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Topic: Superfamily biology

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	Superfamily
		Each sequence may well hit a superfamily more than once as there are several overlapping models for each superfamily, however it is the hit to the superfamily which is meaningful.
		You may view sequences aligned to the models which represent a view of the superfamily although it may be biased towards the seed.
		This server is maintained by Derek Wilson at the MRC Laboratory of Molecular Biology, Cambridge, Martin Madera at UCSD, and Julian Gough at the University of Bristol.
	supfam.org /SUPERFAMILY (659 words)

	PLoS Biology - Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene ...
		Although many superfamilies have been shown to carry out multiple functions, Hegyi and Gerstein [18] found that the majority of structure superfamilies carry out one or a few molecular functions, and conversely, that the majority of functions are carried out by one or a few SCOP superfamilies.
		Superfamily predictions of increased accuracy were obtained by integrating GO function, component, and process annotations [17,22] from the Saccharomyces Genome Database [23] with the structure prediction data using a simple Bayesian approach.
		Superfamilies without members shorter than 200 amino acids were excluded, as were proteins for which Rosetta failed to produce predictions within a reasonable time.
	biology.plosjournals.org /perlserv/?request=get-document&doi=10.1371/journal.pbio.0050076 (6308 words)

	Genome Biology \| Full text \| The alpha/beta fold uracil DNA glycosylases: a common origin with diverse fates
		The sequence conservation in the UDG superfamily is concentrated primarily in three motifs, with the two motifs located near the amino and carboxyl termini corresponding to the substrate-binding pocket (Figures 1,2).
		The ancestral core fold of the UDG superfamily consists of a central parallel four-strand ß sheet with a 2-1-3-4 topology, which is associated with four helices; the substrate-binding pocket is formed by the regions located after strand 1 and strand 4 (Figure 2).
		In both structurally characterized members of this superfamily (Udg and Mug), a conserved aromatic residue located in the loop preceding the conserved helix 1 (Figures 1,2) mediates binding of the attacked uracil from the DNA double helix via stacking interactions [11].
	genomebiology.com /2000/1/4/research/0007 (3421 words)

	Cell-Cell Interactions
		Other members of the Ig superfamily mediate homophilic interactions, in which an adhesion molecule on the surface of one cell binds to the same molecule on the surface of another cell.
		It remains to be determined whether the variable and constant regions of protocadherins are joined at the DNA or the RNA level (for example, by alternative splicing) and to what extent rearrangements of protocadherin genes might contribute to the establishment of specific synaptic connections in the brain.
		In contrast to the stable cell-matrix junctions discussed in the preceding section, the cell-cell interactions mediated by the selectins, integrins, and members of the Ig superfamily are transient adhesions in which the cytoskeletons of adjacent cells are not linked to one another.
	www.ncbi.nlm.nih.gov /books/bv.fcgi?call=bv.View..ShowSection&rid=cooper.section.2058 (1703 words)

	Related WordNet synsets for SUMO concept Organism
		(biology) genus from which the name of a family or subfamily is formed; it is not necessarily the most representative genus by often the largest or best known or earliest described
		(biology) a taxonomic group that is a division of a species; usually arises as a consequence of geographical isolation within a species
		(biology) belonging to or active during the night; "nocturnal animals are active at night"; "nocturnal plants have flowers that open at night and close by day"
	virtual.cvut.cz /kifb/wordnet/_organism.html (1856 words)

	[No title] (Site not responding. Last check: )
		In biology, a superfamily is an intermediate rank between suborder and family.
		A number of genera may be grouped into a family.
		Similarly, a number of families may comprise a superfamily.
	www.wikiwhat.com /encyclopedia/s/su/superfamily__biology_.html (31 words)

	Cell Biology, UVa School of Medicine
		It is also critical to a number of normal physiological processes from fertilization to immune surveillance, and plays a primary role in the progression of disease states that include cancer and metastasis.
		The Department of Cell Biology at the University of Virginia is home to several investigators who are at the forefront of research in the areas of cell adhesion and cell migration.
		A common thread in many of these studies is the integrins, which are a large family of transmembrane receptors that “integrate” the ECM with various cytoskeletal and cell signaling complexes located in the cytoplasm.
	www.virginia.edu /cellbiology/Research/Adhesionpage.htm (305 words)

