SII-SWORD/CoKE huggingface dataset:
Pfam PF18271: Glycoside hydrolase 131 catalytic N-terminal domain (domain)
This is the N-terminal domain found in glycoside hydrolase family 131 (GH131A) protein observed in Coprinopsis cinerea. GH131A exhibits bifunctional exo-beta-1,3-/-1,6- and endo-beta-1,4 activity toward beta-glucan. This domain is catalytic in nature though the catalytic mechanism of C. cinerea GH131A is different from that of typical glycosidases that use a pair of carboxylic acid residues as the catalytic residues. In the case of GH131A, Glu98 and His218 may form a catalytic dyad and Glu98 may activate His218 during catalysis.
Pfam PF11640: Telomere-length maintenance and DNA damage repair (domain)
ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage. It is classified as an [ec:2.7.11.1].
Pfam PF15222: Kidney androgen-regulated (family)
The function of this family is unknown.
Pfam PF03059: Nicotianamine synthase protein (family)
Nicotianamine synthase [ec:2.5.1.43] catalyses the trimerisation of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms.  Plants adopt two strategies (termed I and II) of iron acquisition.  Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold.
Pfam PF18102: Deltex C-terminal domain (domain)
This is the C-terminal domains found in members of the Deltex family of proteins which comprises five members (DTX1, 2, 3, 4, and 3L). This conserved C-terminal region of about 150 residues of the Deltex family, is preceded by a RING E3 ligase domain in four of the members. Crystal structure of the Deltex C-terminal (DTC) domain reveals a fold composed of a central beta-sheet lined with two long parallel alpha-helices.
Pfam PF11165: Protein of unknown function (DUF2949) (family)
This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24998: Domain of unknown function (DUF7778) (domain)
This domain is found in uncharacterised worm proteins. It has a detectable similarity to known PH domains and it is predicted to adopt similar structure.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12687: Protein of unknown function (DUF3801) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 158 and 187 amino acids in length. This family includes the PcfB protein.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12328: Rpp20 subunit of nuclear RNase MRP and P (family)
The nuclear RNase P of Saccharomyces cerevisiae is made up of at least nine protein subunits; Pop1, Pop3, Pop4, Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these subunits seem to be present also in the RNase MRP, with the exception of Rpr2 (Rpp21) which is unique to RNase P. Human nuclear RNase P and MRP appear to contain at least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although there is recent evidence that not all of these subunits are shared between P and MRP. Archaeal RNase P has at least four protein subunits homologous to eukaryotic RNase P/MRP proteins. In the yeast RNase P, Pop6 and Pop7 (the Rpp20 homologue) interact with each other and they are both interaction partners of Pop4; in the human MRP Rpp25 and Rpp20 interact with each other and Rpp25 binds to Rpp29 (Pop4).
Pfam PF16041: E3 ubiquitin-protein ligase APD1-4, middle domain (domain)
This entry includes E3 ubiquitin-protein ligase APD1 to 4 from Arabidopsis. They are involved in pollen mitosis II (PMII) regulation during male gametogenesis. This entry represents a functionally uncharacterised domain found in the middle of APD1-4 and in uncharacterised sequences mainly from arthropods. There are two completely conserved C residues that may be functionally important.
Pfam PF10354: rRNA (uridine-N3-)-methyltransferase BTM5-like (domain)
This is the N-terminal domain found in proteins from plants, yeast and humans, including 25S rRNA (uridine-N(3))-methyltransferase BMT5 from S. cerevisiae and the poorly characterised Ferredoxin-fold anticodon-binding domain-containing protein 1 from human and Heavy metal-associated isoprenylated plant protein 41 from Arabidopsis. This domain has a characteristic Rossmann-like fold of S-adenosyl-L-methionine (SAM) binding domains. BTM5 is a SAM-dependent methyltransferase that specifically methylates the N3 position of uridine in 25S rRNA.
Pfam PF08298: PrkA AAA domain (domain)
This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Pfam PF19712: Acylglycerol kinase C-terminal (domain)
This domain corresponds to the C-terminal of mitochondrial Acylglycerol kinase (AGK, also known as MuLK). AGK is a metazoan-specific protein integrated into the mitochondrial inner membrane through a short N-terminal transmembrane domain. This large C-terminal domain is adjacent the kinase domain and it is oriented to the intermembrane space. AGK is a subunit of the human TIM22 complex which stabilises the complex and regulates the import and assembly of mitochondrial carrier proteins, a function independent of its kinase activity. Disturbances in both functions of AGK (phospholipid metabolism and mitochondrial protein biogenesis) contribute to the pathogenesis of Sengers syndrome.
Pfam PF13894: C2H2-type zinc finger (domain)
This family contains a number of divergent C2H2 type zinc fingers.
Pfam PF05026: Dcp2, box A domain (domain)
This domain is always found to the amino terminal side of [pfam:PF00293].  This domain is specific to mRNA decapping protein 2 and this region has been termed Box A.  Removal of the cap structure is catalysed by the Dcp1-Dcp2 complex.
