SII-SWORD/CoKE huggingface dataset:
Pfam PF14783: Ciliary BBSome complex subunit 2, middle region (repeat)
The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localisation of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia.
Pfam PF15351: Junctional protein associated with coronary artery disease (disordered)
JCAD is a component of VE-cadherin-based cell-cell junctions in endothelial cells.  The cell-cell or adherens junction is an adhesion complex that plays a crucial role in the organisation and function of epithelial and endothelial cellular sheets. These junctions join the actin cytoskeleton to the plasma membrane to form adhesive contacts between cells or between cells and extracellular matrix. The junctions also mediate both cell adhesion and cell-signalling. JCAD localises close to the apical membrane in epithelial cells. This family is found in eukaryotes.
Pfam PF22536: POLR3C, C-terminal winged-helix domain (domain)
This entry represents a C-terminal WH-like domain (WH4) found in the DNA-directed RNA polymerase III subunit RPC3 (POLR3C) from humans (also known as hRPC62). POLR3C exhibits helicase activity.  Helicases are enzymes responsible for unwinding DNA or RNA helices,  facilitating essential processes such as transcription and DNA replication. RNA polymerase (pol) III is responsible for transcribing tRNAs, 5S RNA, and U6 RNA in eukaryotes. The human Pol III complex consists of a total of 17 subunits.
Pfam PF01352: KRAB box (family)
The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers.  The KRAB domain is found to be involved in protein-protein interactions.  The KRAB domain is generally encoded by two exons.  The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.
Wikipedia: The Krüppel associated box (KRAB) domain is a category of transcriptional repression domains present in approximately 400 human zinc finger protein-based transcription factors. The KRAB domain typically consists of about 75 amino acid residues, while the minimal repression module is approximately 45 amino acid residues. It is predicted to function through protein-protein interactions via two amphipathic helices. The most prominent interacting protein is called TRIM28 initially visualized as SMP1, cloned as KAP1 and TIF1-beta. Substitutions for the conserved residues abolish repression.
Pfam PF10970: Spore germination protein GerPE (family)
GerPE is required for the formation of functionally  normal spores. It could be involved in the establishment  of a normal spore coat structure and (or) permeability,  which allows the access of germinants to their receptor.
Pfam PF20334: Family of unknown function (DUF6629) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 212 and 228 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 PF12439: Glycogen debranching enzyme N terminal (family)
This domain family is found in bacteria and archaea, and is typically between 218 and 229 amino acids in length. The family is found in association with [pfam:PF06202]. Glycogen debranching enzyme catalyses the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis.
Pfam PF04223: Citrate lyase, alpha subunit (CitF) (family)
In citrate-utilising prokaryotes, citrate lyase [ec:4.1.3.6] cleaves intracellular citrate into acetate and oxaloacetate, and is organised as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit [ec:2.8.3.10].
Pfam PF13058: Protein of unknown function (DUF3920) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length.
Pfam PF16975: Ly6/PLAUR domain-containing protein 6, Lypd6 (domain)
UPAR_LY6_2 is a family of higher eukaryotic proteins expressed in neurons. It modulates nicotinic acetylcholine receptors by selectively increasing Ca2+-influx through this ion channel. The family carries an LU protein domain - about 80 amino acids long characterised by a conserved pattern of 10 cysteine residues. The family is a positive feedback regulator of Wnt/beta-catenin signalling, eg for patterning of the mesoderm and neuroectoderm in zebrafish gastrulation, where Lypd6 is GPI-anchored to the plasma-membrane and interacts with the Wnt receptor Frizzled8 and the co-receptor Lrp6.
Pfam PF25098: PEX18/PEX21 C-terminal domain (domain)
This domain is found C-terminal in Peroxisomal membrane proteins PEX18 and PEX21 from Saccharomyces cerevisiae. PEX18/PEX21 are involved in peroxisome biogenesis and import of peroxisomal matrix proteins that contain the peroxisomal targeting sequence PTS2. The crystal structure of the heterotrimeric PTS2-recognition complex from S. cerevisiae revealed the molecular mechanism of PTS2 recognition. It showed that the C-terminal domain of PEX21 directly covers the hydrophobic surfaces of both PEX7 and PTS2, and the resulting hydrophobic core is the primary determinant of the stable complex formation.