	University of Nebraska Redox Biology Center (Site not responding. Last check: )
		Results from analysis of several such enzyme superfamilies suggest that chemistry, rather than ability to bind a specific substrate type, is the critical determinant in the evolution of new enzyme functions within each superfamily.
		The laboratory is also interested in extending their approaches to other classes of proteins besides enzymes and in examining the roles of superfamily members in metabolic pathways and other cellular circuits for clues in understanding the evolution of complex systems.
		He is considered the father of the field of oxygen free-radical biology due to the discovery in 1968 when his lab discovered a class of enzymes called superoxide dismutases (SOD).
	www.unl.edu /RedoxBiologyCenter/ext_adv_council.html (1104 words)

	Superfamily
		Each sequence may well hit a superfamily more than once as there are several overlapping models for each superfamily, however it is the hit to the superfamily which is meaningful.
		You may view sequences aligned to the models which represent a view of the superfamily although it may be biased towards the seed.
		This server is maintained by Derek Wilson at the MRC Laboratory of Molecular Biology, Cambridge, Martin Madera at the European Bioinformatics Institute, Hinxton, and Julian Gough at the University of Bristol.
	supfam.mrc-lmb.cam.ac.uk /SUPERFAMILY (668 words)

	Biology Division - Ray Deshaies
		Ubiquitin (Ub) is activated by covalent attachment to E1 enzyme in an ATP-dependent reaction and is subsequently transferred to an E2 (ubiquitin-conjugating) enzyme.
		At the core of this superfamily is a module comprised of a cullin subunit and a RING subunit, and hence these enzymes are referred to as cullin-RING ligases (CRLs).
		We seek to address these questions by applying chemical biology and quantitative proteomics to devise new tools and methods to study CSN and the cycle of cullin neddylation and deneddylation.
	biology.caltech.edu /contact/Members/Deshaies (2360 words)

	Genome Biology \| Full text \| A gold standard set of mechanistically diverse enzyme superfamilies
		In each superfamily, the cognate chemical capability is mapped to specific amino acids, thus allowing uncharacterized proteins identified as candidate superfamily members to be evaluated for their ability to perform the superfamily-specific chemistry based on the presence or absence of this amino acid signature.
		These difficulties largely arise from the complexity of the underlying biology, where the boundaries between different families within a superfamily may be uneven due to different evolutionary rates within each family, and, due to a number of reasons, some enzymes may not fit into the simple family classification at all.
		Armstrong RN: Mechanistic diversity in a metalloenzyme superfamily.
	genomebiology.com /2006/7/1/R8 (6262 words)

	Superfamily (biology)
		In biology, a superfamily is an intermediate rank between suborder and family.
		A number of genera may be grouped into a family.
		Similarly, a number of families may comprise a superfamily.
	www.ebroadcast.com.au /lookup/encyclopedia/su/Superfamily_(biology).html (31 words)

	ScienceDaily: First 'Encyclopedia' Of Nuclear Receptors Reveals Organisms' Focus On Sex, Food (Site not responding. Last check: )
		In creating the first "encyclopedia" of an entire superfamily of nuclear receptors - proteins that turn genes on and off throughout the body — UT Southwestern Medical Center researchers found that certain receptors form networks and interact to regulate disease states and physiology in two main areas, reproduction and nutrient metabolism.
		In the anatomical study, researchers used mice to profile the location and activity of the superfamily of nuclear receptors.
		This also suggests that the superfamily acts as a mega-network to influence metabolism, rather than in a series of independent signaling pathways.
	www.sciencedaily.com /releases/2006/08/060824222321.htm (868 words)

	Dept of Molecular and Cellular Biology, Harvard U: Biology Links
		Evolution Update: The Evolution Research Center for Students and Teachers of Biology
		University of Connecticut Department of Ecology and Evolutionary Biology
		FASEB -- Federation of American Societies for Experimental Biology
	mcb.harvard.edu /BioLinks/Evolution.html (279 words)

