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 "Catalase". 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 email@example.com 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.
Catalase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
PDB rendering based on 1dgb.
|Symbols||; MGC138422; MGC138424|
|RNA expression pattern|
Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as vegetables, fruit or animals). It catalyzes the decomposition of hydrogen peroxide to water and oxygen. It is a very important enzyme in protecting the cell from oxidative damage by reactive oxygen species (ROS). Likewise, catalase has one of the highest turnover numbers of all enzymes; one catalase molecule can convert approximately 5 million molecules of hydrogen peroxide to water and oxygen each second.
Catalase is a tetramer of four polypeptide chains, each over 500 amino acids long. It contains four porphyrin heme (iron) groups that allow the enzyme to react with the hydrogen peroxide. The optimum pH for human catalase is approximately 7, and has a fairly broad maximum (the rate of reaction does not change appreciably at pHs between 6.8 and 7.5). The pH optimum for other catalases varies between 4 and 11 depending on the species. The optimum temperature also varies by species.
Catalase was not noticed until 1818 when Louis Jacques ThÃ©nard, who discovered H2O2 (hydrogen peroxide), suggested its breakdown is caused by an unknown substance. In 1900, Oscar Loew was the first to give it the name catalase, and found it in many plants and animals. In 1937 catalase from beef liver was crystallised by James B. Sumner and Alexander Dounce and the molecular weight was found in 1938.
The reaction of catalase in the decomposition of hydrogen peroxide in living tissue:
- 2 H2O2 â†’ 2 H2O + O2
The presence of catalase in a microbial or tissue sample can be tested by adding a volume of hydrogen peroxide and observing the reaction. The formation of bubbles, oxygen, indicates a positive result. This easy assay, which can be seen with the naked eye, without the aid of instruments, is possible because catalase has a very high specific activity, which produces a detectable response. Alternative splicing may result in different protein variants.
- H2O2 + Fe(III)-E â†’ H2O + O=Fe(IV)-E(.+)
- H2O2 + O=Fe(IV)-E(.+) â†’ H2O + Fe(III)-E + O2
- Here Fe()-E represents the iron center of the heme group attached to the enzyme. Fe(IV)-E(.+) is a mesomeric form of Fe(V)-E, meaning the iron is not completely oxidized to +V, but receives some "supporting electrons" from the heme ligand. This heme has to be drawn then as a radical cation (.+).
As hydrogen peroxide enters the active site, it interacts with the amino acids Asn147 (asparagine at position 147) and His74, causing a proton (hydrogen ion) to transfer between the oxygen atoms. The free oxygen atom coordinates, freeing the newly formed water molecule and Fe(IV)=O. Fe(IV)=O reacts with a second hydrogen peroxide molecule to reform Fe(III)-E and produce water and oxygen. The reactivity of the iron center may be improved by the presence of the phenolate ligand of Tyr357 in the fifth iron ligand, which can assist in the oxidation of the Fe(III) to Fe(IV). The efficiency of the reaction may also be improved by the interactions of His74 and Asn147 with reaction intermediates. In general, the rate of the reaction can be determined by the Michaelis-Menten equation.
Catalase can also catalyze the oxidation, by hydrogen peroxide, of various metabolites and toxins, including formaldehyde, formic acid, phenols, acetaldehyde and alcohols. It does so according to the following reaction:
- H2O2 + H2R â†’ 2H2O + R
The exact mechanism of this reaction is not known.
Any heavy metal ion (such as copper cations in copper(II) sulfate) can act as a noncompetitive inhibitor of catalase. Furthermore, the poison cyanide is a competitive inhibitor of catalase at high concentrations of hydrogen peroxide. Arsenate acts as an activator. Three-dimensional protein structures of the peroxidated catalase intermediates are available at the Protein Data Bank. This enzyme is commonly used in laboratories as a tool for learning the effect of enzymes upon reaction rates.
Hydrogen peroxide is a harmful byproduct of many normal metabolic processes; to prevent damage to cells and tissues, it must be quickly converted into other, less dangerous substances. To this end, catalase is frequently used by cells to rapidly catalyze the decomposition of hydrogen peroxide into less-reactive gaseous oxygen and water molecules.
The true biological significance of catalase is not always straightforward to assess: Mice genetically engineered to lack catalase are phenotypically normal, indicating this enzyme is dispensable in animals under some conditions. A catalase deficiency may increase the likelihood of developing type 2 diabetes. Some humans have very low levels of catalase (acatalasia), yet show few ill effects. The predominant scavengers of H2O2 in normal mammalian cells are likely peroxiredoxins rather than catalase.
