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Category: OntologyTerm
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Type Details Score
Ontology Term
PANTHER:PTHR13675 | LYR MOTIF-CONTAINING PROTEIN 2
 
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Ontology Term
Pfam:PF05347 | Complex 1 protein (LYR family)
Description: Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein (Swiss:Q6Q560) has been shown to play a role in Fe/S cluster biogenesis in mitochondria [1][2]. We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins.
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Ontology Term
PANTHER:PTHR11961 | CYTOCHROME C
 
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Ontology Term
PANTHER:PTHR11961:SF0 | CYTOCHROME C
 
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Ontology Term
Pfam:PF00034 | Cytochrome c
Description: The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.
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Ontology Term
PANTHER:PTHR10516:SF142 | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP17-2, CHLOROPLASTIC-RELATED
 
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Ontology Term
PANTHER:PTHR24015:SF164 | SUBFAMILY NOT NAMED
 
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Ontology Term
PANTHER:PTHR13374 | DET1 HOMOLOG DE-ETIOLATED-1 HOMOLOG
 
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Ontology Term
Pfam:PF09737 | De-etiolated protein 1 Det1
Description: This is the C-terminal conserved 400 residues of Det1 proteins of approximately 550 amino acids [1]. Det1 (de-etiolated-1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Mammalian Det1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 Associated 1), and a member of the UBE2E group of canonical ubiquitin conjugating enzymes and modulates Cul4A function [2].
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Ontology Term
PANTHER:PTHR31579 | OS03G0796600 PROTEIN
 
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Ontology Term
Pfam:PF04720 | PDDEXK-like family of unknown function
Description: PDDEXK_6 is a family of plant proteins that are distant homologues of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteristic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix [1]. The family is not in general fused with any other domains, so its function cannot be predicted [2].
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Ontology Term
PANTHER:PTHR21496 | FERREDOXIN-RELATED
 
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Ontology Term
Pfam:PF13806 | Rieske-like [2Fe-2S] domain
Description: NULL
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Ontology Term
PANTHER:PTHR24095 | ACETYL-COENZYME A SYNTHETASE
 
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Ontology Term
Pfam:PF13193 | AMP-binding enzyme C-terminal domain
Description: This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.
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Ontology Term
Pfam:PF03552 | Cellulose synthase
Description: Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesised by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesise cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity [1].
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Ontology Term
Pfam:PF14570 | RING/Ubox like zinc-binding domain
Description: NULL
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Ontology Term
PANTHER:PTHR13856 | VHS DOMAIN CONTAINING PROTEIN FAMILY
 
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Ontology Term
Pfam:PF00790 | VHS domain
Description: Domain present in VPS-27, Hrs and STAM.
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Ontology Term
Pfam:PF03127 | GAT domain
Description: The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [1] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [2].
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Ontology Term
PANTHER:PTHR12069 | DNA-DIRECTED RNA POLYMERASES III 80 KDA POLYPEPTIDE RNA POLYMERASE III SUBUNIT 5
 
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Ontology Term
PANTHER:PTHR12069:SF0 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC5
 
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Ontology Term
Pfam:PF04801 | RPC5 protein
Description: This family represents the RPC5 protein which is part of the RNA polymerase III complex [1-3].
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Ontology Term
PANTHER:PTHR14744 | N-ALPHA-ACETYLTRANSFERASE 60
 
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Ontology Term
PANTHER:PTHR11851 | METALLOPROTEASE
 
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Ontology Term
PANTHER:PTHR11851:SF34 | INSULINASE (PEPTIDASE FAMILY M16) FAMILY PROTEIN
 
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Ontology Term
Pfam:PF00675 | Insulinase (Peptidase family M16)
Description: NULL
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Ontology Term
Pfam:PF05193 | Peptidase M16 inactive domain
Description: Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].
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Ontology Term
Pfam:PF08378 | Nuclease-related domain
Description: The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing [1].
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Ontology Term
PANTHER:PTHR23160 | SYNAPTONEMAL COMPLEX PROTEIN-RELATED
 
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Ontology Term
PANTHER:PTHR24015:SF62 | SUBFAMILY NOT NAMED
 
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Ontology Term
Pfam:PF14432 | DYW family of nucleic acid deaminases
Description: This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events [1,3,4]. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi [2]. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteristic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems [2].
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Ontology Term
PANTHER:PTHR22880 | FALZ-RELATED BROMODOMAIN-CONTAINING PROTEINS
 
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Ontology Term
Pfam:PF03126 | Plus-3 domain
Description: This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor [1].
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Ontology Term
PANTHER:PTHR19308 | PHOSPHATIDYLCHOLINE TRANSFER PROTEIN
 
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Ontology Term
PANTHER:PTHR22893 | NADH OXIDOREDUCTASE-RELATED
 
