Summary: Apolipoprotein M (ApoM)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

Wikipedia: APOM
Pfam
InterPro

This is the Wikipedia entry entitled "APOM". More...

The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.

Does Pfam agree with the content of the Wikipedia entry ?

Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.

Editing Wikipedia articles

Before you edit for the first time

Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.

You should take a few minutes to view the following pages:

How your contribution will be recorded

Anyone can edit a Wikipedia entry. You can do this either as a new user or you can register with Wikipedia and log on. When you click on the "Edit Wikipedia article" button, your browser will direct you to the edit page for this entry in Wikipedia. If you are a registered user and currently logged in, your changes will be recorded under your Wikipedia user name. However, if you are not a registered user or are not logged on, your changes will be logged under your computer's IP address. This has two main implications. Firstly, as a registered Wikipedia user your edits are more likely seen as valuable contribution (although all edits are open to community scrutiny regardless). Secondly, if you edit under an IP address you may be sharing this IP address with other users. If your IP address has previously been blocked (due to being flagged as a source of 'vandalism') your edits will also be blocked. You can find more information on this and creating a user account at Wikipedia.

If you have problems editing a particular page, contact us at pfam-help@sanger.ac.uk and we will try to help.

Contact us

The community annotation is a new facility of the Pfam web site. If you have problems editing or experience problems with these pages please contact us.

APOM Edit Wikipedia article

This article is an orphan, as no other articles link to it. Please introduce links to this page from related articles; suggestions may be available. (December 2008)

Apolipoprotein M

Rendering based on PDB 2WEW.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
2WEW, 2WEX, 2YG2

Identifiers

Symbols

APOM; G3a; HSPC336; NG20; apo-M

External IDs

OMIM: 606907 MGI: 1930124 HomoloGene: 10308 GeneCards: APOM Gene

Gene Ontology
Molecular function	• lipid transporter activity • phospholipid binding • antioxidant activity
Cellular component	• integral to plasma membrane • very-low-density lipoprotein particle • low-density lipoprotein particle • high-density lipoprotein particle • discoidal high-density lipoprotein particle • spherical high-density lipoprotein particle
Biological process	• response to glucose stimulus • cholesterol efflux • high-density lipoprotein particle remodeling • high-density lipoprotein particle assembly • high-density lipoprotein particle clearance • negative regulation of plasma lipoprotein particle oxidation • lipoprotein metabolic process • cholesterol homeostasis • reverse cholesterol transport
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 6:
31.62 – 31.63 Mb

Chr 17:
35.13 – 35.13 Mb

PubMed search

[1]

[2]

ApoM

Identifiers

Symbol

ApoM

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Apolipoprotein M is a protein that in humans is encoded by the APOM gene.^[1]^[2]^[3]

The protein encoded by this gene is an apolipoprotein and member of the lipocalin protein family. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Two transcript variants encoding two different isoforms have been found for this gene, but only one of them has been fully characterized.^[3]

[edit] References

^ Xu N, Dahlback B (Dec 1999). "A novel human apolipoprotein (apoM)". J Biol Chem 274 (44): 31286–90. doi:10.1074/jbc.274.44.31286. PMID 10531326.
^ Duan J, Dahlback B, Villoutreix BO (Jun 2001). "Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis". FEBS Lett 499 (1–2): 127–32. doi:10.1016/S0014-5793(01)02544-3. PMID 11418126.
^ ^a ^b "Entrez Gene: APOM apolipoprotein M". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=55937.

