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Category: OntologyTerm
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Type Details Score
Ontology Term
Pfam:PF01698 | Floricaula / Leafy protein SAM domain
Description: This family consists of various plant development proteins which are homologues of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species [3].
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Ontology Term
Pfam:PF09192 | Actin-fragmin kinase, catalytic
Description: Members of this family assume a secondary structure consisting of eight beta strands and 11 alpha-helices, organised in two lobes. They are predominantly found in actin-fragmin kinase, where they act as a catalytic domain that mediates the phosphorylation of actin [1].
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Ontology Term
PANTHER:PTHR12461:SF16 | TRANSCRIPTION FACTOR JUMONJI (JMJC) DOMAIN-CONTAINING PROTEIN
 
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Ontology Term
Pfam:PF10184 | Uncharacterized conserved protein (DUF2358)
Description: DUF2358 is a family of conserved proteins found from plants to humans. The function is unknown.
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Ontology Term
PANTHER:PTHR10121:SF0 | COATOMER SUBUNIT DELTA
 
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Ontology Term
Pfam:PF11145 | Protein of unknown function (DUF2921)
Description: This eukaryotic family of proteins has no known function.
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Ontology Term
PANTHER:PTHR13681 | SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30-RELATED
 
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Ontology Term
PANTHER:PTHR10476:SF1 | CHARGED MULTIVESICULAR BODY PROTEIN 3
 
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Ontology Term
PANTHER:PTHR19932 | WD REPEAT AND HMG-BOX DNA BINDING PROTEIN
 
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Ontology Term
PANTHER:PTHR19932:SF10 | WD REPEAT AND HMG-BOX DNA-BINDING PROTEIN 1
 
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Ontology Term
Pfam:PF12341 | Minichromosome loss protein, Mcl1, middle region
Description: Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 Pfam:PF00400 etc, and a Homeobox (HMG) domain, Pfam:PF00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known.
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Ontology Term
PANTHER:PTHR24031:SF122 | UBQ, HELICASE-C AND DEAD-LIKE HELICASE DOMAIN-CONTAINING PROTEIN
 
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Ontology Term
Pfam:PF09369 | MrfA Zn-binding domain
Description: This is the C-terminal MrfA Zn+2-binding domain (MZB, also referred to as DUF1998) which contains a conserved four-cysteine signature motif. These four Cys reside in a short coil between two alpha-helices and form a metal ion-binding site [1]. This domain is frequently found at the C-terminal of ndNTPases, however, it is also found encoded in a standalone gene, downstream of putative helicase domain-encoding genes associated with bacterial anti-phage defense system DISARM. MrfA (Mitomycin repair factor A, also known as YprA in Bacillus subtilis) is a DNA helicase that supports repair of mitomycin C-induced DNA damage. MrfA homologues are widely distributed in bacteria and are also present in archaea, fungi and plants. The MrfA-homologue in yeast, Hrq1, also reduces mitomycin C sensitivity. Hrq1 has high similarity to human RecQ4 and was therefore assigned to the RecQ-like helicase family. MrfA homologues appear to be missing in Enterobacteria, however, certain pathogenic Escherichia coli and Salmonella strains harbour Z5898-like helicases with this domain [1].
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Ontology Term
PANTHER:PTHR22840 | WD REPEAT-CONTAINING PROTEIN 36
 
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Ontology Term
PANTHER:PTHR10000 | PHOSPHOSERINE PHOSPHATASE
 
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Ontology Term
PANTHER:PTHR11752:SF8 | ACTIVATING SIGNAL COINTEGRATOR 1 COMPLEX SUBUNIT 3
 
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Ontology Term
PANTHER:PTHR13193 | CGI-140
 
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Ontology Term
PANTHER:PTHR13193:SF0 | PAT COMPLEX SUBUNIT ASTERIX
 
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Ontology Term
Pfam:PF03669 | PAT complex subunit Asterix
Description: This family represents Asterix proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes [1]. The PAT complex acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins [1]. Asterix is the substrate-interacting subunit of the PAT complex and associates with the first TMD of the nascent chain. The PAT complex favors the binding to TMDs with exposed hydrophilic amino acids within the lipid bilayer and provides a membrane-embedded partially hydrophilic environment in which TMD1 binds [1].
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Ontology Term
PANTHER:PTHR19305:SF0 | SYNAPTOSOMAL-ASSOCIATED PROTEIN 29
 
