SII-SWORD/CoKE huggingface dataset:
Pfam PF10278: Mediator of RNA pol II transcription subunit 19 (family)
Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF08219: Outer membrane protein TOM13 (domain)
The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins.
Pfam PF13737: Transposase DDE domain (domain)
Transposase proteins are necessary for efficient DNA transposition.  This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis.
Pfam PF13690: Chemotaxis phosphatase CheX (domain)
CheX is very closely related to the CheC chemotaxis phosphatase, but it dimerises in a different way, via a continuous beta sheet between the subunits. CheC and CheX both dephosphorylate CheY, although CheC requires binding of CheD to achieve the activity of CheX. The ability of bacteria to modulate their swimming behaviour in the presence of external chemicals (nutrients and repellents) is one of the most rudimentary behavioural responses known, but the the individual components are very sensitively tuned.
Pfam PF13438: Domain of unknown function (DUF4113) (domain)
Although the function is not known this domain occurs almost invariably at the very C-terminus of the IMS family DNA-polymerase repair proteins, IMS, [pfam:PF00817].
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 PF11086: Protein of unknown function (DUF2878) (family)
This bacterial family of proteins has no known function. Some members annotate the proteins as the permease component of a Mn2+/Zn2+ transport system however this cannot be confirmed.
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 PF14551: MCM N-terminal domain (domain)
This family contains the N-terminal domain of MCM proteins.
Pfam PF08434: Calcium-activated chloride channel N terminal (family)
The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions.  Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. This protein cleaves itself into an N-terminal portion and a C-terminal portion. The N-terminus contains an HEXXHXXXGXXDE motif which is essential for proteolytic cleavage.
Wikipedia: Chloride channels are a superfamily of poorly understood ion channels specific for chloride. These channels may conduct many different ions, but are named for chloride because its concentration in vivo is much higher than other anions. Several families of voltage-gated channels and ligand-gated channels have been characterized in humans.
Pfam PF19219: Coronavirus replicase NSP15, N-terminal oligomerisation (domain)
This is the N-terminal domain of the coronavirus nonstructural protein 15 (NSP15), which is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. NSP15, is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) carrying C-terminal catalytic domain belonging to the EndoU family. The SARS-CoV-2 NendoU monomers assemble into a double-ring hexamer, generated by a dimer of trimers. The hexamer is stabilized by the interactions of N-terminal oligomerization domain.
Pfam PF04799: fzo-like conserved region (family)
Family of putative transmembrane GTPase.  The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the  human mitofusin protein.
Pfam PF00418: Tau and MAP protein, tubulin-binding repeat (family)
This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilise microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau ([swissprot:P10636]) is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif.
Pfam PF15050: SCIMP protein (family)
This family contains the SCIMP proteins which are a a transmembrane adaptor protein involved in major histocompatibility complex class II signaling.
Pfam PF23269: Domain of unknown function (DUF7074) (domain)
This domain is found in a group of uncharacterised plant proteins. It is predicted to adopt a globular structure with a Cystatin-like topology consisting of a curved four-stranded beta-sheet and an alpha-helix packed on the concave side of it.
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 PF19163: Family of unknown function (DUF5845) (family)
This is a family of uncharacterised proteins of unknown function found in 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 PF20756: Alpha-amylase SusG, CBM58 domain (domain)
Enzymes of the Glycoside hydrolase family 13 typically show three domains A, B and C. In addition to these, Alpha-amylase SusG from Bacteroides thetaiotaomicron ([swissprot:Q8A1G3]) includes the insertion of a unique carbohydrate binding module (CBM) family 58 (this entry), which gives the protein an elongated shape. SusG, located on the outer membrane of the cell, cleaves starch into oligosaccharides before internalisation for degradation. CBM58 is approximately 120 residues in length. This domain folds into a beta sandwich and adopts an immunoglobulin-like topology with a flat five-stranded antiparallel beta sheet opposing a four-stranded antiparallel beta sheet which features three protruding loops. Y260, W287, and W299 form the starch-binding site.