[edit] Further reading

Albertella MR, Jones H, Thomson W, et al. (1997). "Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B)". Genomics 36 (2): 240–51. doi:10.1006/geno.1996.0459. PMID 8812450.
Xu N, Zhang XY, Dong X, et al. (2002). "Effects of platelet-activating factor, tumor necrosis factor, and interleukin-1alpha on the expression of apolipoprotein M in HepG2 cells". Biochem. Biophys. Res. Commun. 292 (4): 944–50. doi:10.1006/bbrc.2002.6755. PMID 11944906.
Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.ncbi.nlm.nih.gov/pmc/articles/PMC139241/.
Zhang XY, Dong X, Zheng L, et al. (2003). "Specific tissue expression and cellular localization of human apolipoprotein M as determined by in situ hybridization". Acta Histochem. 105 (1): 67–72. doi:10.1078/0065-1281-00687. PMID 12666989.
Mungall AJ, Palmer SA, Sims SK, et al. (2003). "The DNA sequence and analysis of human chromosome 6". Nature 425 (6960): 805–11. doi:10.1038/nature02055. PMID 14574404.
Richter S, Shih DQ, Pearson ER, et al. (2004). "Regulation of apolipoprotein M gene expression by MODY3 gene hepatocyte nuclear factor-1alpha: haploinsufficiency is associated with reduced serum apolipoprotein M levels". Diabetes 52 (12): 2989–95. doi:10.2337/diabetes.52.12.2989. PMID 14633861.
Xie T, Rowen L, Aguado B, et al. (2004). "Analysis of the Gene-Dense Major Histocompatibility Complex Class III Region and Its Comparison to Mouse". Genome Res. 13 (12): 2621–36. doi:10.1101/gr.1736803. PMC 403804. PMID 14656967. //www.ncbi.nlm.nih.gov/pmc/articles/PMC403804/.
Zhang XY, Jiao GQ, Hurtig M, et al. (2005). "Expression pattern of apolipoprotein M during mouse and human embryogenesis". Acta Histochem. 106 (2): 123–8. doi:10.1016/j.acthis.2003.11.004. PMID 15147633.
Kabbara A, Payet N, Cottel D, et al. (2004). "Exclusion of CYP46 and APOM as candidate genes for Alzheimer's disease in a French population". Neurosci. Lett. 363 (2): 139–43. doi:10.1016/j.neulet.2004.03.066. PMID 15172102.
Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. //www.ncbi.nlm.nih.gov/pmc/articles/PMC528928/.
Xu N, Nilsson-Ehle P, Ahrén B (2005). "Correlation of apolipoprotein M with leptin and cholesterol in normal and obese subjects". J. Nutr. Biochem. 15 (10): 579–82. doi:10.1016/j.jnutbio.2004.03.001. PMID 15542348.
Luo G, Hurtig M, Zhang X, et al. (2005). "Leptin inhibits apolipoprotein M transcription and secretion in human hepatoma cell line, HepG2 cells". Biochim. Biophys. Acta 1734 (2): 198–202. doi:10.1016/j.bbalip.2005.02.005. PMID 15904876.
Liu T, Qian WJ, Gritsenko MA, et al. (2006). "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry". J. Proteome Res. 4 (6): 2070–80. doi:10.1021/pr0502065. PMC 1850943. PMID 16335952. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1850943/.
Niu N, Zhu X, Liu Y, et al. (2007). "Single nucleotide polymorphisms in the proximal promoter region of apolipoprotein M gene (apoM) confer the susceptibility to development of type 2 diabetes in Han Chinese". Diabetes Metab. Res. Rev. 23 (1): 21–5. doi:10.1002/dmrr.641. PMID 16572495.
Christoffersen C, Nielsen LB, Axler O, et al. (2006). "Isolation and characterization of human apolipoprotein M-containing lipoproteins". J. Lipid Res. 47 (8): 1833–43. doi:10.1194/jlr.M600055-JLR200. PMID 16682745.
Karlsson H, Lindqvist H, Tagesson C, Lindahl M (2006). "Characterization of apolipoprotein M isoforms in low-density lipoprotein". J. Proteome Res. 5 (10): 2685–90. doi:10.1021/pr060180x. PMID 17022639.
Xu X, Ye Q, Xu N, et al. (2007). "Effects of ischemia-reperfusion injury on apolipoprotein M expression in the liver". Transplant. Proc. 38 (9): 2769–73. doi:10.1016/j.transproceed.2006.08.133. PMID 17112825.
Ahnström J, Faber K, Axler O, Dahlbäck B (2007). "Hydrophobic ligand binding properties of the human lipocalin apolipoprotein M". J. Lipid Res. 48 (8): 1754–62. doi:10.1194/jlr.M700103-JLR200. PMID 17525477.

This article on a gene on chromosome 6 is a stub. You can help Wikipedia by expanding it.

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.

Apolipoprotein M (ApoM) Provide feedback

ApoM is a 25 kDa plasma protein associated with high-density lipoproteins (HDLs). ApoM is important in the formation of pre-ss-HDL and also in increasing cholesterol efflux from macrophage foam cells [1]. Lipoproteins consist of lipids solubilized by apolipoproteins. ApoM lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide [2].

Literature references

Ahnstrom J, Axler O, Jauhiainen M, Salomaa V, Havulinna AS, Ehnholm C, Frikke-Schmidt R, Tybjaerg-Hansen A, Dahlback B; , J Lipid Res. 2008; [Epub ahead of print]: Levels of apolipoprotein M are not associated with the risk of coronary heart disease in two independent case-control studies. PUBMED:18490703 EPMC:18490703
Christoffersen C, Ahnstrom J, Axler O, Christensen EI, Dahlback B, Nielsen LB; , J Biol Chem. 2008; [Epub ahead of print]: The signal peptide anchors apolipoprotein M in plasma lipoproteins and prevents rapid clearance of apolipoprotein M from plasma. PUBMED:18460466 EPMC:18460466

External database links

PANDIT:	PF11032
Pseudofam:	PF11032
SYSTERS:	ApoM

This tab holds annotation information from the InterPro database.

InterPro entry IPR022734

ApoM is a 25 kDa plasma protein associated with high-density lipoproteins (HDLs). ApoM is important in the formation of pre-ss-HDL and also in increasing cholesterol efflux from macrophage foam cells [PUBMED:18490703]. Lipoproteins consist of lipids solubilized by apolipoproteins. ApoM lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide [PUBMED:18460466].

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 Calycin (CL0116), which contains the following 16 members:

ApoM DUF3642 His_binding Lipocalin Lipocalin_2 Lipocalin_3 Lipocalin_4 Lipocalin_5 Lipocalin_6 Lipocalin_7 META Nitrophorin NlpE Triabin VDE YodA

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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 (4)	Full (77)	Representative proteomes				NCBI (102)	Meta (0)
	Seed (4)	Full (77)	RP15 (1)	RP35 (3)	RP55 (18)	RP75 (37)	NCBI (102)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (4)	Full (77)	Representative proteomes				NCBI (102)	Meta (0)
	Seed (4)	Full (77)	RP15 (1)	RP35 (3)	RP55 (18)	RP75 (37)	NCBI (102)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (4)	Full (77)	Representative proteomes				NCBI (102)	Meta (0)
	Seed (4)	Full (77)	RP15 (1)	RP35 (3)	RP55 (18)	RP75 (37)	NCBI (102)	Meta (0)
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.

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

Seed source:

PRODOM

Previous IDs:

none

Type:

Family

Author:

Pollington J, Finn RD

Number in seed:

4

Number in full:

77

Average length of the domain:

164.30 aa

Average identity of full alignment:

37 %

Average coverage of the sequence by the domain:

93.66 %

HMM information

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	20.6	20.6
Trusted cut-off	21.0	20.7
Noise cut-off	20.0	20.5

Model length:

186

Family (HMM) version:

3

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Loading sunburst data...

Tree controls

Hide

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

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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.

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ApoM domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: ApoM (PF11032)

Jump to...