Summary: 7 transmembrane receptor (rhodopsin family)
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "Rhodopsin-like receptors". 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 firstname.lastname@example.org and we will try to help.
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.
Rhodopsin-like receptors Edit Wikipedia article
Structure of rhodopsin: A G protein-coupled receptor.
- 1 Scope
- 2 Function
- 3 Classes
- 3.1 Subfamily A1
- 3.2 Subfamily A2
- 3.3 Subfamily A3
- 3.4 Subfamily A4
- 3.5 Subfamily A5
- 3.6 Subfamily A6
- 3.7 Subfamily A7
- 3.8 Subfamily A8
- 3.9 Subfamily A9
- 3.10 Subfamily A10
- 3.11 Subfamily A11
- 3.12 Subfamily A12
- 3.13 Subfamily A13
- 3.14 Subfamily A14
- 3.15 Subfamily A15
- 3.16 Subfamily A16
- 3.17 Subfamily A17
- 3.18 Subfamily A18
- 3.19 Subfamily A19
- 3.20 Unclassified
- 4 References
- 5 External links
G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine, and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. GPCRs are usually described as "superfamily" because they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence. The currently known superfamily members include the rhodopsin-like GPCRs (this family), the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs.
The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormones, neurotransmitters, and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices.
Rhodopsin-like GPCRs have been classified into the following 19 subgroups (A1-A19) based on a phylogenetic analysis.
- Chemokine receptor IPR000355
- Chemokine (C-C motif) receptor 1 (CCR1, CKR1)
- Chemokine (C-C motif) receptor 2 (CCR2, CKR2)
- Chemokine (C-C motif) receptor 3 (CCR3, CKR3)
- Chemokine (C-C motif) receptor 4 (CCR4, CKR4)
- Chemokine (C-C motif) receptor 5 (CCR5, CKR5)
- Chemokine (C-C motif) receptor 8 (CCR8, CKR8)
- Chemokine (C-C motif) receptor-like 2 (CCRL2, CKRX)
- chemokine (C motif) receptor 1 (XCR1, CXC1) IPR005393
- chemokine (C-X3-C motif) receptor 1 (CX3CR1, C3X1) IPR005387
- GPR137B (GPR137B, TM7SF1)
- Chemokine receptor IPR000355
- CXC chemokine receptors IPR001053
- Interleukin-8 IPR000174 (IL8R)
- Adrenomedullin receptor (GPR182)
- Duffy blood group, chemokine receptor (DARC, DUFF)
- G Protein-coupled Receptor 30 (GPER, CML2, GPCR estrogen receptor)
- Angiotensin II receptor IPR000248
- Bradykinin receptor IPR000496
- GPR15 (GPR15, GPRF)
- GPR25 (GPR25)
- Opioid receptor IPR001418
- Somatostatin receptor IPR000586
- GPCR neuropeptide receptor IPR009150
- GPR1 orphan receptor (GPR1) IPR002275
- Galanin receptor IPR000405
- Cysteinyl leukotriene receptor IPR004071
- Leukotriene B4 receptor IPR003981
- Relaxin receptor IPR008112
- KiSS1-derived peptide receptor (GPR54) (KISS1R) IPR008103
- Melanin-concentrating hormone receptor 1 (MCHR1, GPRO) IPR008361
- Urotensin-II receptor (UTS2R, UR2R) IPR000670
- Cholecystokinin receptor IPR009126
- Neuropeptide FF receptor IPR005395
- Orexin receptor IPR000204
- Vasopressin receptor IPR001817
- Gonadotrophin releasing hormone receptor (GNRHR, GRHR) IPR001658
- Pyroglutamylated RFamide peptide receptor (QRFPR, GPR103)
- GPR22 (GPR22, GPRM)
- GPR176 (GPR176, GPR)
- Bombesin receptor IPR001556
- Endothelin receptor IPR000499
- Neuromedin U receptor IPR005390
- Neurotensin receptor IPR003984
- Thyrotropin-releasing hormone receptor (TRHR, TRFR) IPR009144
- Growth hormone secretagogue receptor (GHSR) IPR003905
- GPR39 (GPR39)
- Motilin receptor (MLNR, GPR38)
- Anaphylatoxin receptors IPR002234
- Formyl peptide receptor IPR000826
- MAS1 oncogene IPR000820
- GPR1 (GPR1)
- GPR32 (GPR32, GPRW)
- GPR44 (GPR44)
