Summary: Exo70 exocyst complex subunit

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

Wikipedia: EXOC7
Pfam
InterPro

This is the Wikipedia entry entitled "EXOC7". 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.

EXOC7 Edit Wikipedia article

Exocyst complex component 7

PDB rendering based on 2pft.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
2pft

Identifiers

Symbols

EXOC7; 2-5-3p; EX070; EXO70; EXOC1; Exo70p; YJL085W

External IDs

OMIM: 608163 MGI: 1859270 HomoloGene: 41019 GeneCards: EXOC7 Gene

Gene Ontology
Molecular function	â¢ protein binding
Cellular component	â¢ exocyst â¢ microtubule organizing center â¢ cytosol â¢ plasma membrane â¢ growth cone membrane â¢ centriolar satellite
Biological process	â¢ exocytosis â¢ protein transport
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 17:
74.08 â 74.12 Mb

Chr 11:
116.29 â 116.31 Mb

PubMed search

[1]

[2]

Exo70 exocyst complex subunit

crystal structure of the s. cerevisiae exocyst component exo70p

Identifiers

Symbol

Exo70

Pfam clan

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

Exocyst complex component 7 is a protein that in humans is encoded by the EXOC7 gene.^[1]^[2] It was formerly known as Exo70.

It forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae, this and other exocyst proteins have been observed in several other eukaryotes, including humans.^[3] In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localised at the tip of the bud, the major site of exocytosis in yeast.^[3] It interacts with the Rho3 GTPase.^[4] This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud).^[5] In humans, the functions of this protein and the exocyst complex are less well characterised: this protein is expressed in several tissues and is thought to also be involved in exocytosis.^[6]

[edit] Interactions

EXOC7 has been shown to interact with EXOC4^[7]^[8] and RHOQ.^[8]

[edit] References

^ Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA (Dec 2002). "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): 16899â16903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.ncbi.nlm.nih.gov/pmc/articles/PMC139241/.
^ "Entrez Gene: EXOC7 exocyst complex component 7". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23265.
^ ^a ^b TerBush DR, Maurice T, Roth D, Novick P (December 1996). "The Exocyst is a multiprotein complex required for exocytosis in Saccharomyces cerevisiae". EMBO J. 15 (23): 6483â94. PMC 452473. PMID 8978675. //www.ncbi.nlm.nih.gov/pmc/articles/PMC452473/.
^ Robinson NG, Guo L, Imai J, Toh-E A, Matsui Y, Tamanoi F (May 1999). "Rho3 of Saccharomyces cerevisiae, which regulates the actin cytoskeleton and exocytosis, is a GTPase which interacts with Myo2 and Exo70". Mol. Cell. Biol. 19 (5): 3580â7. PMC 84150. PMID 10207081. //www.ncbi.nlm.nih.gov/pmc/articles/PMC84150/.
^ Adamo JE, Rossi G, Brennwald P (December 1999). "The Rho GTPase Rho3 has a direct role in exocytosis that is distinct from its role in actin polarity". Mol. Biol. Cell 10 (12): 4121â33. PMC 25747. PMID 10588647. //www.ncbi.nlm.nih.gov/pmc/articles/PMC25747/.
^ Kee Y, Yoo JS, Hazuka CD, Peterson KE, Hsu SC, Scheller RH (December 1997). "Subunit structure of the mammalian exocyst complex". Proc. Natl. Acad. Sci. U.S.A. 94 (26): 14438â43. doi:10.1073/pnas.94.26.14438. PMC 25013. PMID 9405631. //www.ncbi.nlm.nih.gov/pmc/articles/PMC25013/.
^ Sans, Nathalie; Prybylowski Kate, Petralia Ronald S, Chang Kai, Wang Ya-Xian, Racca Claudia, Vicini Stefano, Wenthold Robert J (Jun. 2003). "NMDA receptor trafficking through an interaction between PDZ proteins and the exocyst complex". Nat. Cell Biol. (England) 5 (6): 520â530. doi:10.1038/ncb990. ISSN 1465-7392. PMID 12738960.
^ ^a ^b Inoue, Mayumi; Chang Louise, Hwang Joseph, Chiang Shian-Huey, Saltiel Alan R (Apr. 2003). "The exocyst complex is required for targeting of Glut4 to the plasma membrane by insulin". Nature (England) 422 (6932): 629â633. doi:10.1038/nature01533. ISSN 0028-0836. PMID 12687004.