Catalase is usually located in a cellular, bipolar environment organelle called the peroxisome. Peroxisomes in plant cells are involved in photorespiration (the use of oxygen and production of carbon dioxide) and symbiotic nitrogen fixation (the breaking apart of diatomic nitrogen (N2) to reactive nitrogen atoms). Hydrogen peroxide is used as a potent antimicrobial agent when cells are infected with a pathogen. Catalase-positive pathogens, such as Mycobacterium tuberculosis, Legionella pneumophila, and Campylobacter jejuni, make catalase to deactivate the peroxide radicals, thus allowing them to survive unharmed within the host.
Catalase contributes to ethanol metabolism in the body after ingestion of alcohol, but it only breaks down a small fraction of the alcohol in the body.
Distribution among organisms
The large majority of known organisms use catalase in every organ, with particularly high concentrations occurring in the liver . One unique use of catalase occurs in the bombardier beetle. This beetle has two sets of chemicals ordinarily stored separately in its paired glands. The larger of the pair, the storage chamber or reservoir, contains hydroquinones and hydrogen peroxide, whereas the smaller of the pair, the reaction chamber, contains catalases and peroxidases. To activate the noxious spray, the beetle mixes the contents of the two compartments, causing oxygen to be liberated from hydrogen peroxide. The oxygen oxidizes the hydroquinones and also acts as the propellant. The oxidation reaction is very exothermic (Î”H = âˆ’202.8 kJ/mol) which rapidly heats the mixture to the boiling point.
According to a March 2015 Scientific American Special Report on Aging article, laboratory mice at a University of Washington laboratory who produced more catalase, which is an antioxidant, lived longer. Research on the topic both supports and cautions against the benefit of antioxidants for health effects on aging.
Catalase is used in the food industry for removing hydrogen peroxide from milk prior to cheese production. Another use is in food wrappers where it prevents food from oxidizing. Catalase is also used in the textile industry, removing hydrogen peroxide from fabrics to make sure the material is peroxide-free.
A minor use is in contact lens hygiene - a few lens-cleaning products disinfect the lens using a hydrogen peroxide solution; a solution containing catalase is then used to decompose the hydrogen peroxide before the lens is used again. Recently, catalase has also begun to be used in the aesthetics industry. Several mask treatments combine the enzyme with hydrogen peroxide on the face with the intent of increasing cellular oxygenation in the upper layers of the epidermis.
The catalase test is also one of the main three tests used by microbiologists to identify species of bacteria. The presence of catalase enzyme in the test isolate is detected using hydrogen peroxide. If the bacteria possess catalase (i.e., are catalase-positive), when a small amount of bacterial isolate is added to hydrogen peroxide, bubbles of oxygen are observed.
The catalase test is done by placing a drop of hydrogen peroxide on a microscope slide. Using an applicator stick, a scientist touches the colony, and then smears a sample into the hydrogen peroxide drop.
- If the mixture produces bubbles or froth, the organism is said to be 'catalase-positive'. Staphylococci and Micrococci are catalase-positive. Other catalase-positive organisms include Listeria, Corynebacterium diphtheriae, Burkholderia cepacia, Nocardia, the family Enterobacteriaceae (Citrobacter, E. coli, Enterobacter, Klebsiella, Shigella, Yersinia, Proteus, Salmonella, Serratia), Pseudomonas, Mycobacterium tuberculosis, Aspergillus, Cryptococcus, and Rhodococcus equi.
- If not, the organism is 'catalase-negative'. Streptococcus and Enterococcus spp. are catalase-negative.
While the catalase test alone cannot identify a particular organism, combined with other tests, such as antibiotic resistance, it can aid identification. The presence of catalase in bacterial cells depends on both the growth condition and the medium used to grow the cells.
Capillary tubes may also be used. A small amount of bacteria is collected on the end of the capillary tube (it is essential to ensure that the end is not blocked, otherwise it may present a false negative). The opposite end is then dipped into hydrogen peroxide which will draw up the liquid (through capillary action), and turned upside down, so the bacterial end is closest to the bench. A few taps of the arm should then move the hydrogen peroxide closer to the bacteria. When the hydrogen peroxide and bacteria are touching, bubbles may begin to rise, giving a positive catalase result.
According to recent scientific studies, low levels of catalase may play a role in the graying process of human hair. Hydrogen peroxide is naturally produced by the body and catalase breaks it down. If catalase levels decline, hydrogen peroxide cannot be broken down as well. This allows the hydrogen peroxide to bleach the hair from the inside out. This finding is under investigation in hopes of developing cosmetic treatments for graying hair based on catalase supplements.
- Chelikani P, Fita I, Loewen PC (January 2004). "Diversity of structures and properties among catalases". Cell. Mol. Life Sci. 61 (2): 192â€“208. doi:10.1007/s00018-003-3206-5. PMID 14745498.
- Biology in focus : HSC course / Glenda Chidrawi, Margaret Robson with Stephanie Hollis, 2008
- Goodsell DS (2004-09-01). "Catalase". Molecule of the Month. RCSB Protein Data Bank. Retrieved 2007-02-11.
