SII-SWORD/CoKE huggingface dataset:
Pfam PF19439: CLEC16A C-terminal (domain)
This is the C-terminal domain of C-type lectin domain family 16, member A (CLEC16A, the Drosophila orthologue Ema and GOP-1 in C. elegans), an evolutionarily conserved endosomal membrane protein required for trafficking of fluid-phase and receptor-mediated endocytic cargos. It is required for mitophagy, autophagy and endosome maturation. This protein has been identified as a susceptibility gene for autoimmune diseases like type 1 diabetes, multiple sclerosis and adrenal dysfunction. This domain is also present in GFS9/TT9 (TRANSPARENT TESTA 9) a protein from Arabidopsis required for vacuolar development through membrane fusion at vacuoles and for membrane trafficking machinery and accumulation of flavonoids in the seed coat.
Pfam PF03705: CheR methyltransferase, all-alpha domain (domain)
CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase.
Wikipedia: In enzymology, a protein-glutamate O-methyltransferase is an enzyme that catalyzes the chemical reactionS-adenosyl-L-methionine + protein L-glutamate  S-adenosyl-L-homocysteine + protein L-glutamate methyl ester
Pfam PF16723: Domain of unknown function (DUF5065) (domain)
This family is found in found in Bacillus species. The function is not known.
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 PF07784: Protein of unknown function (DUF1622) (family)
This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species.
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 PF18882: Family of unknown function (DUF5647) (family)
This is a family of unknown function. Family members include the hypothetical protein TTHC002 from Thermus thermophilus. Its has an alpha-beta-alpha-beta(3) structure and forms a dimer with a single beta-sheet, folded in a barrel-like shape.
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 PF14963: Get2-like (family)
Calcium signal-modulating cyclophilin ligand (CAML) was originally identified in a screen for cyclophilin B-interacting proteins. It is involved in calcium signalling and in other signalling pathways as it interacts with many other signalling molecules including proto-oncogene tyrosine-protein kinase LCK, tumor necrosis factor receptor superfamily member 13B and EGFR. It also mediates the membrane insertion of tail-anchored proteins (TA), acting as a TRC40 receptor (the homologue of yeast Get3). Although CAML shows no sequence similarity to yeast Get2, they share similar biochemical properties and topology, thus resulting in the Get2 homologue in mammals, playing the same essential role in the membrane insertion as that of Get2. It also shows similarity with ER membrane protein complex subunit 6 (EMC6).
Pfam PF05588: Clostridium botulinum HA-17 domain (domain)
This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin is composed of neurotoxin (NT) and nontoxic-nonhemagglutinin (NTNHA), whereas the L toxin is composed of the M toxin and hemagglutinin (HA) subcomponents (HA-70, HA-17, and HA-33).
Pfam PF10704: Protein of unknown function (DUF2508) (family)
This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known.
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 PF14466: PLAT/LH2 and C2-like Ca2+-binding lipoprotein (domain)
A small family of bacterial proteins, found in several Bacteroides species. Structure determination (NMR and Xray) shows an immunoglobulin beta-barrel fold.  Multiple homologues have been found in human gut metagenomics data sets. Structural experimentation shows it to share features with two well-established protein architectures in the SCOP database, ie, C2 (calcium/lipid-binding domain) of the Pfam PF00168 and PLAT/LH2 (lipase/lipooxigenase domain) of the Pfam PF01477. The C2 and PLAT/LH2 domains bind Ca2+ in their functions of targeting proteins to cell-membranes; this domain is also shown to bind Ca2+ as well as to be a novel fold.
Pfam PF12738: twin BRCT domain (domain)
This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair.
Pfam PF12444: Sox developmental protein N terminal (family)
This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with [pfam:PF00505]. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.
Wikipedia: SOX genes encode a family of transcription factors that bind to the minor groove in DNA, and belong to a super-family of genes characterized by a homologous sequence called the HMG-box. This HMG box is a DNA binding domain that is highly conserved throughout eukaryotic species. Homologues have been identified in insects, nematodes, amphibians, reptiles, birds and a range of mammals. However, HMG boxes can be very diverse in nature, with only a few amino acids being conserved between species.
Pfam PF21981: RecX, third three-helix domain (domain)
This entry represents the third three-helix domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells. RecX protein is known to inhibit the activity of RecA protein in DNA recombination.