[edit] Further reading

Kee Y, Yoo JS, Hazuka CD et al. (1998). "Subunit structure of the mammalian exocyst complex". Proc. Natl. Acad. Sci. U.S.A. 94 (26): 14438â14443. doi:10.1073/pnas.94.26.14438. PMC 25013. PMID 9405631. //www.ncbi.nlm.nih.gov/pmc/articles/PMC25013/.
Kikuno R, Nagase T, Ishikawa K et al. (1999). "Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (3): 197â205. doi:10.1093/dnares/6.3.197. PMID 10470851.
Soudeyns H, Champagne P, Holloway CL et al. (2000). "Transient T cell receptor beta-chain variable region-specific expansions of CD4+ and CD8+ T cells during the early phase of pediatric human immunodeficiency virus infection: characterization of expanded cell populations by T cell receptor phenotyping". J. Infect. Dis. 181 (1): 107â120. doi:10.1086/315181. PMID 10608757.
Ignatovich O, Tomlinson IM, Popov AV et al. (2000). "Dominance of intrinsic genetic factors in shaping the human immunoglobulin Vlambda repertoire". J. Mol. Biol. 294 (2): 457â465. doi:10.1006/jmbi.1999.3243. PMID 10610771.
Holtmeier W, Hennemann A, Caspary WF (2000). "IgA and IgM V(H) repertoires in human colon: evidence for clonally expanded B cells that are widely disseminated". Gastroenterology 119 (5): 1253â1266. doi:10.1053/gast.2000.20219. PMID 11054383.
Brymora A, Valova VA, Larsen MR et al. (2001). "The brain exocyst complex interacts with RalA in a GTP-dependent manner: identification of a novel mammalian Sec3 gene and a second Sec15 gene". J. Biol. Chem. 276 (32): 29792â29797. doi:10.1074/jbc.C100320200. PMID 11406615.
Inoue M, Chang L, Hwang J et al. (2003). "The exocyst complex is required for targeting of Glut4 to the plasma membrane by insulin". Nature 422 (6932): 629â633. doi:10.1038/nature01533. PMID 12687004.
Moskalenko S, Tong C, Rosse C et al. (2004). "Ral GTPases regulate exocyst assembly through dual subunit interactions". J. Biol. Chem. 278 (51): 51743â51748. doi:10.1074/jbc.M308702200. PMID 14525976.
Ota T, Suzuki Y, Nishikawa T et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40â45. doi:10.1038/ng1285. PMID 14702039.
Wang S, Liu Y, Adamson CL et al. (2005). "The mammalian exocyst, a complex required for exocytosis, inhibits tubulin polymerization". J. Biol. Chem. 279 (34): 35958â35966. doi:10.1074/jbc.M313778200. PMID 15205466.
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): 2121â2127. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334. //www.ncbi.nlm.nih.gov/pmc/articles/PMC528928/.
Xu KF, Shen X, Li H et al. (2005). "Interaction of BIG2, a brefeldin A-inhibited guanine nucleotide-exchange protein, with exocyst protein Exo70". Proc. Natl. Acad. Sci. U.S.A. 102 (8): 2784â2789. doi:10.1073/pnas.0409871102. PMC 549493. PMID 15705715. //www.ncbi.nlm.nih.gov/pmc/articles/PMC549493/.
Rual JF, Venkatesan K, Hao T et al. (2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature 437 (7062): 1173â1178. doi:10.1038/nature04209. PMID 16189514.
Beausoleil SA, VillÃ©n J, Gerber SA et al. (2006). "A probability-based approach for high-throughput protein phosphorylation analysis and site localization". Nat. Biotechnol. 24 (10): 1285â1292. doi:10.1038/nbt1240. PMID 16964243.