	Biology Direct \| Full text \| A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ...
		The former clade is typified by an insert of a β-hairpin after the helix of the β-grasp fold, whereas the latter clade is characterized by an insert between strands 4 and 5 of the core fold.
		A comprehensive multiple alignment for the SLBB superfamily (Figure 1B) was prepared by combining alignments for individual groups constructed using the T-Coffee program, based on the structural superposition of transcobalamin C-terminal domain (2bbc) and Nqo1 middle domain (2fug; chain S).
		The manuscript "A novel superfamily with the β-grasp fold involved in binding diverse soluble ligands" by A. Burroughs is an excellent and insightful comparative genomics study of a very interesting domain family broadly conserved across all kingdoms of Life.
	www.biology-direct.com /content/2/1/4 (6687 words)

	Biosciences Division
		The VL belongs to a large, structurally related family of proteins called the immunoglobulin superfamily.
		In addition to the antibodies, the superfamily includes a wide variety of cell-surface receptors and cell adhesion molecules.
		Members of this superfamily possess one or more copies of a conserved structural domain, the immunoglobulin fold.
	www.bio.anl.gov /structuralbiology/diseases.html (622 words)

	Genome Biology \| Full text \| Higher plant glycosyltransferases
		The amino-terminal regions are more variable than the carboxy-terminal regions, supporting the suggestion that the domain involved in the recognition and binding of the diverse aglycone substrates is located towards the amino terminus of the protein whereas the carboxy-terminal region encodes a domain involved in binding the nucleotide sugar substrate [9].
		Six glycosyltransferases from other superfamilies have been analyzed structurally, however, and these analyses suggest that, although they were previously thought to be unrelated, they may fall into just two superfamilies [10].
		The UGT superfamily in higher plants is thought to encode enzymes that glycosylate a broad array of aglycones, including plant hormones, all major classes of plant secondary metabolites, and xenobiotics such as herbicides [15].
	www.genomebiology.com /2001/2/2/reviews/3004 (2699 words)

	Biology
		Because of the relative abundance of species (mostly undescribed), the worldwide geographic range, the complex biological and often baffling morphological diversity, and the few taxonomists who have studied the superfamily, much remains to be accomplished if ever we are to understand the Chalcidoidea in a comprehensive way.
		Recent work suggests that the Mymarommatidae are the probable sister group to the rest of the superfamily and, as mentioned elsewhere, there is still some debate as to whether or not mymarommatids are true chalcidoids.
		The subject of chalcidoid biology is a study in diversity.
	www.sel.barc.usda.gov /hym/chalcids/biology.html (6074 words)

	First 'encyclopedia' of nuclear receptors reveals organisms' focus on sex, food
		In creating the first "encyclopedia" of an entire superfamily of nuclear receptors – proteins that turn genes on and off throughout the body – UT Southwestern Medical Center researchers found that certain receptors form networks and interact to regulate disease states and physiology in two main areas, reproduction and nutrient metabolism.
		"This 'systems biology' approach to look at the whole superfamily, not just individuals, is a new way to understand how nuclear receptors regulate physiology," said Dr. David Mangelsdorf, chairman of pharmacology and senior author of one study.
		Mangelsdorf said the poster will be a tool for researchers engaged in advanced investigation of the biological role of each receptor individually and as a superfamily.
	www.biologynews.net /archives/2006/08/24/first_encyclopedia_of_nuclear_receptors_reveals_organisms_focus_on_sex_food.html (1053 words)

	Human Molecular Biology - Cambridge University Press (Site not responding. Last check: )
		Human Molecular Biology is an introduction to the molecular basis of health and disease for the new generation of life scientists and medical students.
		This seamless account breaks through the boundaries between molecular biology and medicine, and leads the reader on to a new dimension where the biological basis of health and disease is inescapably molecular.
		Human Molecular Biology scooped both the Richard Asher prize for best new textbook and the overall ‘Medical Book of the Year’ in the Society of Authors and Royal Society of Medicine Medical Book Awards 2003.
	www.cambridge.org /uk/catalogue/catalogue.asp?isbn=052164285X (385 words)

