Summary: Protein kinase domain
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Protein kinase domain Edit Wikipedia article
|Protein kinase domain|
|SCOP2||1apm / SCOPe / SUPFAM|
The protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. Protein kinases are a group of enzymes that move a phosphate group onto proteins, in a process called phosphorylation. This functions as an on/off switch for many cellular processes, including metabolism, transcription, cell cycle progression, cytoskeletal rearrangement and cell movement, apoptosis, and differentiation. They also function in embryonic development, physiological responses, and in the nervous and immune system. Abnormal phosphorylation causes many human diseases, including cancer, and drugs that affect phosphorylation can treat those diseases.
Protein kinases possess a catalytic subunit which transfers the gamma phosphate from nucleoside triphosphates (almost always ATP) to the side chain of an amino acid in a protein, resulting in a conformational and/or dynamic changes affecting protein function. These enzymes fall into two broad classes, characterised with respect to substrate specificity: serine/threonine specific and tyrosine specific.
Protein kinase function has been evolutionarily conserved from Escherichia coli to Homo sapiens. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation. Phosphorylation usually results in a functional change of the target protein by changing structure, dynamics, enzyme activity, cellular location, or association with other proteins.
The catalytic subunits of protein kinases are highly conserved, and the structures of over 270 of the approximately 500 human kinase domains have been determined, leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases.
Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The domain consists of two sub-domains referred to as the N- and C-terminal domains. The N-terminal domain consists of five beta sheet strands and an alpha helix called the C-helix, and the C-terminal domain usually consists of six alpha helices (labeled D, E, F, G, H, and I). The C-terminal domain contains two long loops, called the catalytic loop and the activation loop, which are essential for catalytic activity. The catalytic loop includes the "HRD motif" (for the amino acid sequence His-Arg-Asp), whose aspartic acid residue interacts directly with the hydroxyl group of the target serine, threonine, or tyrosine residue that is phosphorylated.