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Ontology Term
PANTHER:PTHR14091 | PERIODIC TRYPTOPHAN PROTEIN 1
 
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Ontology Term
PANTHER:PTHR14091:SF0 | PERIODIC TRYPTOPHAN PROTEIN 1 HOMOLOG
 
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Ontology Term
PANTHER:PTHR10657 | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
 
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Ontology Term
Pfam:PF00639 | PPIC-type PPIASE domain
Description: Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline.
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Ontology Term
PANTHER:PTHR10536 | DNA PRIMASE SMALL SUBUNIT
 
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Ontology Term
PANTHER:PTHR10536:SF0 | DNA PRIMASE SMALL SUBUNIT
 
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Ontology Term
Pfam:PF01896 | DNA primase small subunit
Description: DNA primase synthesises the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme [1]. The family also contains many bacterial DNA primases.
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Ontology Term
PANTHER:PTHR12388 | MITOCHONDRIA ASSOCIATED GRANULOCYTE MACROPHAGE CSF SIGNALING MOLECULE
 
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Ontology Term
Pfam:PF03656 | Pam16
Description: The Pam16 protein (Swiss:P42949) is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) [1]. In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [1]. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle [2]. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel [3]. Pam18 stimulates the ATPase activity of mtHsp70.
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Ontology Term
PANTHER:PTHR13043 | EXOCYST COMPLEX COMPONENT SEC5
 
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Ontology Term
Pfam:PF15469 | Exocyst complex component Sec5
Description: This entry represents the Sec5 component of the exocyst complex which is an octomeric complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis [1].
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Ontology Term
PANTHER:PTHR23407 | ATPASE INHIBITOR/5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE
 
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Ontology Term
PANTHER:PTHR23407:SF1 | 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE
 
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Ontology Term
Pfam:PF01812 | 5-formyltetrahydrofolate cyclo-ligase family
Description: 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyses the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+ [1]. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin [2].
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Ontology Term
Pfam:PF05089 | Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain
Description: Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate [1]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [2]. The structure shows that the enzyme is composed of three domains. This central domain has a tim barrel fold [3].
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Ontology Term
PANTHER:PTHR12872:SF0 | ALPHA-N-ACETYLGLUCOSAMINIDASE
 
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Ontology Term
Pfam:PF12971 | Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain
Description: Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate [1]. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations [2]. The structure shows that the enzyme is composed of three domains. This N-terminal domain has an alpha-beta fold [3].
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Ontology Term
PANTHER:PTHR14289 | F-BOX ONLY PROTEIN 3
 
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Ontology Term
Pfam:PF04379 | ApaG domain
Description: The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [1,2,3,4].
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Ontology Term
PANTHER:PTHR11871:SF0 | PROTEIN PHOSPHATASE PP2A 55 KDA REGULATORY SUBUNIT
 
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Ontology Term
Pfam:PF00445 | Ribonuclease T2 family
Description: NULL
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Ontology Term
PANTHER:PTHR11800 | DNA-DIRECTED RNA POLYMERASE
 
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Ontology Term
PANTHER:PTHR11800:SF2 | DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
 
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Ontology Term
Pfam:PF01000 | RNA polymerase Rpb3/RpoA insert domain
Description: Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal
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Ontology Term
Pfam:PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain
Description: The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
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Ontology Term
PANTHER:PTHR11135:SF0 | ELONGATOR COMPLEX PROTEIN 3
 
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Ontology Term
Pfam:PF02127 | Aminopeptidase I zinc metalloprotease (M18)
Description: NULL
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Ontology Term
PANTHER:PTHR11203:SF22 | SUBFAMILY NOT NAMED
 
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Ontology Term
Pfam:PF07521 | Zn-dependent metallo-hydrolase RNA specificity domain
Description: The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in Pfam:PF00753 and are common to all metallo-beta-lactamases. This, the fifth motif [1], appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 [4] which are involved in the processing of mRNA [2,3]. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases [2,3,4].
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Ontology Term
PANTHER:PTHR15663 | COMM DOMAIN-CONTAINING PROTEIN 9
 
