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0  structures 28  species 0  interactions 40  sequences 3  architectures

Family: Apolipo_F (PF15148)

Summary: Apolipoprotein F

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

APOF Edit Wikipedia article

Apolipoprotein F
Identifiers
Symbols APOF; Apo-F; LTIP
External IDs OMIM107760 MGI104539 HomoloGene48030 GeneCards: APOF Gene
RNA expression pattern
PBB GE APOF 207262 at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 319 103161
Ensembl ENSG00000175336 ENSMUSG00000047631
UniProt Q13790 Q91V80
RefSeq (mRNA) NM_001638 NM_133997
RefSeq (protein) NP_001629 NP_598758
Location (UCSC) Chr 12:
56.75 – 56.76 Mb
Chr 10:
128.27 – 128.27 Mb
PubMed search [1] [2]
Apolipoprotein F
Identifiers
Symbol APOF
Pfam PF15148

Apolipoprotein F is a protein that in humans is encoded for by the APOF gene.[1][2]

The product of this gene is one of the minor apolipoproteins found in plasma. This protein forms complexes with lipoproteins and may be involved in transport and/or esterification of cholesterol.[2]

References[edit]

  1. ^ Day JR, Albers JJ, Gilbert TL, Whitmore TE, McConathy WJ, Wolfbauer G (Oct 1994). "Purification and molecular cloning of human apolipoprotein F". Biochem Biophys Res Commun 203 (2): 1146–51. doi:10.1006/bbrc.1994.2302. PMID 8093033. 
  2. ^ a b "Entrez Gene: APOF apolipoprotein F". 

Further reading[edit]



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 F Provide feedback

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This tab holds annotation information from the InterPro database.

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Domain organisation

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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...

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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
(8)
Full
(40)
Representative proteomes NCBI
(37)
Meta
(0)
RP15
(1)
RP35
(3)
RP55
(4)
RP75
(20)
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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
(8)
Full
(40)
Representative proteomes NCBI
(37)
Meta
(0)
RP15
(1)
RP35
(3)
RP55
(4)
RP75
(20)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(8)
Full
(40)
Representative proteomes NCBI
(37)
Meta
(0)
RP15
(1)
RP35
(3)
RP55
(4)
RP75
(20)
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.

Pfam alignments:

HMM logo

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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.

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This family is new in this Pfam release.

Seed source: Jackhmmer:Q13790
Previous IDs: none
Type: Family
Author: Eberhardt RY, Coggill P, Hetherington K
Number in seed: 8
Number in full: 40
Average length of the domain: 180.80 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 61.13 %

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 27.0 27.0
Trusted cut-off 27.3 31.9
Noise cut-off 21.4 26.8
Model length: 200
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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