The activation loop starts with the DFG motif (for the amino acid sequence Asp-Phe-Gly), which helps to bind ATP and magnesium in the active site. Broadly, the state or conformation of the kinase may be classified as DFGin or DFGout, depending on whether the Asp residue of the DFG motif is in or out of the active site. In the active form, the first few residues of the activation loop adopt a specific form of the DFGin conformation. Some inactive structures may adopt one of several other DFGin conformations, while other inactive structures are DFGout.
The following is a list of human proteins containing the protein kinase domain:
AAK1Â ; AATKÂ ; ABL1Â ; ABL2Â ; ACVR1Â ; ACVR1BÂ ; ACVR1CÂ ; ACVR2AÂ ; ACVR2BÂ ; ACVRL1Â ; AKT1Â ; AKT2Â ; AKT3Â ; ALKÂ ; AMHR2Â ; ANKK1Â ; ARAFÂ ; AURKAÂ ; AURKBÂ ; AURKCÂ ; AXLÂ ; BLKÂ ; BMP2KÂ ; BMPR1AÂ ; BMPR1BÂ ; BMPR2Â ; BMXÂ ; BRAFÂ ; BRSK1Â ; BRSK2Â ; BTKÂ ; BUB1Â ; BUB1BÂ ; CAMK1Â ; CAMK1DÂ ; CAMK1GÂ ; CAMK2AÂ ; CAMK2BÂ ; CAMK2DÂ ; CAMK2GÂ ; CAMK4Â ; CAMKK1Â ; CAMKK2Â ; CAMKVÂ ; CASKÂ ; CDC42BPAÂ ; CDC42BPBÂ ; CDC42BPGÂ ; CDC7Â ; CDK1Â ; CDK10Â ; CDK11AÂ ; CDK11BÂ ; CDK12Â ; CDK13Â ; CDK14Â ; CDK15Â ; CDK16Â ; CDK17Â ; CDK18Â ; CDK19Â ; CDK2Â ; CDK20Â ; CDK3Â ; CDK4Â ; CDK5Â ; CDK6Â ; CDK7Â ; CDK8Â ; CDK9Â ; CDKL1Â ; CDKL2Â ; CDKL3Â ; CDKL4Â ; CDKL5Â ; CHEK1Â ; CHEK2Â ; CHUKÂ ; CITÂ ; CLK1Â ; CLK2Â ; CLK3Â ; CLK4Â ; CSF1RÂ ; CSKÂ ; CSNK1A1Â ; CSNK1A1LÂ ; CSNK1DÂ ; CSNK1EÂ ; CSNK1G1Â ; CSNK1G2Â ; CSNK1G3Â ; CSNK2A1Â ; CSNK2A2Â ; CSNK2A3Â ; DAPK1Â ; DAPK2Â ; DAPK3Â ; DCLK1Â ; DCLK2Â ; DCLK3Â ; DDR1Â ; DDR2Â ; DMPKÂ ; DSTYKÂ ; DYRK1AÂ ; DYRK1BÂ ; DYRK2Â ; DYRK3Â ; DYRK4Â ; EGFRÂ ; EIF2AK1Â ; EIF2AK2Â ; EIF2AK3Â ; EIF2AK4Â ; EPHA1Â ; EPHA10Â ; EPHA2Â ; EPHA3Â ; EPHA4Â ; EPHA5Â ; EPHA6Â ; EPHA7Â ; EPHA8Â ; EPHB1Â ; EPHB2Â ; EPHB3Â ; EPHB4Â ; EPHB6Â ; ERBB2Â ; ERBB3Â ; ERBB4Â ; ERN1Â ; ERN2Â ; FERÂ ; FESÂ ; FGFR1Â ; FGFR2Â ; FGFR3Â ; FGFR4Â ; FGRÂ ; FLT1Â ; FLT3Â ; FLT4Â ; FRKÂ ; FYNÂ ; GAKÂ ; GRK1Â ; GRK2Â ; GRK3Â ; GRK4Â ; GRK5Â ; GRK6Â ; GRK7Â ; GSG2Â ; GSK3AÂ ; GSK3BÂ ; GUCY2CÂ ; GUCY2DÂ ; GUCY2FÂ ; HCKÂ ; HIPK1Â ; HIPK2Â ; HIPK3Â ; HIPK4Â ; HUNKÂ ; ICKÂ ; IGF1RÂ ; IKBKBÂ ; IKBKEÂ ; ILKÂ ; INSRÂ ; INSRRÂ ; IRAK1Â ; IRAK2Â ; IRAK3Â ; IRAK4Â ; ITKÂ ; JAK1Â ; JAK2Â ; JAK3Â ; KALRNÂ ; KDRÂ ; KITÂ ; KSR1Â ; KSR2Â ; LATS1Â ; LATS2Â ; LCKÂ ; LIMK1Â ; LIMK2Â ; LMTK2Â ; LMTK3Â ; LRRK1Â ; LRRK2Â ; LTKÂ ; LYNÂ ; MAKÂ ; MAP2K1Â ; MAP2K2Â ; MAP2K3Â ; MAP2K4Â ; MAP2K5Â ; MAP2K6Â ; MAP2K7Â ; MAP3K1Â ; MAP3K10Â ; MAP3K11Â ; MAP3K12Â ; MAP3K13Â ; MAP3K14Â ; MAP3K15Â ; MAP3K19Â ; MAP3K2Â ; MAP3K20Â ; MAP3K21Â ; MAP3K3Â ; MAP3K4Â ; MAP3K5Â ; MAP3K6Â ; MAP3K7Â ; MAP3K8Â ; MAP3K9Â ; MAP4K1Â ; MAP4K2Â ; MAP4K3Â ; MAP4K4Â ; MAP4K5Â ; MAPK1Â ; MAPK10Â ; MAPK11Â ; MAPK12Â ; MAPK13Â ; MAPK14Â ; MAPK15Â ; MAPK3Â ; MAPK4Â ; MAPK6Â ; MAPK7Â ; MAPK8Â ; MAPK9Â ; MAPKAPK2Â ; MAPKAPK3Â ; MAPKAPK5Â ; MARK1Â ; MARK2Â ; MARK3Â ; MARK4Â ; MAST1Â ; MAST2Â ; MAST3Â ; MAST4Â ; MASTLÂ ; MATKÂ ; MELKÂ ; MERTKÂ ; METÂ ; MINK1Â ; MKNK1Â ; MKNK2Â ; MLKLÂ ; MOKÂ ; MOSÂ ; MST1RÂ ; MUSKÂ ; MYLKÂ ; MYLK2Â ; MYLK3Â ; MYLK4Â ; MYO3AÂ ; MYO3BÂ ; NEK1Â ; NEK10Â ; NEK11Â ; NEK2Â ; NEK3Â ; NEK4Â ; NEK5Â ; NEK6Â ; NEK7Â ; NEK8Â ; NEK9Â ; NIM1KÂ ; NLKÂ ; NPR1Â ; NPR2Â ; NRBP1Â ; NRBP2Â ; NRKÂ ; NTRK1Â ; NTRK2Â ; NTRK3Â ; NUAK1Â ; NUAK2Â ; OBSCNÂ ; OXSR1Â ; PAK1Â ; PAK2Â ; PAK3Â ; PAK4Â ; PAK5Â ; PAK6Â ; PAN3Â ; PASKÂ ; PBKÂ ; PDGFRAÂ ; PDGFRBÂ ; PDIK1LÂ ; PDPK1Â ; PDPK2PÂ ; PEAK1Â ; PEAK3Â ; PHKG1Â ; PHKG2Â ; PIK3R4Â ; PIM1Â ; PIM2Â ; PIM3Â ; PINK1Â ; PKDCCÂ ; PKMYT1Â ; PKN1Â ; PKN2Â ; PKN3Â ; PLK1Â ; PLK2Â ; PLK3Â ; PLK4Â ; PLK5Â ; PNCKÂ ; POMKÂ ; PRKAA1Â ; PRKAA2Â ; PRKACAÂ ; PRKACBÂ ; PRKACGÂ ; PRKCAÂ ; PRKCBÂ ; PRKCDÂ ; PRKCEÂ ; PRKCGÂ ; PRKCHÂ ; PRKCIÂ ; PRKCQÂ ; PRKCZÂ ; PRKD1Â ; PRKD2Â ; PRKD3Â ; PRKG1Â ; PRKG2Â ; PRKXÂ ; PRKYÂ ; PRPF4BÂ ; PSKH1Â ; PSKH2Â ; PTK2Â ; PTK2BÂ ; PTK6Â ; PTK7Â ; PXKÂ ; RAF1Â ; RETÂ ; RIOK1Â ; RIOK2Â ; RIOK3Â ; RIPK1Â ; RIPK2Â ; RIPK3Â ; RIPK4Â ; RNASELÂ ; ROCK1Â ; ROCK2Â ; ROR1Â ; ROR2Â ; ROS1Â ; RPS6KA1Â ; RPS6KA2Â ; RPS6KA3Â ; RPS6KA4Â ; RPS6KA5Â ; RPS6KA6Â ; RPS6KB1Â ; RPS6KB2Â ; RPS6KC1Â ; RPS6KL1Â ; RSKRÂ ; RYKÂ ; SBK1Â ; SBK2Â ; SBK3Â ; SCYL1Â ; SCYL2Â ; SCYL3Â ; SGK1Â ; SGK2Â ; SGK223Â ; SGK3Â ; SIK1Â ; SIK1BÂ ; SIK2Â ; SIK3Â ; SLKÂ ; SNRKÂ ; SPEGÂ ; SRCÂ ; SRMSÂ ; SRPK1Â ; SRPK2Â ; SRPK3Â ; STK10Â ; STK11Â ; STK16Â ; STK17AÂ ; STK17BÂ ; STK24Â ; STK25Â ; STK26Â ; STK3Â ; STK31Â ; STK32AÂ ; STK32BÂ ; STK32CÂ ; STK33Â ; STK35Â ; STK36Â ; STK38Â ; STK38LÂ ; STK39Â ; STK4Â ; STK40Â ; STKLD1Â ; STRADAÂ ; STRADBÂ ; STYK1Â ; SYKÂ ; TAOK1Â ; TAOK2Â ; TAOK3Â ; TBCKÂ ; TBK1Â ; TECÂ ; TEKÂ ; TESK1Â ; TESK2Â ; TEX14Â ; TGFBR1Â ; TGFBR2Â ; TIE1Â ; TLK1Â ; TLK2Â ; TNIKÂ ; TNK1Â ; TNK2Â ; TNNI3KÂ ; TP53RKÂ ; TRIB1Â ; TRIB2Â ; TRIB3Â ; TRIOÂ ; TSSK1BÂ ; TSSK2Â ; TSSK3Â ; TSSK4Â ; TSSK6Â ; TTBK1Â ; TTBK2Â ; TTKÂ ; TTNÂ ; TXKÂ ; TYK2Â ; TYRO3Â ; UHMK1Â ; ULK1Â ; ULK2Â ; ULK3Â ; ULK4Â ; VRK1Â ; VRK2Â ; VRK3Â ; WEE1Â ; WEE2Â ; WNK1Â ; WNK2Â ; WNK3Â ; WNK4Â ; YES1Â ; ZAP70