- Boon EM, Downs A, Marcey D. "Catalase: H2O2: H2O2 Oxidoreductase". Catalase Structural Tutorial Text. Retrieved 2007-02-11.
- Maehly AC, Chance B (1954). "The assay of catalases and peroxidases". Methods Biochem Anal. Methods of Biochemical Analysis 1: 357â€“424. doi:10.1002/9780470110171.ch14. ISBN 978-0-470-11017-1. PMID 13193536.
- Aebi H (1984). Aebi H, ed. "Catalase in vitro". Meth. Enzymol. Methods in Enzymology 105: 121â€“126. doi:10.1016/S0076-6879(84)05016-3. ISBN 0-12-182005-X. PMID 6727660.
- "EC 22.214.171.124 - catalase". BRENDA: The Comprehensive Enzyme Information System. Department of Bioinformatics and Biochemistry, Technische UniversitÃ¤t Braunschweig. Retrieved 2009-05-26.
- Toner K, Sojka G, Ellis R. "A Quantitative Enzyme Study; CATALASE". bucknell.edu. Archived from the original on 2000-06-12. Retrieved 2007-02-11.
- Loew O (May 1900). "A New Enzyme of General Occurrence in Organisms". Science 11 (279): 701â€“702. doi:10.1126/science.11.279.701. PMID 17751716.
- Sumner JB, Dounce AL (April 1937). "Crystalline catalase". Science 85 (2206): 366â€“367. doi:10.1126/science.85.2206.366. PMID 17776781.
- Sumner JB, GralÃ©n N (March 1938). "The molecular weight of crystalline catalase". Science 87 (2256): 284â€“284. doi:10.1126/science.87.2256.284. PMID 17831682.
- Schroeder WA, Shelton JR, Shelton JB, Robberson B, Apell G (May 1969). "The amino acid sequence of bovine liver catalase: a preliminary report". Arch. Biochem. Biophys. 131 (2): 653â€“655. doi:10.1016/0003-9861(69)90441-X. PMID 4892021.
- Murthy MR, Reid TJ, Sicignano A, Tanaka N, Rossmann MG (October 1981). "Structure of beef liver catalase". J. Mol. Biol. 152 (2): 465â€“499. doi:10.1016/0022-2836(81)90254-0. PMID 7328661.
- Boon EM, Downs A, Marcey D. "Proposed Mechanism of Catalase". Catalase: H2O2: H2O2 Oxidoreductase: Catalase Structural Tutorial. Retrieved 2007-02-11.
- Maass E (1998-07-19). "How does the concentration of hydrogen peroxide affect the reaction". MadSci Network. Retrieved 009-03-02. Check date values in:
- Ogura, Y.; Yamazaki, I. (Aug 1983). "Steady-state kinetics of the catalase reaction in the presence of cyanide.". J Biochem 94 (2): 403â€“8. PMID 6630165.
- Kertulis-Tartar GM, Rathinasabapathi B, Ma LQ (2009). "Characterization of glutathione reductase and catalase in the fronds of two Pteris ferns upon arsenic exposure". Plant Physiology and Biochemistry 47 (10): 960â€“5. doi:10.1016/j.plaphy.2009.05.009. PMID 19574057.
- Gaetani GF, Ferraris AM, Rolfo M, Mangerini R, Arena S, Kirkman HN (1996). "Predominant role of catalase in the disposal of hydrogen peroxide within human erythrocytes". Blood 87 (4): 1595â€“9. PMID 8608252.
- Ho YS, Xiong Y, Ma W, Spector A, Ho DS (2004). "Mice Lacking Catalase Develop Normally but Show Differential Sensitivity to Oxidant Tissue Injury". J Biol Chem 279 (31): 32804â€“32812. doi:10.1074/jbc.M404800200. PMID 15178682.
- GÃ³th L, Bigler WN (2001). "Blood Catalase Deficiency and Diabetes in Hungary". Diabetes Care 24 (10): 1839â€“1840. doi:10.2337/diacare.24.10.1839. PMID 11574451.
- GÃ³th L (2008). "Catalase Deficiency and Type 2 Diabetes". Diabetes Care 24 (10): e93â€“e93. doi:10.2337/dc08-1607. PMID 19033415.
- Amo T, Atomi H, Imanaka T (June 2002). "Unique presence of a manganese catalase in a hyperthermophilic archaeon, Pyrobaculum calidifontis VA1". J. Bacteriol. 184 (12): 3305â€“3312. doi:10.1128/JB.184.12.3305-3312.2002. PMC 135111. PMID 12029047.
- Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Peroxisomes". Molecular Biology of the Cell (4th ed.). New York: Garland Science. ISBN 0-8153-3218-1.