Pfam PF14894: Lsm C-terminal (domain)
This domain is found at the C-terminus of archaeal Lsm (like-Sm) proteins.
Pfam PF23557: Leprecan family TPR-like repeat region (repeat)
This entry represents the alpha-helical N-terminal alpha helical domain of members of the leprecan family. Members of this family often have an associated C-terminal enzymatic domain.  The Leprecan family proteins are involved in the hydroxylation of proline residues in collagen, an essential post-translational modification for the stability and assembly of collagen fibrils. Members of this family form complexes with other enzymes to hydroxylate lysine residues in collagen alpha chains, which is crucial for the proper assembly and cross-linking of collagen fibrils in various tissues, including skin, bone, tendon, aorta, and cornea. Some family members also exhibit growth suppressive activity and may play a role in the secretory pathway of cells. The family's enzymatic activity is particularly important for the structural integrity of type I, IV, and V collagens, contributing to normal bone density and skin stability.
Pfam PF13870: CCDC113/CCDC96, coiled-coil (coiled_coil)
This entry represents the coiled-coil region of Coiled-coil domain-containing protein 113 (CCDC113, also known as cilia- and flagella-associated protein 263, CFAP263) and coiled-coil domain-containing protein 96 (CCDC96, also known as cilia- and flagella-associated protein 184, CFAP184). These proteins form a complex and regulate ciliary beating that connects radial spoke 3 (RS3) to the inner dynein arm (IDA) and the nexin-dynein regulatory complex (N-DRC). The complex is positioned parallel to N-DRC and forms a connection between the arch at the base of RS3, the IDA tail and N-DRC.
Pfam PF13486: Reductive dehalogenase subunit (domain)
This family is most frequently associated with a Fer4 iron-sulfur cluster towards the C-terminal region.
Pfam PF19660: Family of unknown function (DUF6163) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 141 and 157 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 PF11488: Transcriptional regulatory protein LGE1 (family)
This family of proteins is conserved from fungi to human. In yeasts it is involved in the ubiquitination of histones H2A and H2B.  This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In S. cerevisiae, Rad6 and Bre1 are present in a complex, also containing Lge1, that is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters. In S. pombe the equivalent protein to Lge1 appears to be Shf1. In human,  periphilin acts a transcriptional co-repressor and regulates cell cycle progression.
Pfam PF22898: BOS complex subunit NOMO1-like, first beta sandwich domain (domain)
This domain is found at the N-terminal end of human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. NOMO1 is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. This domain is predicted to adopt a seven stranded beta sandwich fold.
Pfam PF00412: LIM domain (domain)
This family represents two copies of the LIM structural domain.
Wikipedia: LIM domains are protein structural domains, composed of two contiguous zinc fingers, separated by a two-amino acid residue hydrophobic linker. The domain name is an acronym of the three genes in which it was first identified. LIM is a protein interaction domain that is involved in binding to many structurally and functionally diverse partners. The LIM domain appeared in eukaryotes sometime prior to the most recent common ancestor of plants, fungi, amoeba and animals. In animal cells, LIM domain-containing proteins often shuttle between the cell nucleus where they can regulate gene expression, and the cytoplasm where they are usually associated with actin cytoskeletal structures involved in connecting cells together and to the surrounding matrix, such as stress fibers, focal adhesions and adherens junctions.
Pfam PF04458: Protein of unknown function (DUF505) (family)
Family of uncharacterised prokaryotic proteins.
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 PF01806: Paramyxovirinae P phosphoprotein C-terminal region (domain)
The subfamily Paramyxovirinae of the family Paramyxoviridae now contains as main genera the Rubulaviruses, avulaviruses, respiroviruses, Henipavirus-es and morbilliviruses.  Protein P is the best characterised, structurally of the replicative complex of N, P and L proteins and consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT. The P protein is an essential part of the viral RNA polymerase complex formed from the P and L proteins. P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional.The C-terminal part of P (PCT) is only functional as an oligomer and forms with L the polymerase complex. PNT is poorly conserved and unstructured in solution while PCT contains the oligomerisation domain (PMD) that folds as a homotetrameric coiled coil (40) containing the L binding region and a C-terminal partially folded domain, PX (residues 474 to 568), identified as the nucleocapsid binding site. Interestingly, PX is also expressed as an independent polypeptide in infected cells. PX has a C-subdomain (residues 516 to 568) that consists of three {alpha}-helices arranged in an antiparallel triple-helical bundle linked to an unfolded flexible N-subdomain (residues 474 to 515).