Pfam PF06341: Protein of unknown function (DUF1056) (family)
This family consists of several putative head-tail joining bacteriophage 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 PF16919: Protein kinase G rubredoxin domain (domain)
This rubredoxin domain is found at the N-terminus of protein kinase G, and is essential for kinase activity.
Pfam PF04079: Segregation and condensation complex subunit ScpB (family)
This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerises and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies.
Wikipedia: Condensins are large protein complexes that play a central role in chromosome assembly and segregation during mitosis and meiosis. Their subunits were originally identified as major components of mitotic chromosomes assembled in Xenopus egg extracts.
Pfam PF01667: Ribosomal protein S27 (family)
S27 is involved in rRNa processing, direct binding to mRNA and degradation of damaged mRNAs. S27 is a C4 zinc finger protein of the CX2CX14-16CX2C class. Zinc finger motifs in ribosomal proteins mediate protein-RNA interactions, however it has been suggested the zinc finger in S27 possibly has no functional importance for modern S27 proteins, and is rather a fossil from ancient evolution. This view is supported by the sequence alignment, showing that the zinc finger motif is not strictly conserved . A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 .
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 PF06973: Domain of unknown function (DUF1297) (domain)
This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme.
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 PF13356: Arm DNA-binding domain (domain)
This DNA-binding domain is found at the N-terminus of a wide variety of phage integrase proteins.
Pfam PF00815: Histidinol dehydrogenase (family)
Histidinol dehydrogenase (HDH) catalyses the terminal step in the biosynthesis of histidine in bacteria, fungi, and plants, the four-electron oxidation of L-histidinol to histidine.

In 4-electron dehydrogenases, a single active site catalyses 2 separate oxidation steps: oxidation of the substrate alcohol to an intermediate aldehyde; and oxidation of the aldehyde to the product acid, in this case His . The reaction proceeds via a tightly- or covalently-bound inter-mediate, and requires the presence of 2 NAD molecules . By contrast with most dehydrogenases, the substrate is bound before the NAD coenzyme . A Cys residue has been implicated in the catalytic mechanism of the second oxidative step .

In bacteria HDH is a single chain polypeptide; in fungi it is the C-terminal domain of a multifunctional enzyme which catalyses three different steps of histidine biosynthesis; and in plants it is expressed as nuclear encoded protein precursor which is exported to the chloroplast .
Wikipedia: In enzymology, histidinol dehydrogenase (HIS4) (HDH) (EC 1.1.1.23) is an enzyme that catalyzes the chemical reactionL-histidinol + 2 NAD+  L-histidine + 2 NADH + 2 H+
Pfam PF20769: YpeB N-terminal (domain)
This is the N-terminal region of YpeB, a protein restricted to endospore-forming species in the Firmicutes lineage of bacteria, that have been found in all such species to date except Clostridium perfringens. YpeB and the spore-cortex-lytic enzyme SleB are required for normal germination. This protein is essential in stabilising SleB enzyme in Bacillus spores, and may regulate its activity during germination.
Pfam PF18373: Spectrin like domain (domain)
Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. The N-terminal region of DP contains a plakin domain common to members of the plakin family. Plakin domains contain multiple copies of spectrin repeats (SRs) [pfam:PF00435]. Spectrin repeats (SRs) consist of three alpha-helices (A, B, and C) that form an antiparallel triple-helical bundle. This entry describes SR6 which has a divergent structure relative to the other SRs. SR6 shows significant deviations in helices A and B where they are significantly shorter than in other repeats. Structural comparison revealed that SR6 is more similar to other three-helix-bundle proteins, including target of Myb1 and the syntaxin Habc domain, than to other SR proteins. Due to these differences with other spectrin repeats, this region is termed spectrin-like repeat.