- Srinivasa Rao PS, Yamada Y, Leung KY (September 2003). "A major catalase (KatB) that is required for resistance to H2O2 and phagocyte-mediated killing in Edwardsiella tarda". Microbiology (Reading, Engl.) 149 (Pt 9): 2635â€“2644. doi:10.1099/mic.0.26478-0. PMID 12949187.
- Eisner T, Aneshansley DJ (August 1999). "Spray aiming in the bombardier beetle: photographic evidence". Proc. Natl. Acad. Sci. U.S.A. 96 (17): 9705â€“9709. doi:10.1073/pnas.96.17.9705. PMC 22274. PMID 10449758.
- Beheshti N, McIntosh AC (2006). "A biomimetic study of the explosive discharge of the bombardier beetle" (PDF). Int. Journal of Design & Nature 1 (1): 1â€“9.
- Isobe K, Inoue N, Takamatsu Y, Kamada K, Wakao N (January 2006). "Production of catalase by fungi growing at low pH and high temperature". J. Biosci. Bioeng. 101 (1): 73â€“76. doi:10.1263/jbb.101.73. PMID 16503295.
- Brioukhanov AL, Netrusov AI, Eggen RI (June 2006). "The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri". Microbiology (Reading, Engl.) 152 (Pt 6): 1671â€“1677. doi:10.1099/mic.0.28542-0. PMID 16735730.
- "Catalase". Worthington Enzyme Manual. Worthington Biochemical Corporation. Retrieved 2009-03-01.
- Hengge A (1999-03-16). "Re: how is catalase used in industry?". General Biology. MadSci Network. Retrieved 2009-03-01.
- "textile industry". Case study 228. International Cleaner Production Information Clearinghouse. Retrieved 2009-03-01.
- US patent 5521091, Cook JN, Worsley JL, "Compositions and method for destroying hydrogen peroxide on contact lens", issued 1996-05-28
- Rollins DM (2000-08-01). "Bacterial Pathogen List". BSCI 424 Pathogenic Microbiology. University of Maryland. Retrieved 2009-03-01.
- Johnson M. "Catalase Production". Biochemical Tests. Mesa Community College. Retrieved 2009-03-01.
- Fox A. "Streptococcus pneumoniae and Staphylococci". University of South Carolina. Retrieved 2009-03-01.
- "Why Hair Turns Gray Is No Longer A Gray Area: Our Hair Bleaches Itself As We Grow Older". Science News. ScienceDaily. 2009-02-24. Retrieved 2009-03-01.
- Hitti M (2009-02-25). "Why Hair Goes Gray". Health News. WebMD. Retrieved 2009-03-01.
- Wood JM, Decker H, Hartmann H, Chavan B, Rokos H, Spencer JD et al. (February 2009). "Senile hair graying: H2O2-mediated oxidative stress affects human hair color by blunting methionine sulfoxide repair". FASEB J. 23 (7): 2065â€“2075. doi:10.1096/fj.08-125435. PMID 19237503.
- Cao C, Leng Y, Kufe D (August 2003). "Catalase activity is regulated by c-Abl and Arg in the oxidative stress response". J. Biol. Chem. 278 (32): 29667â€“75. doi:10.1074/jbc.M301292200. PMID 12777400.
- "GenAge entry for CAT (Homo sapiens)". Human Ageing Genomic Resources. Retrieved 2009-03-05.
- "Catalase". MadSci FAQ. madsci.org. Retrieved 2009-03-05.
- "Catalase and oxidase test video". Regnvm Prokaryotae. Retrieved 2009-03-05.
- "EC 126.96.36.199 - catalase". Brenda: The Comprehensive Enzyme Information System. Retrieved 2009-03-05.
- "PeroxiBase - The peroxidase database". Swiss Institute of Bioinformatics. Retrieved 2009-03-05.
- "Catalase Procedure". MicrobeID.com. Retrieved 2009-04-22.
- "Catalase Molecule of the Month". Protein Data Bank. Retrieved 2013-01-08.
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.
Catalase Provide feedback
No Pfam abstract.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011614
Catalases (EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects [PUBMED:11351128]. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (INTERPRO) that are found in bacteria [PUBMED:14745498]. Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants [PUBMED:9287428, PUBMED:12557185].This entry represent the core-forming domain of mono-functional, haem-containing catalases. It does not cover the region that carries an immune-responsive amphipathic octa-peptide that is found in the C-terminal of some catalases (INTERPRO).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||heme binding (GO:0020037)|
|catalase activity (GO:0004096)|
|Biological process||oxidation-reduction process (GO:0055114)|
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.
|Number in seed:||417|
|Number in full:||21162|
|Average length of the domain:||355.40 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||67.79 %|
|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:||15|
|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 6 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 Catalase domain has been found. There are 391 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...