SII-SWORD/CoKE huggingface dataset:
Pfam PF16012: Domain of unknown function (DUF4780) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 132 and 144 amino acids in length. There is a single completely conserved residue W that may be functionally important.
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 PF12922: non-SMC mitotic condensation complex subunit 1, N-term (repeat)
The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. This is the conserved N-terminus of the subunit 1.
Pfam PF14538: Raptor N-terminal CASPase like domain (domain)
This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure. It conserves the characteristic cys/his dyad of the caspases suggesting it may have a peptidase activity.
Pfam PF08752: Coatomer gamma subunit appendage platform subdomain (domain)
COPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport.  This is the platform subdomain of the coatomer gamma subunit appendage domain.           It carries a protein-protein interaction site at UniProt:P53620, residue W776, which in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2.
Pfam PF13632: Glycosyl transferase family group 2 (domain)
Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis.
Pfam PF16195: SUMO-activating enzyme subunit 2 C-terminus (disordered)
This is the C-terminal domain found in SUMO-activating enzyme subunit 2 (Uba2) . Uba2 forms a heterodimer with Aos1 which acts as a E1 ligase for SUMO (small ubiquitin-like modifier) proteins .
Pfam PF05520: Citrus tristeza virus P18 protein (family)
This family contains the P18 proteins of citrus tristeza virus (CTV). CTV is a member of the closterovirus group and is one of the more complex single-stranded RNA viruses. Assembly of the viral genome into virions is a critical process of the virus life cycle often defining the ability of the virus to move within the plant and to be transmitted horizontally to other plants. Closteroviridae virions are polar helical rods assembled primarily by a major coat protein, but with a related minor coat protein at one end. It is the only virus family that encodes a protein with similarity to cellular chaperones, a 70kDa heat-shock protein homologue (HSP70h). Deletion mutagenesis reveals that p33, p6, p18, p13, p20, and p23 genes are not needed for virion formation. Their function is unknown .
Pfam PF10007: Uncharacterized protein conserved in archaea (DUF2250) (family)
Members of this family of hypothetical archaeal proteins have no known function.
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 PF03952: Enolase, N-terminal domain (domain)
Enolase (2-phospho-D-glycerate hydrolase) is an essential, homodimeric enzyme that catalyses the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways . The reaction is facilitated by the presence of metal ions . In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer . The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown  to be evolutionary related to enolase.

Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.
Wikipedia: Phosphopyruvate hydratase, usually known as enolase, is a metalloenzyme (EC 4.2.1.11) that catalyses the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The chemical reaction is:2-phospho-D-glycerate  phosphoenolpyruvate + H2O
Pfam PF14931: Intraflagellar transport complex B, subunit 20 (family)
IFT20 is subunit 20 of the intraflagellar transport complex B. The intraflagellar transport complex assembles and maintains eukaryotic cilia and flagella. IFT20 is localised to the Golgi complex and is anchored there by the Golgi polypeptide, GMAP210, whereas all other subunits except IFT172 localise to cilia and the peri-basal body or centrosomal region at the base of cilia.  IFT20 accompanies Golgi-derived vesicles to the point of exocytosis near the basal bodies where the other IFT polypeptides are present, and where the intact IFT particle is assembled in association with the inner surface of the cell membrane.  Passage of the IFT complex then follows, through the flagellar pore recognition site at the transition region, into the ciliary compartment.  There also appears to be a role of intraflagellar transport (IFT) polypeptides in the formation of the immune synapse in non ciliated cells. The flagellum, in addition to being a sensory and motile organelle, is also a secretory organelle. A number of IFT components are expressed in haematopoietic cells, which have no cilia, indicating an unexpected role of IFT proteins in immune synapse-assembly and intracellular membrane trafficking in T lymphocytes; this suggests that the immune synapse could represent the functional homologue of the primary cilium in these cells.
Wikipedia: Intraflagellar transport (IFT) is a bidirectional motility along axoneme microtubules that is essential for the formation (ciliogenesis) and maintenance of most eukaryotic cilia and flagella. It is thought to be required to build all cilia that assemble within a membrane projection from the cell surface. Plasmodium falciparum cilia and the sperm flagella of Drosophila are examples of cilia that assemble in the cytoplasm and do not require IFT. The process of IFT involves movement of large protein complexes called IFT particles or trains from the cell body to the ciliary tip and followed by their return to the cell body. The outward or anterograde movement is powered by kinesin-2 while the inward or retrograde movement is powered by cytoplasmic dynein 2/1b. The IFT particles are composed of about 20 proteins organized in two subcomplexes called complex A and B.