- Knighton DR, Bell SM, Zheng J, etÂ al. (May 1993). "2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent". Acta Crystallogr. D. 49 (Pt 3): 357â€“61. doi:10.1107/S0907444993000502. PMIDÂ 15299526.
- Hanks SK, Quinn AM (1991). "Protein kinase catalytic domain sequence database: Identification of conserved features of primary structure and classification of family members". Meth. Enzymol. Methods in Enzymology. 200: 38â€“62. doi:10.1016/0076-6879(91)00126-H. ISBNÂ 978-0-12-182101-2. PMIDÂ 1956325.
- Hanks SK, Hunter T (May 1995). "Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification". FASEB J. 9 (8): 576â€“96. doi:10.1096/fasebj.9.8.7768349. PMIDÂ 7768349. S2CIDÂ 21377422.
- Scheeff ED, Bourne PE (October 2005). "Structural evolution of the protein kinase-like superfamily". PLOS Comput. Biol. 1 (5): e49. Bibcode:2005PLSCB...1...49S. doi:10.1371/journal.pcbi.0010049. PMCÂ 1261164. PMIDÂ 16244704.
- Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (December 2002). "The Protein Kinase Complement of the Human Genome". Science. 298 (5600): 1912â€“1934. Bibcode:2002Sci...298.1912M. doi:10.1126/science.1075762. PMIDÂ 12471243. S2CIDÂ 26554314.
- Hunter T, Hanks SK, Quinn AM (1988). "The protein kinase family: conserved features and deduced phylogeny of the catalytic domains". Science. 241 (4861): 42â€“51. Bibcode:1988Sci...241...42H. doi:10.1126/science.3291115. PMIDÂ 3291115.
- Manning G, Plowman GD, Hunter T, Sudarsanam S (October 2002). "Evolution of protein kinase signaling from yeast to man". Trends Biochem. Sci. 27 (10): 514â€“20. doi:10.1016/S0968-0004(02)02179-5. PMIDÂ 12368087.
- Modi, V; Dunbrack, RL (24 December 2019). "A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains". Scientific Reports. 9 (1): 19790. Bibcode:2019NatSR...919790M. doi:10.1038/s41598-019-56499-4. PMCÂ 6930252. PMIDÂ 31875044.
- Li B, Liu Y, Uno T, Gray N (August 2004). "Creating chemical diversity to target protein kinases". Comb. Chem. High Throughput Screen. 7 (5): 453â€“72. doi:10.2174/1386207043328580. PMIDÂ 15320712. Archived from the original on 14 April 2013.
- Hanks SK (2003). "Genomic analysis of the eukaryotic protein kinase superfamily: a perspective". Genome Biol. 4 (5): 111. doi:10.1186/gb-2003-4-5-111. PMCÂ 156577. PMIDÂ 12734000.
