Summary: Casein kinase II regulatory subunit
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 "CSNK2B". 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.
CSNK2B Edit Wikipedia article
|Casein kinase 2, beta polypeptide|
PDB rendering based on 1jwh.
|Symbols||; CK2B; CK2N; CSK2B; G5A|
|External IDs||IUPHAR: ChEMBL: GeneCards:|
|RNA expression pattern|
|Casein kinase II regulatory subunit|
structure of ck2 beta subunit crystallized in the presence of a p21waf1 peptide
This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus.
Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Serine or Threonine in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta'). The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase.
CSNK2B has been shown to interact with CD163, CSNK2A2, Casein kinase 2, alpha 1, FGF1, TRIB3, CDC34, Ribosomal protein L5, BTF3, BRCA1, RNF7, P70-S6 Kinase 1 and APC.
- Yang-Feng TL, Teitz T, Cheung MC, Kan YW, Canaani D (March 1991). "Assignment of the human casein kinase II beta-subunit gene to 6p12----p21". Genomics 8 (4): 741â€“2. doi:10.1016/0888-7543(90)90266-W. PMID 2276748.
- Mucher G, Becker J, Knapp M, Buttner R, Moser M, Rudnik-Schoneborn S, Somlo S, Germino G, Onuchic L, Avner E, Guay-Woodford L, Zerres K (April 1998). "Fine mapping of the autosomal recessive polycystic kidney disease locus (PKHD1) and the genes MUT, RDS, CSNK2 beta, and GSTA1 at 6p21.1-p12". Genomics 48 (1): 40â€“5. doi:10.1006/geno.1997.5145. PMID 9503014.
- "Entrez Gene: CSNK2B casein kinase 2, beta polypeptide".
- Jakobi R, Voss H, Pyerin W (July 1989). "Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full-length cDNA encoding subunit beta". Eur. J. Biochem. 183 (1): 227â€“33. doi:10.1111/j.1432-1033.1989.tb14917.x. PMID 2666134.
- Voss H, Wirkner U, Jakobi R, Hewitt NA, Schwager C, Zimmermann J, Ansorge W, Pyerin W (July 1991). "Structure of the gene encoding human casein kinase II subunit beta". J. Biol. Chem. 266 (21): 13706â€“11. PMID 1856204.
- Bidwai AP, Reed JC, Glover CV (May 1995). "Cloning and disruption of CKB1, the gene encoding the 38-kDa beta subunit of Saccharomyces cerevisiae casein kinase II (CKII). Deletion of CKII regulatory subunits elicits a salt-sensitive phenotype". J. Biol. Chem. 270 (18): 10395â€“404. doi:10.1074/jbc.270.18.10395. PMID 7737972.
- Reed JC, Bidwai AP, Glover CV (July 1994). "Cloning and disruption of CKB2, the gene encoding the 32-kDa regulatory beta'-subunit of Saccharomyces cerevisiae casein kinase II". J. Biol. Chem. 269 (27): 18192â€“200. PMID 8027080.
- Ritter, M; Buechler C; Kapinsky M; Schmitz G (April 2001). "Interaction of CD163 with the regulatory subunit of casein kinase II (CKII) and dependence of CD163 signaling on CKII and protein kinase C". Eur. J. Immunol. (Germany) 31 (4): 999â€“1009. doi:10.1002/1521-4141(200104)31:4<999::AID-IMMU999>3.0.CO;2-R. ISSN 0014-2980. PMID 11298324.
- Lehner, Ben; Semple Jennifer I; Brown Stephanie E; Counsell Damian; Campbell R Duncan; Sanderson Christopher M (January 2004). "Analysis of a high-throughput yeast two-hybrid system and its use to predict the function of intracellular proteins encoded within the human MHC class III region". Genomics (United States) 83 (1): 153â€“67. doi:10.1016/S0888-7543(03)00235-0. ISSN 0888-7543. PMID 14667819.
