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2  structures 3156  species 0  interactions 6131  sequences 48  architectures

Family: HlyIII (PF03006)

Summary: Haemolysin-III related

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.

Haemolysin-III related Provide feedback

Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus [1]. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism [2]. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins [3]. The mammalian members include progesterone binding proteins [4]. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea. This family belongs to the CREST superfamily [5] which are distantly related to GPCRs.

Literature references

  1. Baida GE, Kuzmin NP; , Biochim Biophys Acta 1995;1264:151-154.: Cloning and primary structure of a new hemolysin gene from Bacillus cereus. PUBMED:7495855 EPMC:7495855

  2. Karpichev IV, Cornivelli L, Small GM; , J Biol Chem 2002;0:0-1.: Multiple regulatory roles of a novel Saccharomyces cerevisiae protein, encoded by YOL002c, in lipid and phosphate metabolism. PUBMED:11916977 EPMC:11916977

  3. Tang YT, Hu T, Arterburn M, Boyle B, Bright JM, Emtage PC, Funk WD;, J Mol Evol. 2005;61:372-380.: PAQR proteins: a novel membrane receptor family defined by an ancient 7-transmembrane pass motif. PUBMED:16044242 EPMC:16044242

  4. Thomas P, Pang Y, Dong J, Groenen P, Kelder J, de Vlieg J, Zhu Y, Tubbs C;, Endocrinology. 2007;148:705-718.: Steroid and G protein binding characteristics of the seatrout and human progestin membrane receptor alpha subtypes and their evolutionary origins. PUBMED:17082257 EPMC:17082257

  5. Pei J, Millay DP, Olson EN, Grishin NV;, Biol Direct. 2011;6:37.: CREST--a large and diverse superfamily of putative transmembrane hydrolases. PUBMED:21733186 EPMC:21733186


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004254

Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus [PUBMED:7495855]. YOL002c (AdipoR-like receptor IZH2) from Saccharomyces cerevisiae encodes a protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism [PUBMED:11916977, PUBMED:15664187]. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adiponectin (AdipoQ) receptors (AdipoR), and hence have been named PAQR proteins [PUBMED:16044242]. The mammalian members include progesterone binding proteins [PUBMED:17082257]. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea.

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 GPCR_A (CL0192), which has the following description:

This clan contains various seven-transmembrane receptors and related proteins. A major member is Pfam:PF00001, members of which have been considered to be typical members of the rhodopsin superfamily. Many members of this clan are Caenorhabditis proteins, suggesting great expansion of the relevant families in these nematode worms.

The clan contains the following 43 members:

7TM-7TMR_HD 7tm_1 7tm_2 7tm_3 7tm_4 7TM_GPCR_Sra 7TM_GPCR_Srab 7TM_GPCR_Srb 7TM_GPCR_Srbc 7TM_GPCR_Srd 7TM_GPCR_Srh 7TM_GPCR_Sri 7TM_GPCR_Srj 7TM_GPCR_Srsx 7TM_GPCR_Srt 7TM_GPCR_Sru 7TM_GPCR_Srv 7TM_GPCR_Srw 7TM_GPCR_Srx 7TM_GPCR_Srz 7TM_GPCR_Str 7TMR-DISM_7TM Bac_rhodopsin Ceramidase Dicty_CAR DUF1182 DUF3522 DUF621 Frizzled Git3 GpcrRhopsn4 GPR_Gpa2_C HisKA_7TM HlyIII Lung_7-TM_R Ocular_alb Per1 Serpentine_r_xa SID-1_RNA_chan Sre Srg TAS2R V1R

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(38)
Full
(6131)
Representative proteomes UniProt
(13912)
NCBI
(20412)
Meta
(457)
RP15
(1235)
RP35
(3181)
RP55
(5401)
RP75
(7929)
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PP/heatmap 1                

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

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

Format an alignment

  Seed
(38)
Full
(6131)
Representative proteomes UniProt
(13912)
NCBI
(20412)
Meta
(457)
RP15
(1235)
RP35
(3181)
RP55
(5401)
RP75
(7929)
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
(38)
Full
(6131)
Representative proteomes UniProt
(13912)
NCBI
(20412)
Meta
(457)
RP15
(1235)
RP35
(3181)
RP55
(5401)
RP75
(7929)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_1581 (release 6.4)
Previous IDs: UPF0073;
Type: Family
Author: Bateman A
Number in seed: 38
Number in full: 6131
Average length of the domain: 205.30 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 70.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 26.1 26.1
Model length: 224
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 HlyIII domain has been found. There are 2 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.

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