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. 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.
Key: available, not generated, — not available. 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. 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. 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 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. 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.
Align selected sequences to HMM. Clear selection. This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab.
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.
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:. 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. There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary. The tree is built by looking at each sequence in the full alignment for the family. 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.
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. 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. Activation of humoral immunity and eosinophils in neuromyelitis optica.
Association between Alzheimer's disease and a functional polymorphism in the myeloperoxidase gene. Experimental Neurology. Myeloperoxidase, a catalyst for lipoprotein oxidation, is expressed in human atherosclerotic lesions. Journal of Clinical Investigations. Glutathione depletion increases tyrosinase activity in human melanoma cells. Spectral and kinetic evidence for reaction of superoxide with compound I of myeloperoxidase.
Journal of Immunology. A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment. Journal of Biological Chemistry. Free radicals in the physiological control of cell function. Physiological Reviews. Myeloperoxidase, a leukocyte derived vascular NO oxidase. The cytotoxic activity of lactoperoxidase: enhancement and Inhibition by neuroactive compounds. Role of peroxidases in Parkinson disease: A hypothesis.
Myeloperoxidase predicts progression of carotid stenosis in states of low high-density lipoprotein cholesterol. Journal of the American College of Cardiology. Loss of glutathione peroxidase 3 expression is correlated with epigenetic mechanisms in endometrial adenocarcinoma. Cancer Cell Int. Increase in uterine peroxidase activity in the rat uterus during oestrogen hyperaemia. Journal of Inorganic Biochemistry. Selenoproteins of the glutathione system. In: Selenium.
Hatfield D. Targeted expression of the human uncoupling protein 2 Hucp2 to adult neurons extends life span in the fly. Cell Metabolism.
Active site structure and catalytic mechanisms of human peroxidases. Archives of Biochemistry and Biophysics. Challenge testing the lactoperoxidase system against a range of bacteria using different activation agents.
Journal of Dairy Science. Opposite effects of peroxidase in the initial stages of tyrosinase-catalysed melanin biosynthesis biosynthesis. Distinct immunological and biochemical properties of thyroid peroxidase purified from human thyroid glands and recombinant protein produced in insect cells. Neuronal expression of myeloperoxidase is increased in Alzheimer's disease. Growing significance of myeloperoxidase in non-infectious diseases. Thiocyanate mediated antifungal and antibacterial property of goat milk.
Life Sciences Including Pharmacology Letter. Inhibition of myeloperoxidase- and neutrophil-mediated oxidant production by tetraethyl and tetramethyl nitroxides.
Free Radical Biology and Medicine. Brain and Development. Glutathione peroxidase: A potential marker for the most common diseases and disorders. Recent Patents on Biomarkers. Myeloperoxidase: friend and foe. Journal of Leukocyte Biology. The role of eosinophils in host defense against helminth parasites. Lactoperoxidase: physicochemical properties, occurrence, mechanism of action and applications. British Journal of Nutrition. Eosinophilic and neutrophilic inflammation in asthma, chronic bronchitis, and chronic obstructive pulmonary disease.
Eosinophils in atopic dermatitis. Oral Microbiology and Immunology. Role of mitochondria in oxidative stress and ageing. Biochimica Biophysica Acta.
Glutathione peroxidase-1 in health and disease: from molecular mechanisms to therapeutic opportunities. Antioxidant Redox Signal. Journal of Investigative Dermatology.
Development of insulin resistance and obesity in mice overexpressing cellular glutathione peroxidase. Inhibition of herpes simplex virus type 1, respiratory syncytial virus and echovirus type 11 by peroxidase-generated hypothiocyanite. Antiviral Research. Plasma concentrations of myeloperoxidase predict mortality after myocardial infarction. Journal of American College of Cardiology. National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines: clinical characteristics and utilization of biochemical markers in acute coronary syndromes.