Pfam PF22748: Effector PexRD54, WY-domain (domain)
This entry represents homologous WY domains of the RxLR effector PexRD54 and other related proteins. The WY domain is a conserved structural unit consisting of three alpha-helices and two characteristic hydrophobic amino acids, frequently W (Trp) and Y (Tyr), which contribute to a stable hydrophobic core.
Pfam PF19581: Glyoxalase superfamily protein (domain)
Bleomycin (Blm) is a glycopeptide antibiotic produced naturally by actinomycetes. It is a strong DNA-cutting agent and thus finds use as a potent anti-cancer drug. The DNA-cutting mechanism is complex, involving concomitant oxidation of FeII and reduction of oxygen. In addition to iron, Blm binds other transition metals: cobalt, nickel, copper and zinc. Actinomycetes have developed a defence mechanism against this lethal compound, producing a protein that confers resistance to Blm through drug sequestering. The crystal structure of the bleomycin resistance protein reveals 2 identically-folded halves, each having an Î±/Î² fold but showing no sequence similarity . Each half comprises a 4-stranded Î²-sheet and a short Î±-helix (3 turns). The sheets within each half lie roughly at right-angles and are related by an approximate 2-fold axis. The crystal packing shows compact dimers that have a hydrophobic interface and are involved in mutual chain exchange.
Pfam PF10960: BhlA holin family (family)
The Phage_holin_BhlA family is a family of holin-like proteins from both bacteriophages and bacterial chromosomes. In bacteriophage, holins are small membrane proteins that accumulate and oligomerise to form non-specific lesions in the cytoplasmic membrane allowing the release of the second protein, endolysins, to access the peptidoglycan. Most holins share common structural features: two or three transmembrane domains separated by a beta-turn, a short hydrophilic N-terminus, a highly charged C-terminus and a dual translational start motif. The BhlA holin of Bacillus is found to be toxic to the host cell where the site of action of is on the cell membrane and causes bacterial death by cell membrane disruption.
Pfam PF03861: ANTAR domain (domain)
ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the  domain consists of a coiled-coil.
Pfam PF18248: RalF C-terminal Sec-7 capping domain (domain)
This is the C-terminal domain of RalF protein present in Legionella pneumophilia. RalF is secreted into host cytosol via the Dot/Icm type IV transporter where it acts to recruit ADP-ribosylation factor (Arf) to pathogen-containing phagosomes in the establishment of a replicative organelle. This domain forms a cap over the active site in the Sec7 domain and so is referred to as the Sec7-capping domain.
Pfam PF08978: Reoviridae VP9 (domain)
This domain is found in various VP9 viral outer-coat proteins. It has no known function.
Pfam PF16578: Interleukin 17 receptor D (domain)
IL17R_fnIII_D2 is the second extracellular fibronectin III-like domain on interleukin17-receptor-D molecules. The exact ligands of IL17R-D are not known.
Pfam PF02352: Decorin binding protein (family)
This family consists of decorin binding proteins from Borrelia. The decorin binding protein of Borrelia  burgdorferi the lyme disease spirochetes adheres to the  proteoglycan decorin found on collagen fibres.
Pfam PF24719: Imm33-like domain (domain)
This entry represents a family of bacterial proteins that are structurally related to the Imm33 family of putative immunity proteins.
Pfam PF14081: Domain of unknown function (DUF4262) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 147 and 227 amino acids in length. [swissprot:Q50763] is incorrectly annotated as the KatG protein.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF03638: Tesmin/TSO1-like CXC domain, cysteine-rich domain (domain)
This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin [swissprot:Q9Y4I5] and TSO1 [swissprot:Q9LE32]. This family is called a CXC domain in.
Pfam PF00066: LNR domain (domain)
The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion.  Three repeats are also found in the PAPP-A peptidase.
Wikipedia: Notch proteins are a family of type 1 transmembrane proteins that form a core component of the Notch signaling pathway, which is highly conserved in animals. The Notch extracellular domain mediates interactions with DSL family ligands, allowing it to participate in juxtacrine signaling. The Notch intracellular domain acts as a transcriptional activator when in complex with CSL family transcription factors. Members of this type 1 transmembrane protein family share several core structures, including an extracellular domain consisting of multiple epidermal growth factor (EGF)-like repeats and an intracellular domain transcriptional activation domain (TAD). Notch family members operate in a variety of different tissues and play a role in a variety of developmental processes by controlling cell fate decisions. Much of what is known about Notch function comes from studies done in Caenorhabditis elegans (C.elegans) and Drosophila melanogaster. Human homologs have also been identified, but details of Notch function and interactions with its ligands are not well known in this context.