	JIS: Tschinkel 2.12.2002
		Moreover its biology and ecology makes it an ideal mechanical vector for human and animal pathogens, including viruses, bacteria, protozoan cysts and helminth eggs (Sukontason et al., 2000; Graczyk et al., 2001).
		Analyses of the predicted secondary structure of the polypeptides encoded by MdHexL1 and MdHeF1 revealed that the positions of several -helixes and -sheets, and also of the three protein domains described for proteins belonging to the hemocyanin superfamily are highly conserved in the house fly hexamerins (results not shown).
		Hemocyanins and hexamerins are members of the same superfamily and it has been estimated that hemocyanins from primitive crustaceans diverged more than 360 million years ago giving rise to the insect hexamerins (Beintema et al., 1994; Burmester and Scheller, 1996; Burmester, 2001).
	www.insectscience.org /4.2 (5747 words)

	John A. Gerlt
		Using the paradigm that the reactions catalyzed by members of this superfamily are initiated by abstraction of the
		We are using directed evolution to explore the functional restrictions available to members of this superfamily, aiming to obtain novel catalysts for new reactions.
		In contrast to the enolase superfamily, the positions of the essential functional groups in this superfamily cannot be restricted to known positions within the structure.
	www.scs.uiuc.edu /chem/gerlt.html (602 words)

	The A-superfamily of Conotoxins: STRUCTURAL AND FUNCTIONAL DIVERGENCE -- Santos et al. 279 (17): 17596 -- Journal of ...
		in the conotoxin precursors encoded by the gene superfamily.
		polypeptide backbone of all peptides that belong to the superfamily.
		framework of the peptides belonging to that superfamily.
	www.jbc.org /cgi/content/full/279/17/17596 (5121 words)

	The University of Iowa - Department of Biology
		Cell-cell and cell-substrate adhesion molecules play a crucial role in guiding cells and axons along their paths during tissue and organ formation and the formation of the intricate patterns of nerve connections.
		The cytoplasmic domains of these adhesion receptors interact with signaling molecules and adaptor molecules that propagate signals initiated by adhesive interactions, in some cases directly altering the function of the adhesion molecule and in other cases initiating signal cascades that alter cell function in many different ways.
		Another goal is to understand the role of the adhesion molecule P0, the smallest member of the immunoglobulin superfamily, in myelination of the peripheral nervous system.
	www.biology.uiowa.edu /faculty_info.php?ID=46 (595 words)

	BIOLOGICAL SCIENCE :: AudioEnglish.net dictionary
		coarctation ((biology) a narrowing or constriction of a vessel or canal; especially a congenital narrowing of the aorta)
		valence; valency ((biology) a relative capacity to unite or react or interact as with antigens or a biological substrate)
		dehiscence ((biology) release of material by splitting open of an organ or tissue; the natural bursting open at maturity of a fruit or other reproductive body to release seeds or spores or the bursting open of a surgically closed wound)
	www.audioenglish.net /dictionary/biological_science.htm (2400 words)

	Biopharmaceutical protein structure glossary
		It is assumed, although in most cases this has not been investigated in detail, that the molecules in a homeomorphic superfamily share a common evolutionary history since the acquisition of their constituent domains.
		Prior to about 1990, the superfamily classification permitted a sequence to be assigned to a single superfamily only.
		The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily.
	www.genomicglossaries.com /content/protein_structure_glossary.asp (2741 words)

	The Superfamilies of the Order Stomatopoda
		This section is arranged such that links lead to ever more detailed information on each of the superfamilies, families, etc. At this time, I will only have time to include info down to the superfamily (I did not scan these in --- I TYPED them in).
		This superfamily includes some of the largest known stomatopods, many of whom are flattened burrowers with elaborate spear-type appendages.
		It has a preponderance of smasher types, and if there is any one group that marine aquarists would want to wish out of existence, this would be it.
	www.blueboard.com /mantis/taxon/species/stmpd.htm (525 words)

	Ceilometer
		An optical ceilometer uses triangulation to determine the height of a spot of light projected onto the base of the cloud; a laser ceilometer determines the height by measuring the time required for a pulse of light to be scattered back from the cloud base.
		Taeniolabidoidea Scientific classification Kingdom biology Kingdom: Animalia Therapsida Class biology Class: Mammalia Order biology Order: Multituberculata Superfamily biology Superfamily: Taeniolabidoidea Family biology Family Taeniolabididae Genus biology...
		After defeating State Senator John Marchi in the 1973 mayoral election, Beame faced the worst fiscal crisis in the city s history and spent the bulk of his term attempting to ward off bankruptcy.
	www.uk.fraquisanto.net /Ceilometer (339 words)

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