- Hunter T (1991). "Protein kinase classification". Meth. Enzymol. Methods in Enzymology. 200: 3â€“37. doi:10.1016/0076-6879(91)00125-G. ISBNÂ 978-0-12-182101-2. PMIDÂ 1835513.
- Knighton DR, Zheng JH, Ten Eyck LF, Ashford VA, Xuong NH, Taylor SS, Sowadski JM (July 1991). "Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase". Science. 253 (5018): 407â€“14. Bibcode:1991Sci...253..407K. doi:10.1126/science.1862342. PMIDÂ 1862342.
- Modi, V; Dunbrack, RL (2 April 2019). "Defining a new nomenclature for the structures of active and inactive kinases". Proceedings of the National Academy of Sciences of the United States of America. 116 (14): 6818â€“6827. doi:10.1073/pnas.1814279116. PMCÂ 6452665. PMIDÂ 30867294.
- "Human and mouse protein kinases: classification and index". pkinfam.txt. UniProt Consortium. Retrieved 10 June 2019.
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.
Protein kinase domain Provide feedback
No Pfam abstract.
Hanks SK, Quinn AM; , Methods Enzymol 1991;200:38-62.: Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members. PUBMED:1956325 EPMC:1956325
Internal database links
External database links
|PROSITE:||PDOC00100 PDOC00212 PDOC00213 PDOC00629|
|SMART:||STYKc S_TKc TyrKc|
This tab holds annotation information from the InterPro database.
InterPro entry IPR000719
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity [ PUBMED:3291115 ]:
- Serine/threonine-protein kinases
- Tyrosine-protein kinases
- Dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins)
Protein kinase function is evolutionarily conserved from Escherichia coli to human [ PUBMED:12471243 ]. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation [ PUBMED:12368087 ]. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [ PUBMED:15078142 ], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases [ PUBMED:15320712 ].
Eukaryotic protein kinases [ PUBMED:3291115 , PUBMED:12734000 , PUBMED:7768349 , PUBMED:1835513 , PUBMED:1956325 ] are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. There are a number of conserved regions in the catalytic domain of protein kinases. In the N-terminal extremity of the catalytic domain there is a glycine-rich stretch of residues in the vicinity of a lysine residue, which has been shown to be involved in ATP binding. In the central part of the catalytic domain there is a conserved aspartic acid residue which is important for the catalytic activity of the enzyme [ PUBMED:1862342 ].
This entry represents the protein kinase domain containing the catalytic function of protein kinases [ PUBMED:1956325 ]. This domain is found in serine/threonine-protein kinases, tyrosine-protein kinases and dual specificity protein kinases.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|protein kinase activity (GO:0004672)|
|Biological process||protein phosphorylation (GO:0006468)|
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 superfamily includes the Serine/Threonine- and Tyrosine- protein kinases as well as related kinases that act on non-protein substrates.
The clan contains the following 40 members:ABC1 AceK_kinase Act-Frag_cataly Alpha_kinase APH APH_6_hur Choline_kinase CotH DUF1679 DUF2252 DUF4135 DUF5898 EcKL Fam20C Fructosamin_kin FTA2 Haspin_kinase HipA_C Ins_P5_2-kin IPK IucA_IucC Kdo Kinase-like Kinase-PolyVal KIND Pan3_PK PI3_PI4_kinase PIP49_C PIP5K PK_Tyr_Ser-Thr Pkinase Pkinase_fungal Pox_ser-thr_kin RIO1 Seadorna_VP7 TCAD9 UL97 WaaY YrbL-PhoP_reg YukC
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 and the UniProtKB 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 UniProtKB 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.
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.
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:||38|
|Number in full:||636438|
|Average length of the domain:||241.40 aa|
|Average identity of full alignment:||21 %|
|Average coverage of the sequence by the domain:||36.71 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||28|
|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.
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 Pkinase domain has been found. There are 6176 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 sequence.
Loading structure mapping...
AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.