Pfam PF11449: Putative, 10TM heavy-metal exporter (family)
This is a family of putative manganese transporters with 9-11 TMs. Members carry two well-conserved characteristic sequence- motifs of 'PGCG'.
Pfam PF11694: Protein of unknown function (DUF3290) (family)
This family of proteins with unknown function appears to be restricted to Firmicutes.
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 PF23672: Domain of unknown function (DUF7153) (domain)
This domain is found in Caenorhabditis elegans uncharacterized protein C01C4.2 and related proteins. It is predicted to adopt an alpha+beta barrel with some similarity to the dimeric alpha+beta barrel structures, in particular REDY-like protein Hapk ([pfam:PF11639]).
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 PF07823: Cyclic phosphodiesterase-like protein (domain)
Cyclic phosphodiesterase (CPDase, [swissprot:O04147]) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft.  Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site.
Pfam PF19547: Family of unknown function (DUF6071) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family contains a  protein from the herboxidiene biosynthetic gene cluster from  Streptomyces chromofuscus.
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 PF25069: Med14 C-terminal domain (domain)
This entry represents a domain found in the human Mediator of RNA polymerase II transcription subunit 14 (Med14) and related proteins. Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents a domain located at the C terminus and predicted to adopt a globular alpha/beta structure.
Pfam PF12608: Type IVb secretion, IcmS, effector-recruitment (family)
This is a family of Gram-negative bacterial proteins involved in the Dot/Icm type IVb transport system. Members are small acidic cytoplasmic proteins required for Dot/Icm-dependent activities. Binary complexes of IcmW-IcmS and of IcmS-LvgA have been consistently reported, suggestive of the binary WXG100 system. The IcmW-IcmS complex may play a role in recruitment of effector proteins to the transport apparatus.
Wikipedia: Secretion is the movement of material from one point to another, such as a secreted chemical substance from a cell or gland. In contrast, excretion is the removal of certain substances or waste products from a cell or organism. The classical mechanism of cell secretion is via secretory portals at the plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures embedded in the cell membrane, where secretory vesicles transiently dock and fuse to release intra-vesicular contents from the cell.
Pfam PF11427: Tc3 transposase (family)
Tc3 is transposase with a specific DNA-binding domain which contains three alpha-helices, two of which form a helix-turn-helix motif which makes four base-specific contacts with the major groove. The N-terminus makes contacts with the minor groove. There is a base specific recognition between Tc3 and the transposon DNA. The DNA binding domain forms a dimer in which each monomer binds a separate transposon end. This implicates that the dimer has a role in synapsis and is necessary for the simultaneous cleavage of both transposon termini.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF10918: Protein of unknown function (DUF2718) (family)
This viral family of proteins has 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 PF24527: Nucleoporin pom152-like, ninth immunoglobulin-like domain (domain)
This domain is found in Nucleoporin pom152 from Schizosaccharomyces pombe and similar fungal proteins. Pom152 functions as a component of the nuclear pore complex (NPC). This domain is predicted to adopt an immunoglobulin-like structure.
Pfam PF16717: Ribosome-associated complex head domain (domain)
The RAC head domain is involved in ribosome binding.
Pfam PF11937: Protein of unknown function (DUF3455) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 174 to 251 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 PF14586: Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 (domain)
Members of this family are known as retinoic-acid-inducible proteins. They are ligands for the activating immunoreceptor NKG2D, which is widely expressed on natural killer cells, T cells, and macrophages.
Pfam PF22830: CATSPERB head domain (domain)
CATSPERB (Cation channel sperm-associated protein subunit beta) is an auxiliary subunit of the CatSper complex which is involved in sperm cell hyperactivation, a process needed for sperm motility which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which consists of an N-terminal domain ([pfam:PF21541]), followed by a beta-propeller ([pfam:PF21548]) that is also present in the other auxiliary subunits gamma, delta and epsilon. This entry represents the head domain, only present in the beta subunit.