Clinical Chemistry. Characterization of the differentiated antioxidant profile of human saliva. Immunohistochemical and genetic evidence of Myeloperoxidase involvement in multiple sclerosis. Journal of Neuroimmunology, 78, Myeloperoxidase level in patients with stable coronary artery disease and acute coronary syndromes.
European Journal of Clinical Investigations. Involvement of mitochondrial phospholipid hydroperoxide glutathione peroxidase as an antiapoptotic factor. Chemico-Biological Interactions. From selenium to selenoproteins: synthesis, identity, and their role in human health.
Antioxidand Redox Signal. Crevicular fluid levels of plasma glutathione peroxidase eGPx in periodontal health and disease. Archives of Oral Biology. Inactivation of human myeloperoxidase by hydrogen peroxide.
Quantitative, standardized assays for determining the concentrations of bovine lactoperoxidase, human salivary peroxidase, and human myeloperoxidase. Analytical Biochemistry. Thyroid peroxidase autoantibodies in euthyroid subjects.
Myeloperoxidase polymorphism is associated with gender specific risk for Alzheimer's disease. Inhibition of oral peroxidase activity by cigarette smoke: In vivo and in vitro studies. Tumor suppressive effects of MnSOD overexpression may involve imbalance in peroxide generation versus peroxide removal.
Abernathy's surgical secrets. Chapter 58; pp. Thyroid peroxidase antibodies, levels of thyroid stimulating hormone and development of hypothyroidism in euthyroid subjects. European Journal of Internal Medicine. Pathogenesis and clinical features of eosinophilic esophagitis. Markers of oxidative stress and erythrocyte antioxidant enzyme activity in older men and women with differing physical activity.
Experimental Gerontology. Eosinophils and human cancer. Tyrosyl radical generated by myeloperoxidase is a physiological catalyst for the initiation of lipid peroxidation in low density lipoprotein. Journal of Biological Chemistry Allergic fungal sinusitis. Identification of a glutathione peroxidase inhibitor that reverses resistance to anticancer drugs in human B-cell lymphoma cell lines. Autoantibodies as predictors of disease. Significance of the lactoperoxidase system in the dairy industry and its potential applications: a review.
Alterations in gene expression and activity during squamous cell carcinoma development. Cancer Research. Nuclease sensitive element binding protein 1 associates with the selenocysteine insertion sequence and functions in mammalian selenoprotein translation.
Journal of Cellular Physiology. Effects of orally administered bovine lactoperoxidase on dextran sulfate sodium-induced colitis in mice.
Bioscience Biotechnology Biochemistry. Identification of lactoperoxidase in mature human milk. Experimental Setup We extracted catalase from turnips, and investigated the effects of four factors on the speed of the enzymatic reaction.
The factors were: temperature, pH, substrate here, H 2 O 2 concentration, and enzyme concentration. To track the rate of the reactions, we used the spectrophotometers and a reagent called guiacol. In the presence of oxygen, guiacol oxidizes from clear to brown. The more oxygen produced, the darker brown the guiacol becomes. We set up 10 mL reaction mixtures including guiacol, hydrogen peroxide, turnip extract, and a pH 7 buffer.
We then took an absorbance measurement every second for a minute, and graphed absorbance y versus time x. The slope of the resulting line was the rate of the reaction. We began by running a standard reaction. To test each variable of interest, we then ran sets of three reactions to compare to our standard.
For example, to determine the effects of substrate concentration, we made three sets of tubes that varied from the standard and from each other in only one way: how much hydrogen peroxide had been added. We recorded the slopes of the resulting lines and graphed the average reaction rates y -- here, the dependent variable against the factor being tested x, which was our independent variable. The resulting curves showed the enzyme's optimum value for each factor and what happened to the reaction rate as the conditions moved away from the optimum.
Temperature Effects. Temperature affects all chemical reactions, enzyme-catalyzed or not. In general, higher temperatures equal faster reaction rates. So why did our reaction slow down and eventually stop as we warmed up our test tubes? The optimum temperature for turnip peroxidase fell near room temperature.
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