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0  structures 567  species 0  interactions 711  sequences 16  architectures

Family: LPAM_1 (PF08139)

Summary: Prokaryotic membrane lipoprotein lipid attachment site

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.

Prokaryotic membrane lipoprotein lipid attachment site Provide feedback

In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [1].

Literature references

  1. Hayashi S, Wu HC;, J Bioenerg Biomembr. 1990;22:451-471.: Lipoproteins in bacteria. PUBMED:2202727 EPMC:2202727

  2. Klein P, Somorjai RL, Lau PC;, Protein Eng. 1988;2:15-20.: Distinctive properties of signal sequences from bacterial lipoproteins. PUBMED:3253732 EPMC:3253732


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012640

In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [PUBMED:2202727,PUBMED:3253732].

This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection [PUBMED:11309113].

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 LppaM (CL0421), which has the following description:

Superfamily consists of those protein families wherein the lipo-protein attachmnet motif, usually at the N-terminus, is found. regions of sequence downstream of this motif may not be conserved between families in the clan.

The clan contains the following 4 members:

Entericidin Lambda_Bor LPAM_1 MLTD_N

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
(71)
Full
(711)
Representative proteomes NCBI
(226)
Meta
(22)
RP15
(6)
RP35
(22)
RP55
(43)
RP75
(60)
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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
(71)
Full
(711)
Representative proteomes NCBI
(226)
Meta
(22)
RP15
(6)
RP35
(22)
RP55
(43)
RP75
(60)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(71)
Full
(711)
Representative proteomes NCBI
(226)
Meta
(22)
RP15
(6)
RP35
(22)
RP55
(43)
RP75
(60)
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: Short protein clustering
Previous IDs: VirB;
Type: Motif
Author: Lee SC, Bateman A
Number in seed: 71
Number in full: 711
Average length of the domain: 24.40 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 12.78 %

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: 25
Family (HMM) version: 7
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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