- GPR77 (GPR77, C5L2)
- Melatonin receptor IPR000025
- Neurokinin receptor IPR001681
- Neuropeptide Y receptor IPR000611
- Prolactin-releasing peptide receptor (PRLHR, GPRA) IPR001402
- Prokineticin receptor 1 (PROKR1, GPR73)
- Prokineticin receptor 2 (PROKR2, PKR2)
- GPR19 (GPR19, GPRJ)
- GPR50 (GPR50, ML1X)
- GPR75 (GPR75)
- GPR83 (GPR83, GPR72)
- Glycoprotein hormone receptor IPR002131
- Leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4, GPR48)
- Leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5, GPR49)
- Leucine-rich repeat-containing G protein-coupled receptor 6 (LGR6)
- GPR40-related receptor IPR013312
- P2 purinoceptor IPR002286
- Hydroxycarboxylic acid receptor 1 (HCAR1, GPR81)
- Hydroxycarboxylic acid receptor 2, Niacin receptor 1 (HCAR2, GPR109A)
- Hydroxycarboxylic acid receptor 3, Niacin receptor 2 (HCAR3, GPR109B, HM74)
- GPR31 (GPR31, GPRV)
- GPR82 (GPR82)
- Oxoglutarate (alpha-ketoglutarate) receptor 1 (OXGR1, GPR80)
- Succinate receptor 1 (SUCNR1, GPR91)
- P2 purinoceptor IPR002286
- GPR34 (GPR34)
- GPR87 (GPR87)
- GPR171 (GPR171, H963)
- Platelet-activating factor receptor (PTAFR, PAFR) IPR002282
- Cannabinoid receptor IPR002230
- Lysophosphatidic acid receptor IPR004065
- Sphingosine 1-phosphate receptor IPR004061
- Melanocortin/ACTH receptor IPR001671
- GPR3 (GPR3)
- GPR6 (GPR6)
- GPR12 (GPR12, GPRC)
- Eicosanoid receptor IPR008365
- Prostaglandin D2 receptor (PTGDR, PD2R)
- Prostaglandin E1 receptor (PTGER1, PE21)
- Prostaglandin E2 receptor (PTGER2, PE22)
- Prostaglandin E3 receptor (PTGER3, PE23)
- Prostaglandin E4 receptor (PTGER4, PE24)
- Prostaglandin F receptor (PTGFR, PF2R)
- Prostaglandin I2 (prostacyclin) receptor (PTGIR, PI2R)
- Thromboxane A2 receptor (TBXA2R, TA2R)
- Lysophosphatidic acid receptor IPR004065
- P2 purinoceptor IPR002286
- Protease-activated receptor IPR003912
- Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor) (GPR183)
- Proton-sensing G protein-coupled receptors
- GPR17 (GPR17, GPRH)
- GPR18 (GPR18, GPRI)
- GPR20 (GPR20, GPRK)
- GPR35 (GPR35)
- GPR55 (GPR55)
- Coagulation factor II receptor (F2R, THRR)
- Opsins IPR001760
- Rhodopsin (RHO, OPSD)
- Opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan) (OPN1SW, OPSB) (blue-sensitive opsin)
- Opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan) (OPN1MW, OPSG) (green-sensitive opsin)
- Opsin 1 (cone pigments), long-wave-sensitive (color blindness, protan) (OPN1LW, OPSR) (red-sensitive opsin)
- Opsin 3, Panopsin (OPN3)
- Opsin 4, Melanopsin (OPN4)
- Opsin 5 (OPN5, GPR136)
- Retinal G protein coupled receptor (RGR)
- Retinal pigment epithelium-derived rhodopsin homolog (RRH, OPSX) (visual pigment-like receptor opsin) IPR001793
- 5-Hydroxytryptamine (5-HT) receptor IPR002231
- Adrenergic receptor IPR002233
- Dopamine receptor IPR000929
- Trace amine receptor IPR009132
- Histamine H2 receptor (HRH2, HH2R) IPR000503
- Histamine H1 receptor (HRH1, HH1R) IPR000921
- Histamine H3 receptor (HRH3) IPR003980
- Histamine H4 receptor (HRH4) IPR008102
- Adenosine receptor IPR001634
- Muscarinic acetylcholine receptor IPR000995
- GPR21 (GPR21, GPRL)
- GPR27 (GPR27)
- GPR45 (GPR45, PSP24)
- GPR52 (GPR52)
- GPR61 (GPR61)
- GPR62 (GPR62)
- GPR63 (GPR63)
- GPR78 (GPR78)
- GPR84 (GPR84)
- GPR85 (GPR85)
- GPR88 (GPR88)
- GPR101 (GPR101)
- GPR161 (GPR161, RE2)
- GPR173 (GPR173, SREB3)
- 5-Hydroxytryptamine (5-HT) receptor IPR002231
- Palczewski K, Kumasaka T, Hori T; et al. (August 2000). "Crystal structure of rhodopsin: A G protein-coupled receptor". Science 289 (5480): 739–45. doi:10.1126/science.289.5480.739. PMID 10926528.