Pfam PF19420: N,N dimethylarginine dimethylhydrolase, eukaryotic (family)
This family contains N(G),N(G)-dimethylarginine dimethylaminohydrolases (DDAH) from eukaryotes. It also includes arginine deiminases and DDAH from prokaryotes. These enzymes are involved in arginine metabolism and belong to the amidinotransferase (AT) superfamily as they share the alpha/beta propeller fold, which includes structurally important residues (buried hydrophobic residues, buried hydrophilic residues hydrogen-bonded with mainchain groups and the hallmark of three consecutive buried Gly residues near the C-terminus, conserved among its members.
Pfam PF03264: NapC/NirT cytochrome c family, N-terminal region (family)
Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC [swissprot:P33932] and NirT [swissprot:P24038], bind four haem groups, while others, such as TorC [swissprot:P33226], bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs.
Wikipedia: Cytochrome c nitrite reductase (ccNiR) is a bacterial enzyme that catalyzes the six electron reduction of nitrite to ammonia; an important step in the biological nitrogen cycle. The enzyme catalyses the second step in the two step conversion of nitrate to ammonia, which allows certain bacteria to use nitrite as a terminal electron acceptor, rather than oxygen, during anaerobic conditions. During this process, ccNiR draws electrons from the quinol pool, which are ultimately provided by a dehydrogenase such as formate dehydrogenase or hydrogenase. These dehydrogenases are responsible for generating a proton motive force.
Pfam PF17906: HTH domain in Mos1 transposase (domain)
The N-terminal domain of the Mos1 Mariner transposase comprises two HTH domains. This HTH domain binds in the DNA major groove to the transposons inverted repeats.
Wikipedia: Tc1/mariner is a class and superfamily of interspersed repeats DNA transposons. The elements of this class are found in all animals, including humans. They can also be found in protists and bacteria.
Pfam PF20346: Family of unknown function (DUF6641) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19141: Family of unknown function (DUF5824) (family)
This family contains a domain of unknown function,  which is predominantly found in Phycodnaviridae and Caudovirale viruses.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13385: Concanavalin A-like lectin/glucanases superfamily (domain)
This domain belongs to the Concanavalin A-like lectin/glucanases superfamily.
Pfam PF05204: Homing endonuclease (domain)
Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life.
Wikipedia: The homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them, but do so at very few, or even singular, locations. Repair of the hydrolyzed DNA by the host cell frequently results in the gene encoding the homing endonuclease having been copied into the cleavage site, hence the term 'homing' to describe the movement of these genes. Homing endonucleases can thereby transmit their genes horizontally within a host population, increasing their allele frequency at greater than Mendelian rates.
Pfam PF12053: N-terminal of Par3 and HAL proteins (family)
This domain is about 150 amino acids in length found associated with [pfam:PF00595] in eukaryotes. It has a conserved GILD sequence motif.  Family members have been found to be essential for cell polarity establishment and maintenance such as Par3 (partitioning defective) [swissprot:Q8TEW0] and involved in conversion of histidine into ammonia (a crucial step for forming histamine in humans) such as Histidine ammonia lyase (HAL) [swissprot:P42357]. This N-terminal domain is found to mediate oligomerization critical for the membrane localization of Par-3. It is also found to possess a self-association capacity via a front-to-back mode in Par-3 and HAL proteins. However, unlike the Par-3 N-terminal domain which self-assembles into a left-handed helical filament, the HAL N-terminal domain does not tend to form a helical filament but rather self-assembles into circular oligomeric particles. This has been suggested to be likely due to the absence of equivalent charged residues that are essential for the longitudinal packing of the Par-3 N-terminal domain filament.
Pfam PF20704: NucS shadow ORF (family)
This entry represents a shadow ORF found on the opposite strand to Endonuclease NucS. Unlike most shadow ORFs this appears to be a genuine protein coding gene. A structural model suggests the protein has some similarity to the KH domain suggesting it may be an RNA-binding protein of unknown function. This family was formerly in the AntiFam database with accession ANF00096.
Pfam PF08137: DVL family (family)
This family consists of the DVL family of proteins.  In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, DEVIL (DVL) gene was identified. DVL is a small protein and overexpression of the protein results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development.
Pfam PF14835: zf-RING of BARD1-type protein (domain)
The RING domain of the breast and ovarian cancer tumour-suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. A dimer is formed between the RING domains of BRCA1 and BARD1. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level. The corresponding BRCA1-RING domain is on family zf-C3HC4_2, [pfam:PF13923].
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF23042: Transcription elongation factor SPT5, KOW1 domain (domain)
This domain is found in human Transcription elongation factor SPT5 and related proteins from eukaryotes. SPT5 is a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain, a tandem of KOW domains and and a mobile C-terminal-repeat region. This entry represents the KOW1 domain that is located between the N-terminal NusG domain and KOW2. In the RNA polymerase II (Pol II)-DSIF elongation complex, KOW1 and NGN-SPT4 domains together form a 'DNA clamp'. In the Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex, the rewrapped DNA displaces SPT4 and the SPT5 NGN and KOW1 domains of DSIF from their previously observed binding positions on Pol II.