- Kim, M S; Lee Y T; Kim J M; Cha J Y; Bae Y S (February 1998). "Characterization of protein interaction among subunits of protein kinase CKII in vivo and in vitro". Mol. Cells (KOREA) 8 (1): 43â€“8. ISSN 1016-8478. PMID 9571630.
- Marin, O; Meggio F; Sarno S; Pinna L A (June 1997). "Physical dissection of the structural elements responsible for regulatory properties and intersubunit interactions of protein kinase CK2 beta-subunit". Biochemistry (UNITED STATES) 36 (23): 7192â€“8. doi:10.1021/bi962885q. ISSN 0006-2960. PMID 9188720.
- Bosc, D G; Graham K C; Saulnier R B; Zhang C; Prober D; Gietz R D; Litchfield D W (May 2000). "Identification and characterization of CKIP-1, a novel pleckstrin homology domain-containing protein that interacts with protein kinase CK2". J. Biol. Chem. (UNITED STATES) 275 (19): 14295â€“306. doi:10.1074/jbc.275.19.14295. ISSN 0021-9258. PMID 10799509.
- Ahn, B H; Kim T H; Bae Y S (October 2001). "Mapping of the interaction domain of the protein kinase CKII beta subunit with target proteins". Mol. Cells (Korea (South)) 12 (2): 158â€“63. ISSN 1016-8478. PMID 11710515.
- Kusk, M; Ahmed R; Thomsen B; Bendixen C; Issinger O G; Boldyreff B (January 1999). "Interactions of protein kinase CK2beta subunit within the holoenzyme and with other proteins". Mol. Cell. Biochem. (NETHERLANDS) 191 (1â€“2): 51â€“8. doi:10.1023/A:1006840613986. ISSN 0300-8177. PMID 10094392.
- Skjerpen, Camilla Skiple; Nilsen Trine; Wesche JÃ¸rgen; Olsnes Sjur (August 2002). "Binding of FGF-1 variants to protein kinase CK2 correlates with mitogenicity". EMBO J. (England) 21 (15): 4058â€“69. doi:10.1093/emboj/cdf402. ISSN 0261-4189. PMC 126148. PMID 12145206.
- Zhou, Ying; Li Lu; Liu Qiongming; Xing Guichun; Kuai Xuezhang; Sun Jing; Yin Xiushan; Wang Jian; Zhang Lingqiang; He Fuchu (May 2008). "E3 ubiquitin ligase SIAH1 mediates ubiquitination and degradation of TRB3". Cell. Signal. (England) 20 (5): 942â€“8. doi:10.1016/j.cellsig.2008.01.010. ISSN 0898-6568. PMID 18276110.
- Block, K; Boyer T G; Yew P R (November 2001). "Phosphorylation of the human ubiquitin-conjugating enzyme, CDC34, by casein kinase 2". J. Biol. Chem. (United States) 276 (44): 41049â€“58. doi:10.1074/jbc.M106453200. ISSN 0021-9258. PMID 11546811.
- Boldyreff, B; Issinger O G (February 1997). "A-Raf kinase is a new interacting partner of protein kinase CK2 beta subunit". FEBS Lett. (NETHERLANDS) 403 (2): 197â€“9. doi:10.1016/S0014-5793(97)00010-0. ISSN 0014-5793. PMID 9042965.
- Kim, J M; Cha J Y; Marshak D R; Bae Y S (September 1996). "Interaction of the beta subunit of casein kinase II with the ribosomal protein L5". Biochem. Biophys. Res. Commun. (UNITED STATES) 226 (1): 180â€“6. doi:10.1006/bbrc.1996.1330. ISSN 0006-291X. PMID 8806611.
- Grein, S; Pyerin W (January 1999). "BTF3 is a potential new substrate of protein kinase CK2". Mol. Cell. Biochem. (NETHERLANDS) 191 (1â€“2): 121â€“8. doi:10.1023/A:1006806226764. ISSN 0300-8177. PMID 10094400.