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Ontology Term
Pfam:PF07258 | COMM domain
Description: The leucine-rich, 70-85 amino acid long COMM domain is predicted to form a beta-sheet and an extreme C-terminal alpha- helix. The COMM domain containing proteins are about 200 residues in length and passed the C-terminal COMM domain [1].
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Ontology Term
PANTHER:PTHR14939 | F-BOX ONLY PROTEIN 22
 
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Ontology Term
Pfam:PF10442 | FIST C domain
Description: The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids [1].
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Ontology Term
Pfam:PF03540 | Transcription initiation factor TFIID 23-30kDa subunit
Description: NULL
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Ontology Term
PANTHER:PTHR20854:SF17 | PHOSPHATASE IMPL1, CHLOROPLASTIC
 
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Ontology Term
PANTHER:PTHR12651 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 9
 
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Ontology Term
Pfam:PF08744 | Plant transcription factor NOZZLE
Description: NOZZLE is a transcription factor that plays a role in patterning the proximal-distal and adaxial-abaxial axes [1][2].
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Ontology Term
Pfam:PF01649 | Ribosomal protein S20
Description: Bacterial ribosomal protein S20 interacts with 16S rRNA [1].
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Ontology Term
PANTHER:PTHR13554 | 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 5-RELATED
 
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Ontology Term
Pfam:PF10508 | Proteasome non-ATPase 26S subunit
Description: The 26S proteasome, a eukaryotic ATP-dependent, dumb-bell shaped, protease complex with a molecular mass of approx 20kDa consists of a central 20S proteasome,functioning as a catalytic machine, and two large V-shaped terminal modules, having possible regulatory roles,composed of multiple subunits of 25- 110 kDa attached to the central portion in opposite orientations. It is responsible for degradation of abnormal intracellular proteins, including oxidatively damaged proteins, and may play a role as a component of a cellular anti-oxidative system. Expression of catalytic core subunits including PSMB5 and peptidase activities of the proteasome were elevated following incubation with 3-methylcholanthrene. The 20S proteasome comprises a cylindrical stack of four rings, two outer rings formed by seven alpha-subunits (alpha1-alpha7) and two inner rings of seven beta-subunits (beta1-beta7). Two outer rings of alpha subunits maintain structure, while the central beta rings contain the proteolytic active core subunits beta1 (PSMB6), beta2 (PSMB7), and beta5 (PSMB5). Expression of PSMB5 can be altered by chemical reactants, such as 3-methylcholanthrene [1].
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Ontology Term
Pfam:PF11282 | Protein of unknown function (DUF3082)
Description: This family of proteins has no known function.
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Ontology Term
PANTHER:PTHR23044 | 3'-5' EXONUCLEASE ERI1-RELATED
 
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Ontology Term
PANTHER:PTHR11056 | HOMOGENTISATE 1,2-DIOXYGENASE
 
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Ontology Term
Pfam:PF04209 | Homogentisate 1,2-dioxygenase C-terminal
Description: Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers [1]. This entry represents the C-terminal active site domain.
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Ontology Term
Pfam:PF09728 | Myosin-like coiled-coil protein
Description: Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed. It is a novel binding partner of several syntaxin family members and is possibly involved in Ca2+-dependent exocytosis in neuroendocrine cells [1]. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription [2].
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Ontology Term
Pfam:PF13251 | Domain of unknown function (DUF4042)
Description: This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 amino acids in length.
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Ontology Term
PANTHER:PTHR13366 | MALARIA ANTIGEN-RELATED
 
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Ontology Term
PANTHER:PTHR13366:SF0 | HEAT REPEAT-CONTAINING PROTEIN 6
 
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Ontology Term
PANTHER:PTHR11046 | OLIGORIBONUCLEASE, MITOCHONDRIAL
 
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Ontology Term
PANTHER:PTHR31656 | ROOT CAP DOMAIN-CONTAINING PROTEIN
 
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Ontology Term
PANTHER:PTHR31656:SF0 | ROOT CAP DOMAIN-CONTAINING PROTEIN
 
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Ontology Term
Pfam:PF06830 | Root cap
Description: The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die [1].This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.
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Ontology Term
PANTHER:PTHR12604 | KU AUTOANTIGEN DNA HELICASE
 