Pfam PF23751: WDR11 first beta-propeller (repeat)
This entry represents the first beta-propeller found at the N-terminal of WD repeat-containing protein 11 (WDR11) from animals and similar eukaryotic proteins. Members of this family share a domain architecture consisting of two beta-propellers followed by a TPR domain. WDR11 has been implicated in human developmental genetic disorders characterised by delayed puberty and infertility. WDR11 modulates the Hedgehog (Hh) signalling pathway and is essential for adequate ciliogenesis. The beta-propellers in WDR11 are involved in protein-protein interaction. This are essential for proper interaction with EMX1, a homeodomain transcription factor involved in the development of olfactory neurons. Impaired pubertal development is suggested to result from a deficiency of productive WDR11 protein interaction. WDR11 is also involved in vesicle traffic as it binds TBC1D23, a vesicle-golgin adaptor required for endosome-to-Golgi trafficking.
Pfam PF05892: Trichovirus coat protein (family)
This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus.
Pfam PF01969: Nickel insertion protein (family)
Members of this family may be involved in the activation of nickel-pincer cofactor-dependent enzymes. LarC from Lactobacillus plantarum is involved, together with LarB and LarE, in the synthesis of the enzyme-bound cofactor of lactate racemase (LarA). Larc C binds Ni2+, and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor.
Pfam PF02827: cAMP-dependent protein kinase inhibitor (family)
Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains.
Pfam PF23527: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AS18] from the parasite Babesia bovis.
Pfam PF14014: Protein of unknown function (DUF4230) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 228 amino acids in length.
Pfam PF08407: Chitin synthase N-terminal (family)
This is the N-terminal domain of Chitin synthase ([pfam:PF01644]).
Wikipedia: In enzymology, a chitin synthase is an enzyme that catalyzes the chemical reactionUDP-N-acetyl-D-glucosamine + [1,4-(N-acetyl-beta-D-glucosaminyl)]n  UDP + [1,4-(N-acetyl-beta-D-glucosaminyl)]n+1
Pfam PF22177: XylR N-terminal domain (domain)
This entry represents the N-terminal domain of XylR, an atypical AraC protein. This D-xylose-binding domain contains a periplasmic-binding protein (PBP) fold, similar to LacI/GalR transcription regulators, and mediates dimerization.
Pfam PF18810: phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2 (domain)
A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages. The predicted active site contains a conserved arginine and threonine residues.
Pfam PF08818: Domain of unknown function (DU1801) (domain)
This domain is found in the Intracellular iron chaperone frataxin YdhG and the uncharacterised protein YdeI from Bacillus subtilis.
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 PF08048: Tap RepA1 leader peptide (family)
This family consists of the RepA1 leader peptides.  The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid. The tap gene encodes a 24-amino acids protein. The translation of tap is required for translation of repA.
Pfam PF18567: Toll/interleukin-1 receptor domain (domain)
This is a Toll/interleukin-1 receptor (TIR) domain found in the N-terminal region of B-cell adaptor for phosphoinositide 3-kinase (BCAP). BCAP functions in linking the B-cell receptor (BCR) and the co-receptor CD19 to the activation of PI3K via interaction with the SH2 domains on the regulatory p85 subunit. BCAP TIR associates with the MAL/TIRAP adaptor and the TIR domains of Toll-like receptors (TLRs).
Wikipedia: The toll-interleukin-1 receptor (TIR) homology domain is an intracellular signaling domain found in MyD88, SARM1, interleukin-1 receptors, toll receptors and many plant R proteins. It contains three highly conserved regions, and mediates protein-protein interactions between the toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins where they are involved in resistance to disease and in bacteria where they are associated with virulence. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 (UniProt Q99836) and TOLLIP (toll-interacting protein, UniProt Q9H0E2). In turn, these associate with various kinases to set off signaling cascades. Some TIR domains have also been found to have intrinsic NAD+ cleavage activity, such as in SARM1. In the case of SARM1, the TIR NADase activity leads to the production of Nam, ADPR and cADPR and the activation of downstream pathways involved in Wallerian degeneration and neuron death.
Pfam PF17820: PDZ domain (domain)
This entry represents the PDZ domain from a wide variety of proteins.
Pfam PF00795: Carbon-nitrogen hydrolase (family)
This family contains hydrolases that break carbon-nitrogen bonds.  The family includes: Nitrilase [ec:3.5.5.1] [swissprot:Q42965], Aliphatic amidase [ec:3.5.1.4] [swissprot:Q01360], Biotidinase [ec:3.5.1.12] [swissprot:P43251], Beta-ureidopropionase [ec:3.5.1.6] [swissprot:Q03248].  Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins.