- O'Brien, K A; Lemke S J; Cocke K S; Rao R N; Beckmann R P (July 1999). "Casein kinase 2 binds to and phosphorylates BRCA1". Biochem. Biophys. Res. Commun. (UNITED STATES) 260 (3): 658â€“64. doi:10.1006/bbrc.1999.0892. ISSN 0006-291X. PMID 10403822.
- Panasyuk, Ganna; Nemazanyy Ivan; Zhyvoloup Alexander; Bretner Maria; Litchfield David W; Filonenko Valeriy; Gout Ivan T (October 2006). "Nuclear export of S6K1 II is regulated by protein kinase CK2 phosphorylation at Ser-17". J. Biol. Chem. (United States) 281 (42): 31188â€“201. doi:10.1074/jbc.M602618200. ISSN 0021-9258. PMID 16895915.
- Homma, Miwako Kato; Li Dongxia; Krebs Edwin G; Yuasa Yasuhito; Homma Yoshimi (April 2002). "Association and regulation of casein kinase 2 activity by adenomatous polyposis coli protein". Proc. Natl. Acad. Sci. U.S.A. (United States) 99 (9): 5959â€“64. doi:10.1073/pnas.092143199. ISSN 0027-8424. PMC 122884. PMID 11972058.
- Schubert U, Schneider T, Henklein P et al. (1992). "Human-immunodeficiency-virus-type-1-encoded Vpu protein is phosphorylated by casein kinase II". Eur. J. Biochem. 204 (2): 875â€“83. doi:10.1111/j.1432-1033.1992.tb16707.x. PMID 1541298.
- Teitz T, Eli D, Penner M et al. (1990). "Expression of the cDNA for the beta subunit of human casein kinase II confers partial UV resistance on xeroderma pigmentosum cells". Mutat. Res. 236 (1): 85â€“97. doi:10.1016/0921-8777(90)90036-5. PMID 1694965.
- Voss H, Wirkner U, Jakobi R et al. (1991). "Structure of the gene encoding human casein kinase II subunit beta". J. Biol. Chem. 266 (21): 13706â€“11. PMID 1856204.
- Litchfield DW, Lozeman FJ, Cicirelli MF et al. (1991). "Phosphorylation of the beta subunit of casein kinase II in human A431 cells. Identification of the autophosphorylation site and a site phosphorylated by p34cdc2". J. Biol. Chem. 266 (30): 20380â€“9. PMID 1939094.
- Ackerman P, Glover CV, Osheroff N (1990). "Stimulation of casein kinase II by epidermal growth factor: relationship between the physiological activity of the kinase and the phosphorylation state of its beta subunit". Proc. Natl. Acad. Sci. U.S.A. 87 (2): 821â€“5. doi:10.1073/pnas.87.2.821. PMC 53358. PMID 2300566.
- Heller-Harrison RA, Meisner H, Czech MP (1990). "Cloning and characterization of a cDNA encoding the beta subunit of human casein kinase II". Biochemistry 28 (23): 9053â€“8. doi:10.1021/bi00449a014. PMID 2513884.
- Jakobi R, Voss H, Pyerin W (1989). "Human phosvitin/casein kinase type II. Molecular cloning and sequencing of full-length cDNA encoding subunit beta". Eur. J. Biochem. 183 (1): 227â€“33. doi:10.1111/j.1432-1033.1989.tb14917.x. PMID 2666134.
- Vincent MJ, Abdul Jabbar M (1996). "The human immunodeficiency virus type 1 Vpu protein: a potential regulator of proteolysis and protein transport in the mammalian secretory pathway". Virology 213 (2): 639â€“49. doi:10.1006/viro.1995.0035. PMID 7491787.
- Litchfield DW, Bosc DG, Slominski E (1995). "The protein kinase from mitotic human cells that phosphorylates Ser-209 on the casein kinase II beta-subunit is p34cdc2". Biochim. Biophys. Acta 1269 (1): 69â€“78. doi:10.1016/0167-4889(95)00100-7. PMID 7578274.