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Ontology Term
Pfam:PF00724 | NADH:flavin oxidoreductase / NADH oxidase family
Description: NULL
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Ontology Term
Pfam:PF09187 | RNA-directed DNA methylation 1
Description: This family of plant proteins includes RDM1 from Arabidopsis, which is a component of the RNA-directed DNA methylation (RdDM) effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation [1]. As part of the DDR complex with two other RdDM components, it has been shown to facilitate association of PolV to chromatin [2,3].
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Ontology Term
PANTHER:PTHR32258 | PROTEIN NETWORKED 4A
 
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Ontology Term
PANTHER:PTHR32258:SF0 | CENTROMERE PROTEIN-RELATED
 
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Ontology Term
Pfam:PF07765 | KIP1-like protein
Description: This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase [1]. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions [1]. It has also been suggested that the protein's coiled- coils allow it to dimerise in vivo [1].
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Ontology Term
Pfam:PF13302 | Acetyltransferase (GNAT) domain
Description: This domain catalyses N-acetyltransferase reactions.
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Ontology Term
PANTHER:PTHR11830 | 40S RIBOSOMAL PROTEIN S3A
 
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Ontology Term
Pfam:PF01015 | Ribosomal S3Ae family
Description: NULL
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Ontology Term
Pfam:PF07911 | Protein of unknown function (DUF1677)
Description: The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.
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Ontology Term
Pfam:PF07227 | PHD - plant homeodomain finger protein
Description: PHD_oberon is a plant homeodomain finger domain of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Oberon proteins are made up of a PHD finger domain and a coiled-coil domain. The PHD-finger domain is found in a wide variety of proteins involved in the regulation of chromatin structure [1]. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (MP) (or Auxin response factor 7) [2].
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Ontology Term
Pfam:PF10273 | Pre-rRNA-processing protein TSR2
Description: This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown.
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Ontology Term
Pfam:PF00111 | 2Fe-2S iron-sulfur cluster binding domain
Description: NULL
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Ontology Term
PANTHER:PTHR24098 | OUTER SEGMENT 5
 
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Ontology Term
PANTHER:PTHR24098:SF0 | OUTER SEGMENT 5
 
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Ontology Term
PANTHER:PTHR30457 | 5'-NUCLEOTIDASE SURE
 
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Ontology Term
PANTHER:PTHR30457:SF0 | PHOSPHATASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_4G01070)-RELATED
 
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Ontology Term
Pfam:PF01975 | Survival protein SurE
Description: E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase [1]. It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family Swiss:P38254. Swiss:P30887 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.
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Ontology Term
PANTHER:PTHR19375 | HEAT SHOCK PROTEIN 70KDA
 
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Ontology Term
PANTHER:PTHR19375:SF101 | HEAT SHOCK 70 KDA PROTEIN 8
 
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Ontology Term
Pfam:PF00012 | Hsp70 protein
Description: Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
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Ontology Term
PANTHER:PTHR10281 | MEMBRANE-ASSOCIATED PROGESTERONE RECEPTOR COMPONENT-RELATED
 
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Ontology Term
PANTHER:PTHR10281:SF1 | VACUOLE MEMBRANE PROTEIN 1
 
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Ontology Term
Pfam:PF09335 | SNARE associated Golgi protein
Description: This is a family of SNARE associated Golgi proteins. The yeast member of this family (Swiss:P36164) localises with the t-SNARE Tlg2 [1].
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Ontology Term
Pfam:PF02298 | Plastocyanin-like domain
Description: This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family (eg Swiss:P93328) may not bind copper due to the lack of key residues.
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Ontology Term
PANTHER:PTHR11689 | CHLORIDE CHANNEL PROTEIN CLC FAMILY MEMBER
 
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Ontology Term
Pfam:PF00654 | Voltage gated chloride channel
Description: This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 (Swiss:P35523) is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney [3]. These proteins contain two Pfam:PF00571 domains.
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Ontology Term
PANTHER:PTHR10026 | CYCLIN
 
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Ontology Term
PANTHER:PTHR23024 | ARYLACETAMIDE DEACETYLASE
 
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Ontology Term
Pfam:PF07859 | alpha/beta hydrolase fold
Description: This catalytic domain is found in a very wide range of enzymes.
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Ontology Term
PANTHER:PTHR10799:SF209 | ATP-DEPENDENT HELICASE BRM
 
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Ontology Term
Pfam:PF14619 | Snf2-ATP coupling, chromatin remodelling complex
Description: This domain appears to play a crucial role in chromatin remodelling for yeast SWI/SNF. It binds histones. It is required for mobilising nucleosomes and lies within the catalytic subunit of the yeast SWI/SNF. It is found to be universally conserved [1].
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Ontology Term
Pfam:PF11250 | Fantastic Four meristem regulator
Description: FAF is a family of plant proteins that regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop. The proteins are expressed in the centre of the shoot meristem, overlapping with the site of WUS - the homeodomain transcription factor WUSCHEL- expression. FAF proteins are capable of modulating shoot growth by repressing WUS in the organising centre of the shoot meristem. The ability of plants to form new organs throughout their life cycle requires tight control of the meristems to avoid unregulated growth. Plants have evolved an elaborate genetic network that controls meristem size and maintenance. WUS and the CLAVATA (CLV) ligand-receptor system are at the core of the network that regulates the size of the stem cell population in the shoot meristem.
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Ontology Term
PANTHER:PTHR11758 | 40S RIBOSOMAL PROTEIN S15A
 