Pfam PF16836: Shu complex component Psy3, DNA-binding description (domain)
PSY3 is one of the components of the yeast Shu complex that maintains genomic stability during replication. Psy3 complexes first with Cms2, and their L2 loops confer the DNA-binding activity to the Shu complex.  The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. The heterodimer of Psy3-Csm2 stabilises the Rad51-single-stranded DNA complex independently of nucleotide cofactor because Psy3-Csm2 is a structural mimic of the Rad51-dimer.
Pfam PF20234: Family of unknown function (DUF6591) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, mainly Firmicutes and Actinobacteria, and is approximately 80 amino acids in length. It contains a highly conserved tryptophan residue and the conserved sequence YxxxxxxY.
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 PF00935: Ribosomal protein L44 (family)
A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian L44 (also known as L36A and eL42) , Trypanosoma brucei and fungal L44, Caenorhabditis elegans rpl-36.A, and Haloarcula marismortui LA .
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF16426: Domain of unknown function (DUF5023) (family)
This family consists of several uncharacterised proteins around 300 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown.
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 PF00571: CBS domain (domain)
CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet.  CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP.
Wikipedia: In molecular biology, the CBS domain is a protein domain found in a range of proteins in all species from bacteria to humans. It was first identified as a conserved sequence region in 1997 and named after cystathionine beta synthase, one of the proteins it is found in. CBS domains are also found in a wide variety of other proteins such as inosine monophosphate dehydrogenase, voltage gated chloride channels and AMP-activated protein kinase (AMPK). CBS domains regulate the activity of associated enzymatic and transporter domains in response to binding molecules with adenosyl groups such as AMP and ATP, or s-adenosylmethionine.
Pfam PF07111: Alpha helical coiled-coil rod protein (HCR) (coiled_coil)
This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation.
Pfam PF03784: Cyclotide family (domain)
This family contains a set of cyclic peptides with a variety of activities. The structure consists of a distorted triple-stranded beta-sheet and a cysteine-knot arrangement of the disulfide bonds. Cyclotides can be separated into two subfamilies, namely bracelet and moebius. The bracelet cyclotide subfamily tends to contain a larger number of positively charged residues and has a bracelet-like circularisation of the backbone. The moebius cyclotide subfamily contains a backbone twist due to a cis-Pro peptide bond and may conceptually be regarded as a molecular Moebius strip.
Wikipedia: In biochemistry, cyclotides are small, disulfide-rich peptides isolated from plants. Typically containing 28-37 amino acids, they are characterized by their head-to-tail cyclised peptide backbone and the interlocking arrangement of their three disulfide bonds. These combined features have been termed the cyclic cystine knot (CCK) motif. To date, over 100 cyclotides have been isolated and characterized from species of the families Rubiaceae, Violaceae, and Cucurbitaceae. Cyclotides have also been identified in agriculturally important families such as the Fabaceae and Poaceae.
Pfam PF07728: AAA domain (dynein-related subfamily) (domain)
This Pfam entry includes some of the AAA proteins not detected by the [pfam:PF00004] model.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF10230: Lipid-droplet associated hydrolase (family)
This family of proteins is conserved from plants to humans. The function is as a lipid-droplet hydrolase. Human LDAH plays a role in cholesterol homeostasis.
Pfam PF12972: Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain (domain)
Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. 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. The structure shows that the enzyme is composed of three domains.  This C-terminal domain has an all alpha helical fold.
Wikipedia: In molecular biology, glycoside hydrolase family 89 is a family of glycoside hydrolases.
Pfam PF01410: Fibrillar collagen C-terminal domain (family)
Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
Pfam PF02706: Chain length determinant protein (family)
This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases such as [swissprot:P38134].
Pfam PF10334: Aromatic acid exporter family member 2 (family)
This is a family of proteins conserved in fungi. The function is not known.
Pfam PF23669: DNA replication licensing factor MCM2-like, winged-helix domain (domain)
This is the winged-helix (WH) domain found at the C-terminal end of human DNA replication licensing factor MCM2 and similar eukaryotic proteins. MCM2 is a component of the MCM2-7 complex, the replicative helicase essential for DNA replication initiation and elongation in eukaryotic cells, and a core component of the CDC45-MCM-GINS (CMG) helicase, the molecular machine that unwinds template DNA during replication, and around which the replisome is built.