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Ontology Term
PANTHER:PTHR12604:SF3 | X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 5
 
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Ontology Term
Pfam:PF02735 | Ku70/Ku80 beta-barrel domain
Description: The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 Swiss:P12956 and Ku80 Swiss:P13010 proteins that form a DNA binding heterodimer [1].
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Ontology Term
Pfam:PF03730 | Ku70/Ku80 C-terminal arm
Description: The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C terminal arm. This alpha helical region embraces the beta-barrel domain Pfam:PF02735 of the opposite subunit [1].
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Ontology Term
Pfam:PF03731 | Ku70/Ku80 N-terminal alpha/beta domain
Description: The Ku heterodimer (composed of Ku70 Swiss:P12956 and Ku80 Swiss:P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [1].
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Ontology Term
PANTHER:PTHR16719 | CYTOCHROME C OXIDASE COPPER CHAPERONE
 
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Ontology Term
Pfam:PF05051 | Cytochrome C oxidase copper chaperone (COX17)
Description: Cox17 is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in yeast [1]. The structure of Cox17 [2] shows the protein to have an unstructured N-terminal region followed by two helices and several unstructured C-terminal residues. The Cu(I) binding site has been modelled as two-coordinate with ligation by conserved residues Cys23 and Cys26.
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Ontology Term
PANTHER:PTHR12867 | GLYCOSYL TRANSFERASE-RELATED
 
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Ontology Term
PANTHER:PTHR12210 | DULLARD PROTEIN PHOSPHATASE
 
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Ontology Term
PANTHER:PTHR32219 | RNA-BINDING PROTEIN YLMH-RELATED
 
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Ontology Term
PANTHER:PTHR20371 | ENOLASE-PHOSPHATASE E1
 
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Ontology Term
PANTHER:PTHR20371:SF0 | ENOLASE-PHOSPHATASE E1
 
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Ontology Term
PANTHER:PTHR10640 | METHYLTHIORIBULOSE-1-PHOSPHATE DEHYDRATASE
 
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Ontology Term
Pfam:PF00596 | Class II Aldolase and Adducin N-terminal domain
Description: This family includes class II aldolases and adducins which have not been ascribed any enzymatic function.
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Ontology Term
PANTHER:PTHR23193 | NUCLEAR PORE COMPLEX PROTEIN NUP
 
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Ontology Term
PANTHER:PTHR13902:SF3 | GB|AAF34833.1-RELATED
 
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Ontology Term
PANTHER:PTHR24361:SF207 | SERINE/THREONINE-PROTEIN KINASE 24
 
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Ontology Term
PANTHER:PTHR11638:SF68 | DOUBLE CLP-N MOTIF-CONTAINING P-LOOP NUCLEOSIDE TRIPHOSPHATE HYDROLASE DOMAIN-CONTAINING PROTEIN-RELATED
 
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Ontology Term
PANTHER:PTHR18895:SF3 | METHYLTRANSFERASE-LIKE PROTEIN 20
 
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Ontology Term
Pfam:PF06325 | Ribosomal protein L11 methyltransferase (PrmA)
Description: This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.
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Ontology Term
PANTHER:PTHR24067:SF31 | UBIQUITIN-CONJUGATING ENZYME E2N-RELATED
 
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Ontology Term
PANTHER:PTHR30523 | PHOSPHOENOLPYRUVATE CARBOXYLASE
 
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Ontology Term
Pfam:PF00311 | Phosphoenolpyruvate carboxylase
Description: NULL
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Ontology Term
PANTHER:PTHR12472 | RAB3-GAP REGULATORY DOMAIN
 
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Ontology Term
Pfam:PF14655 | Rab3 GTPase-activating protein regulatory subunit N-terminus
Description: This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily [1].
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Ontology Term
PANTHER:PTHR32108 | DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA
 
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Ontology Term
PANTHER:PTHR32108:SF0 | DNA-DIRECTED RNA POLYMERASE SUBUNIT ALPHA
 
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Ontology Term
PANTHER:PTHR12220 | 50S/60S RIBOSOMAL PROTEIN L16
 
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The Legume Information System (LIS) is a research project of the USDA-ARS:Corn Insects and Crop Genetics Research in Ames, IA.
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