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Ontology Term
Pfam:PF00410 | Ribosomal protein S8
Description: NULL
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Ontology Term
PANTHER:PTHR10314:SF3 | TRYPTOPHAN SYNTHASE
 
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Ontology Term
PANTHER:PTHR24325 | FAMILY NOT NAMED
 
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Ontology Term
PANTHER:PTHR31052 | COBRA-LIKE PROTEIN 7
 
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Ontology Term
Pfam:PF04833 | COBRA-like protein
Description: Family of plant proteins are designated COBRA-like (COBL) proteins. The 12 Arabidopsis members of the family are all GPI-liked [1]. Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect [3].
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Ontology Term
PANTHER:PTHR11139:SF9 | SERINE/THREONINE-PROTEIN KINASE MTOR
 
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Ontology Term
Pfam:PF11865 | Domain of unknown function (DUF3385)
Description: This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 160 to 172 amino acids in length. This domain is found associated with Pfam:PF00454, Pfam:PF02260, Pfam:PF02985, Pfam:PF02259 and Pfam:PF08771.
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Ontology Term
Pfam:PF02260 | FATC domain
Description: The FATC domain is named after FRAP, ATM, TRRAP C-terminal [1]. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability [2].
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Ontology Term
Pfam:PF08771 | FKBP12-rapamycin binding domain
Description: The macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapamycin binding domain (FRB) of the TOR proteins. This entry represents the FRB domain [1, 2].
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Ontology Term
PANTHER:PTHR31412 | ZINC METALLOPROTEASE EGY1
 
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Ontology Term
PANTHER:PTHR31412:SF0 | ZINC METALLOPROTEASE EGY1, CHLOROPLASTIC-RELATED
 
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Ontology Term
PANTHER:PTHR11700 | 30S RIBOSOMAL PROTEIN S10 FAMILY MEMBER
 
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Ontology Term
Pfam:PF00338 | Ribosomal protein S10p/S20e
Description: This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.
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Ontology Term
PANTHER:PTHR13890 | RNA SPLICING PROTEIN MRS2, MITOCHONDRIAL
 
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Ontology Term
Pfam:PF01544 | CorA-like Mg2+ transporter protein
Description: The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. The family includes the MRS2 protein Swiss:Q01926 from yeast that is thought to be an RNA splicing protein [3]. However its membership of this family suggests that its effect on splicing is due to altered magnesium levels in the cell.
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Ontology Term
PANTHER:PTHR11076 | DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER
 
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Ontology Term
PANTHER:PTHR11076:SF12 | DNA POLYMERASE KAPPA
 
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Ontology Term
Pfam:PF00817 | impB/mucB/samB family
Description: These proteins are involved in UV protection (Swiss).
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Ontology Term
PANTHER:PTHR22765 | RING FINGER AND PROTEASE ASSOCIATED DOMAIN-CONTAINING
 
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Ontology Term
Pfam:PF12662 | Complement Clr-like EGF-like
Description: cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.
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Ontology Term
PANTHER:PTHR12010 | 40S RIBOSOMAL PROTEIN S29
 
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Ontology Term
PANTHER:PTHR12010:SF2 | 40S RIBOSOMAL PROTEIN S29
 
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Ontology Term
Pfam:PF00253 | Ribosomal protein S14p/S29e
Description: This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
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Ontology Term
PANTHER:PTHR10625 | HISTONE DEACETYLASE
 
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Ontology Term
Pfam:PF02148 | Zn-finger in ubiquitin-hydrolases and other protein
Description: NULL
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Ontology Term
PANTHER:PTHR31084 | ALPHA-L-FUCOSIDASE 2
 
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Ontology Term
PANTHER:PTHR31084:SF0 | ALPHA-L-FUCOSIDASE 2
 
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Ontology Term
Pfam:PF14498 | Glycosyl hydrolase family 65, N-terminal domain
Description: This domain represents a domain found to the N-terminus of the glycosyl hydrolase 65 family catalytic domain.
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Ontology Term
PANTHER:PTHR11076:SF13 | DNA REPAIR PROTEIN REV1
 
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Ontology Term
Pfam:PF00533 | BRCA1 C Terminus (BRCT) domain
Description: The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs [2]. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilised head-to-tail BRCT-BRCT oligomerisation mode [3]. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants [5].
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Ontology Term
Pfam:PF11799 | impB/mucB/samB family C-terminal domain
Description: These proteins are involved in UV protection (Swiss).
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