PDB gallery

2pft: The Crystal Structure of Mouse Exo70 Reveals Unique Features of the Mammalian Exocyst

This article incorporates text from the public domain Pfam and InterPro IPR004140

This article on a gene on chromosome 17 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.

Exo70 exocyst complex subunit Provide feedback

The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae [1] Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localised at the tip of the bud, the major site of exocytosis in yeast [1]. Exo70 interacts with the Rho3 GTPase [4]. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) [3]. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [2].

Literature references

TerBush DR, Maurice T, Roth D, Novick P; , EMBO J 1996;15:6483-6494.: The Exocyst is a multiprotein complex required for exocytosis in Saccharomyces cerevisiae. PUBMED:8978675 EPMC:8978675
Kee Y, Yoo JS, Hazuka CD, Peterson KE, Hsu SC, Scheller RH; , Proc Natl Acad Sci U S A 1997;94:14438-14443.: Subunit structure of the mammalian exocyst complex. PUBMED:9405631 EPMC:9405631
Adamo JE, Rossi G, Brennwald P; , Mol Biol Cell 1999;10:4121-4133.: The Rho GTPase Rho3 has a direct role in exocytosis that is distinct from its role in actin polarity. PUBMED:10588647 EPMC:10588647
Robinson NG, Guo L, Imai J, Toh-E A, Matsui Y, Tamanoi F; , Mol Cell Biol 1999;19:3580-3587.: Rho3 of Saccharomyces cerevisiae, which regulates the actin cytoskeleton and exocytosis, is a GTPase which interacts with Myo2 and Exo70. PUBMED:10207081 EPMC:10207081
Hamburger ZA, Hamburger AE, West AP Jr, Weis WI; , J Mol Biol. 2005; [Epub ahead of print]: Crystal Structure of the S.cerevisiae Exocyst Component Exo70p. PUBMED:16359701 EPMC:16359701

External database links

PANDIT:	PF03081
Pseudofam:	PF03081
SYSTERS:	Exo70

This tab holds annotation information from the InterPro database.

InterPro entry IPR004140

The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [PUBMED:8978675], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast [PUBMED:8978675]. Exo70 interacts with the Rho3 GTPase [PUBMED:10207081]. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) [PUBMED:10588647]. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [PUBMED:9405631].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	exocyst (GO:0000145)
Biological process	exocytosis (GO:0006887)

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 Vps51 (CL0295), which contains the following 16 members:

COG2 COG5 COG6 Dor1 DUF2450 Exo70 Sec15 Sec3_C Sec3_C_2 Sec5 Sec6 Sec8_exocyst Vps51 Vps52 Vps53_N Zw10

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 (58)	Full (882)	Representative proteomes				NCBI (852)	Meta (0)
	Seed (58)	Full (882)	RP15 (109)	RP35 (289)	RP55 (425)	RP75 (540)	NCBI (852)	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 (58)	Full (882)	Representative proteomes				NCBI (852)	Meta (0)
	Seed (58)	Full (882)	RP15 (109)	RP35 (289)	RP55 (425)	RP75 (540)	NCBI (852)	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 (58)	Full (882)	Representative proteomes				NCBI (852)	Meta (0)
	Seed (58)	Full (882)	RP15 (109)	RP35 (289)	RP55 (425)	RP75 (540)	NCBI (852)	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:

Pfam-B_2462 (release 6.4)

Previous IDs:

none

Type:

Family

Author:

Mifsud W

Number in seed:

58

Number in full:

882

Average length of the domain:

323.30 aa

Average identity of full alignment:

22 %

Average coverage of the sequence by the domain:

57.29 %

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	23.7	23.7
Trusted cut-off	24.3	23.8
Noise cut-off	23.3	23.6

Model length:

371

Family (HMM) version:

10

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 Exo70 domain has been found. There are 7 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: Exo70 (PF03081)

Jump to...