Pfam PF04218: CENP-B N-terminal DNA-binding domain (domain)
Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Pfam PF07277: SapC (family)
This family contains a number of bacterial SapC proteins approximately 250 residues long. In Campylobacter fetus, SapC forms part of a paracrystalline surface layer (S-layer) that confers serum resistance.
Pfam PF02208: Sorbin homologous domain (family)
Sorbin is an active peptide present in the digestive tract, where it has pro-absorptive and anti-secretory effects in different parts of the intestine, including the ability to decrease VIP (vasoactive intestinal peptide) and cholera toxin-induced secretion. It is expressed in some intestinal and pancreatic endocrine tumours in humans .

Sorbin-homology (SoHo) domains are found in adaptor proteins such as vinexin, CAP/ponsin and argBP2, which regulate various cellular functions, including cell adhesion, cytoskeletal organisation, and growth factor signalling . In addition to the sorbin domain, these proteins contain three SH3 (src homology 3) domains. The sorbin homology domain mediates the interaction of vinexin and CAP with flotillin, which is crucial for the localisation of SH3-binding proteins to the lipid raft, a region of the plasma membrane rich in cholesterol and sphingolipids that acts to concentrate certain signalling molecules. The sorbin homology domain of adaptor proteins may mediate interactions with the lipid raft that are crucial to intracellular communication .
Human sorbin is generated via splicing of an alternative transcript from the ArgBP2 gene locus .
Pfam PF13924: Lipocalin-like domain (domain)
This family includes domains distantly related to lipocalins. However, they do contain the important GXW motif in the first strand. The protein in this family include aln5 [swissprot:B6SEG2] which is involved in biosynthesis of alnumycin. The family also includes the ZFK protein from Trypanosoma brucei which is a protein kinase. This domain is at the C-terminus of that protein. The domain is also found as the C-terminal domain in StiJ a protein involved in producing stigmatellin. This domain has been assumed to catalyse a final cyclisation reaction.
Pfam PF15097: Immunoglobulin J chain (family)
Immunoglobulin J serves to link two monomer units of either IgM or IgA. In the case of IgM, the J chain-joined dimer is a nucleating unit for the IgM pentamer, and in the case of IgA it induces larger polymers. It also help to bind these immunoglobulins to the secretory component .
Wikipedia: The Joining (J) chain is a protein component that links monomers of antibodies IgM and IgA to form polymeric antibodies capable of secretion. The J chain is well conserved in the animal kingdom, but its specific functions are yet to be fully understood. It is a 137 residue polypeptide, encoded by the IGJ gene.
Pfam PF22304: Adenylosuccinate Lyase, C-terminal domain (domain)
This entry represents a C-terminal helical domain present in the adenylosuccinate lyase from Pyrobaculum aerophilum. This domain is remotely related to [pfam:PF10397] (Adenylosuccinate lyase C-terminus).
Pfam PF02426: Muconolactone delta-isomerase (domain)
This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway [ec:5.3.3.4]. The protein has a ferredoxin-like fold according to SCOP.
Pfam PF00426: Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain (domain)
This entry represents the N-terminal concanavalin-like domain from the VP4 protein of rotavirus.
Pfam PF06900: Protein of unknown function (DUF1270) (family)
This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. 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 PF06769: YoeB-like toxin of bacterial type II toxin-antitoxin system (domain)
YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in [pfam:PF02604].  The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as an antitoxin-toxin pair. When the plasmid is lost, the antitoxin is degraded relatively quickly by host enzymes. This allows the toxin to interact with its intracellular target, thus killing the cell or impeding cell growth. These toxins are highly potent protein synthesis inhibitors, specifically blocking the initiation of translation. In the case of YoeB, it binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA is released from ribosomes, and translation initiation is effectively inhibited.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF20617: Family of unknown function (DUF6803) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 162 and 222 amino acids in length. Structurally, proteins in this family are made of a Four Helix Bundle.
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 PF20952: Influenza RNA polymerase PB2 C-terminal domain (domain)
Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. This entry represents the C-terminal domain of Flu PB2 protein.
Pfam PF00610: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) (domain)
The DEP domain is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit.
Wikipedia: In molecular biology, the DEP domain is a globular protein domain of about 80 amino acids that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in:Dishevelled, which plays a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarised cells and segments in embryos, and plays a role in wingless signalling.
Egl-10, which regulates G-protein signalling in the central nervous system in RGS9.Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain.
Pfam PF20380: Family of unknown function (DUF6675) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 242 and 267 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.