- Jin YJ, Burakoff SJ (1993). "The 25-kDa FK506-binding protein is localized in the nucleus and associates with casein kinase II and nucleolin". Proc. Natl. Acad. Sci. U.S.A. 90 (16): 7769â€“73. doi:10.1073/pnas.90.16.7769. PMC 47224. PMID 7689229.
- Gietz RD, Graham KC, Litchfield DW (1995). "Interactions between the subunits of casein kinase II". J. Biol. Chem. 270 (22): 13017â€“21. doi:10.1074/jbc.270.22.13017. PMID 7768894.
- Szebeni A, Herrera JE, Olson MO (1995). "Interaction of nucleolar protein B23 with peptides related to nuclear localization signals". Biochemistry 34 (25): 8037â€“42. doi:10.1021/bi00025a009. PMID 7794916.
- Arnold SF, Obourn JD, Jaffe H, Notides AC (1995). "Serine 167 is the major estradiol-induced phosphorylation site on the human estrogen receptor". Mol. Endocrinol. 8 (9): 1208â€“14. doi:10.1210/me.8.9.1208. PMID 7838153.
- Pyerin W (1994). "Human casein kinase II: structures, genes, expression and requirement in cell growth stimulation". Adv. Enzyme Regul. 34: 225â€“46. doi:10.1016/0065-2571(94)90018-3. PMID 7942276.
- el Benna J, Faust LP, Babior BM (1994). "The phosphorylation of the respiratory burst oxidase component p47phox during neutrophil activation. Phosphorylation of sites recognized by protein kinase C and by proline-directed kinases". J. Biol. Chem. 269 (38): 23431â€“6. PMID 8089108.
- Schubert U, Henklein P, Boldyreff B et al. (1994). "The human immunodeficiency virus type 1 encoded Vpu protein is phosphorylated by casein kinase-2 (CK-2) at positions Ser52 and Ser56 within a predicted alpha-helix-turn-alpha-helix-motif". J. Mol. Biol. 236 (1): 16â€“25. doi:10.1006/jmbi.1994.1114. PMID 8107101.
- Schubert U, Strebel K (1994). "Differential activities of the human immunodeficiency virus type 1-encoded Vpu protein are regulated by phosphorylation and occur in different cellular compartments". J. Virol. 68 (4): 2260â€“71. PMC 236702. PMID 8139011.
- Tanasijevic MJ, Myers MG, Thoma RS et al. (1993). "Phosphorylation of the insulin receptor substrate IRS-1 by casein kinase II". J. Biol. Chem. 268 (24): 18157â€“66. PMID 8349691.
- Friborg J, Ladha A, GÃ¶ttlinger H et al. (1996). "Functional analysis of the phosphorylation sites on the human immunodeficiency virus type 1 Vpu protein". J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 8 (1): 10â€“22. doi:10.1097/00042560-199501000-00004. PMID 8548340.
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.
Casein kinase II regulatory subunit Provide feedback
No Pfam abstract.
Internal database links
|SCOOP:||RRN3 DpnI Spt5_N CCDC24|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000704
Casein kinase, a ubiquitous well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [PUBMED:2666134, PUBMED:1856204]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') [PUBMED:7737972].
The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif [PUBMED:7737972]. The beta subunit contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc [PUBMED:8027080]. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [PUBMED:7737972].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||protein kinase CK2 complex (GO:0005956)|
|Molecular function||protein kinase regulator activity (GO:0019887)|
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...
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.
|Author:||Finn RD, Bateman A|
|Number in seed:||196|
|Number in full:||1493|
|Average length of the domain:||181.80 aa|
|Average identity of full alignment:||48 %|
|Average coverage of the sequence by the domain:||69.04 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|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 3 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 CK_II_beta domain has been found. There are 40 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...