- Attwood TK, Findlay JB (1994). "Fingerprinting G-protein-coupled receptors". Protein Eng. 7 (2): 195–203. doi:10.1093/protein/7.2.195. PMID 8170923.
- "Information system for G protein-coupled receptors". GPCRDB. www.gpcr.org. Retrieved 2008-12-05.
- Birnbaumer L (1990). "G proteins in signal transduction". Annu. Rev. Pharmacol. Toxicol. 30: 675–705. doi:10.1146/annurev.pa.30.040190.003331. PMID 2111655.
- Gilman AG, Casey PJ (1988). "G protein involvement in receptor-effector coupling". J. Biol. Chem. 263 (6): 2577–2580. PMID 2830256.
- Attwood TK, Findlay JB (1993). "Design of a discriminating fingerprint for G-protein-coupled receptors". Protein Eng. 6 (2): 167–176. doi:10.1093/protein/6.2.167. PMID 8386361.
- Joost P, Methner A (2002). "Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands". Genome Biol 3 (11): research0063.1–0063.16. doi:10.1186/gb-2002-3-11-research0063. PMC 133447. PMID 12429062.
- Terakita A (2005). "The opsins". Genome Biol. 6 (3): 213. doi:10.1186/gb-2005-6-3-213. PMC 1088937. PMID 15774036.
- Vriend G, Horn F, Oliveira L, Bywater RP, Cohen FE. "GPCRDB (G Protein-Coupled Receptor Data Base): sequence-derived data.". Archived from the original on 2007-11-14. Retrieved 2007-12-10.
- Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003). "GPCRDB information system for G protein-coupled receptors". Nucleic Acids Res. 31 (1): 294–7. doi:10.1093/nar/gkg103. PMC 165550. PMID 12520006. This database includes multiple sequence alignments of all GPCR families and sub-families.
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.
7 transmembrane receptor (rhodopsin family) Provide feedback
This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins .
External database links
|PRINTS:||PR00237 PR00652 PR00425 PR00527 PR00857 PR00245|
This tab holds annotation information from the InterPro database.
InterPro entry IPR000276
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups [PUBMED:12679517]. The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence [PUBMED:8170923]. The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [PUBMED:8170923, PUBMED:8081729, PUBMED:15914470, PUBMED:18948278, PUBMED:16753280]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice [PUBMED:12679517]. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [PUBMED:23020293].
The rhodopsin-like GPCRs (GPCRA) represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [PUBMED:2111655, PUBMED:2830256, PUBMED:8386361].
This entry represents the G protein-coupled receptor, rhodopsin-like family.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||integral component of membrane (GO:0016021)|
|Molecular function||G-protein coupled receptor activity (GO:0004930)|
|Biological process||G-protein coupled receptor signaling pathway (GO:0007186)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
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 36 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 Bac_rhodopsin Dicty_CAR DUF1182 DUF621 Frizzled Git3 Git3_C GpcrRhopsn4 Lung_7-TM_R Ocular_alb Serpentine_r_xa Sre Srg TAS2R V1R
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.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- 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
- 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
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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.
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.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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 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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Number in seed:||64|
|Number in full:||58080|
|Average length of the domain:||229.40 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||73.19 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the 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:
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".
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.
The tree shows the occurrence of this domain across different species. More...
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.
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
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.
There are 12 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 7tm_1 domain has been found. There are 194 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...