new family of amino-acid-efflux proteins. PUBMED:10322417 EPMC:10322417


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001123

Lysine exporter protein is involved in the efflux of excess L-lysine as a control for intracellular levels of L-lysine. A number of proteins belong to this family. These include the chemotactic transduction protein from Pseudomonas aeruginosa, the threonine efflux protein and a number of uncharacterised proteins from a variety of sources.

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 LysE (CL0292), which contains the following 10 members:

BacA Cad Colicin_V DUF204 DUF475 LysE MarC TauE TerC UPF0016

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
(19)
Full
(13176)
Representative proteomes NCBI
(9500)
Meta
(5031)
RP15
(649)
RP35
(1498)
RP55
(2340)
RP75
(3080)
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PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(19)
Full
(13176)
Representative proteomes NCBI
(9500)
Meta
(5031)
RP15
(649)
RP35
(1498)
RP55
(2340)
RP75
(3080)
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
(19)
Full
(13176)
Representative proteomes NCBI
(9500)
Meta
(5031)
RP15
(649)
RP35
(1498)
RP55
(2340)
RP75
(3080)
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.

Pfam alignments:

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_1537 (release 4.2) & Pfam-B_7916 (Release 8.0)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 19
Number in full: 13176
Average length of the domain: 188.60 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 91.83 %

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 25.6 25.6
Trusted cut-off 25.6 25.6
Noise cut-off 25.5 25.5
Model length: 191
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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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