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Search results 101 to 200 out of 202262 for *

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Category: OntologyTerm
Type Details Score
Ontology Term  
Ontology Term
Description: The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger [1].
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term  
Ontology Term
Description: This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].
Ontology Term  
Ontology Term
Description: Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain, such as Swiss:O64965. The function of this region is uncertain.
Ontology Term
Description: A conserved region of auxin-responsive transcription factors.
Ontology Term  
Ontology Term
Description: NULL
Ontology Term
Description: This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, Pfam:PF00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y).
Ontology Term  
Ontology Term
Description: p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain [1]. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain.
Ontology Term
Description: DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients [3]. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family [1]. This domain is also found in chitin synthase proteins like Swiss:Q8TF96, and in protein phosphastases such as Swiss:Q6NN85.
Ontology Term  
Ontology Term
Description: The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.
Ontology Term
Description: The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival.
Ontology Term
Description: This is a 100 residue conserved region of a family of proteins found from fungi to humans. This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.
Ontology Term  
Ontology Term
Description: The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain Pfam:PF00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [1] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [2,3]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in Pfam:PF00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.
Ontology Term  
Ontology Term
Description: Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292.
Ontology Term
Description: The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilises the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands [1]. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, Pfam:PF09459, the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, Pfam:PF02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families.
Ontology Term  
Ontology Term  
Ontology Term  
Ontology Term
Description: This cysteine-rich GUB_WAK_bind domain is the extracellular part of this serine/threonine kinase that binds to the cell-wall pectins.
Ontology Term  
Ontology Term  
Ontology Term
Description: Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N-terminus, which must be cleaved by the ubiquitin-specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome [1]. This entry represents the ubiquitin fold N-terminal domain found in Sde2 proteins.
Ontology Term
Description: This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage [1].
Ontology Term
Description: This family is composed of trypsin-alpha amylase inhibitors, seed storage proteins and lipid transfer proteins from plants.
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term
Description: This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term
Description: This eukaryotic family of proteins has no known function.
Ontology Term  
Ontology Term  
Ontology Term  
Ontology Term
Description: This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 Swiss:P32522 that may be involved in RNA stabilisation [1]. This domain occurs in crp1 that is involved in RNA processing [2]. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR [3].
Ontology Term  
Ontology Term  
Ontology Term
Description: PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilise nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates [1].
Ontology Term  
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term
Description: This family of membrane proteins transport nucleotide sugars from the cytoplasm into Golgi vesicles. Swiss:P78382 transports CMP-sialic acid, Swiss:P78381 transports UDP-galactose and Swiss:Q9Y2D2 transports UDP-GlcNAc.
Ontology Term  
Ontology Term  
Ontology Term
Description: This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.
Ontology Term
Description: This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).
Ontology Term
Description: This entry represents the arabinogalactan peptide family found in plants [1].
Ontology Term  
Ontology Term  
Ontology Term
Description: Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].
Ontology Term  
Ontology Term  
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term
Description: The Pfam entry includes the basic region and the leucine zipper region.
Ontology Term
Description: This region is found to the N-terminus of the Pfam:PF00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain) [2], whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C [1], classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions [1]. The MFMR region contains a nuclear localisation signal in bZIP opaque and GBF-2 [2]. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals [2].
Ontology Term  
Ontology Term
Description: The BTB (for BR-C, ttk and bab) [1] or POZ (for Pox virus and Zinc finger) [2] domain is present near the N-terminus of a fraction of zinc finger (Pfam:PF00096) proteins and in proteins that contain the Pfam:PF01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation [2]. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule [3]. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [4,5,6]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.
Ontology Term
Description: This domain is found associated with Pfam:PF00651 and Pfam:PF01344 [1]. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues [1]. This family appears to be closely related to the BTB domain (Finn RD, personal observation).
Ontology Term  
Ontology Term
Description: This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.
Ontology Term  
Ontology Term
Description: This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; Pfam:PF00560 and Pfam:PF07723) and the WD repeat (Pfam:PF00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression [1-2].
Ontology Term  
Ontology Term
Description: NULL
Ontology Term  
Ontology Term  
Ontology Term
Description: This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements [1,2]. These transposons contain two ORFs. The molecular function of this region is unknown.
Ontology Term
Description: This domain is found in bacterial, archaeal and eukaryotic proteins. It is predicted to be organised into two N-terminal beta-strands and a C-terminal alpha helix, thus possibly adopting a fold similar to that of the C2H2 zinc finger (Pfam:PF00096). SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts [1].
Ontology Term  
Ontology Term
Description: Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances [1].
Ontology Term  
Ontology Term
Description: This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [1].
Ontology Term  
Ontology Term
Description: Members of this family are similar to late embryogenesis abundant proteins. Members of the family have been isolated in a number of different screens. However, the molecular function of these proteins remains obscure.
Ontology Term  
Ontology Term
Description: The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process [1-3]. This domain is related to the Ring finger Pfam:PF00097 but lacks the zinc binding residues [4].
Ontology Term  
Ontology Term
Description: This entry includes Cytoplasmic fragile X mental retardation interacting proteins 1/2 (CYFIP1/2) from humans and their homologues, such as Sra-1 (specifically Rac1-associated protein 1) from Drosophila and PIROGI from Arabidopsis. CYFIP1/2 interact with FMRP (fragile X mental retardation protein) which is responsible for pathologic manifestations in the Fragile X Syndrome. CYFIP1 interacts with the small GTPase Rac1 [1,2]. CYFIP1 represses cap-dependent translation of mRNA by interacting with the initiation factor eIF4E [3]. CYFIP1 and CYFIP2 are part of the Wiskott-Aldrich syndrome protein-family verprolin-homologous protein (WAVE) complex that regulates actin polymerization at synapses [4]. Drosophila Sra-1 interacts with the Kette and Wasp. It is required for neuronal and bristle development in Drosophila [5]. PIROGI is part of a WAVE complex that activates the ARP2/3 complex and is Involved in regulation of actin organisation [6].
Ontology Term  
Ontology Term  
Ontology Term
Description: This family includes multiple HEAT repeats.
Ontology Term  
Ontology Term
Description: Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide. The neprosin domain corresponds to the mature peptidase [1]. It is not known if other proteins with this domain are peptidases.
Ontology Term
Description: Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide [1]. This domain corresponds to the presumed activation peptide.
Ontology Term  
Ontology Term
Description: This family contains the plant whirly transcription factors.
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