Pfam PF12315: Protein DA1 (family)
Proteins in this family include protein DA1 and its homologues. In Arabidopsis thaliana, DA1 is an ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. It may act maternally to control seed mass.
Pfam PF12973: ChrR Cupin-like domain (domain)
Members of this family are part of the cupin superfamily. This family includes the transcriptional activator ChrR [swissprot:P40685].
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF21064: Reovirus core-spike protein lambda-2 (L2), N-terminal (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the N-terminal domain which adopts an alpha/beta topology.
Pfam PF04738: Lantibiotic dehydratase, N terminus (family)
Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides.  They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin.  Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues.  This family constitutes the N-terminus of the enzyme proposed to catalyse the dehydration step, via glutamylation of the substrate during lantibiotic biosynthesis. The enzyme dehydrates Ser/Thr residues in the precursor by glutamylation.
Pfam PF21063: Reovirus core-spike protein lambda-2 (L2), GTase domain (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second one, which contains the nucleotide-binding histidine triad (HIT)-like motif from the GTase (guanylyltransferase) domain.
Pfam PF24223: Fimbrial adhesin MrpH C-terminal domain (domain)
This entry represents the C-terminal domain of fimbrial adhesin MrpH from bacteria. This protein is associated to strain virulence and is involved in surface adherence, biofilm formation and autoaggregation, essential for bladder and kidney colonization. This domain attaches to bacterial fimbrial tip.
Pfam PF00816: H-NS histone C-terminal domain (domain)
This entry represents the C-terminal DNA binding domain of H-NS histone protein.
Wikipedia: Histone-like nucleoid-structuring protein (H-NS), is one of twelve nucleoid-associated proteins (NAPs) whose main function is the organization of genetic material, including the regulation of gene expression via xenogeneic silencing. H-NS is characterized by an N-terminal domain (NTD) consisting of two dimerization sites, a linker region that is unstructured and a C-terminal domain (CTD) that is responsible for DNA-binding. Though it is a small protein, it provides essential nucleoid compaction and regulation of genes and is highly expressed, functioning as a dimer or multimer. Change in temperature causes H-NS to be dissociated from the DNA duplex, allowing for transcription by RNA polymerase, and in specific regions lead to pathogenic cascades in enterobacteria such as Escherichia coli and the four Shigella species.
Pfam PF21201: Tertiapin (family)
THis is tertiapin, a honeybee peptide identified as a presynaptic neurotoxin that blocks the inwardly rectifying Kir1.1/KCNJ1 and Kir3.1/3.4 (KCNJ3/KCNJ5) potassium channels with high affinity. It can prevent dose-dependently acetylcholine(ACh)-induced atrioventricular blocks in mammalian hearts, as KCNJ3/KCNJ5 channels (also named I(KACh), because these channels are activated by ACh) are found in mammalian myocytes. Interacts specifically with calmodulin in the presence of calcium
Pfam PF18175: CCDC81-like prokaryotic HU domain 2 (domain)
Second of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope.
Pfam PF06046: Exocyst complex component Sec6 (repeat)
Sec6 is a component of the multiprotein exocyst complex.  Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner.
Pfam PF24798: CFAP74 forth Ig-like domain (domain)
This entry represents the forth Ig-like domain of CFAP74, a protein that is part of the central apparatus of the cilium axoneme and may play a role in cilium movement. It may play an important role in sperm architecture and function.
Pfam PF19803: Family of unknown function (DUF6286) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 181 and 228 amino acids in length. There is a conserved GV motif.
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 PF01366: Herpesvirus processing and transport protein (family)
The members of this family are associate with capsid intermediates during packaging of the virus.
Pfam PF04765: TOD1/MUCI70, glycosyltransferase-like domain (domain)
This entry represents a glycosyltransferase-like domain found in alkaline ceramidase TOD1 and the probable hexosyltransferase MUCI70 from Arabidopsis. MUCI70 is a predicted glycosyltransferase essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched rhamnogalacturonan I (RG I), and for shaping the surface morphology of seeds. TOD1 is an  endoplasmic reticulum ceramidase that catalyses the hydrolysis of ceramides into sphingosine and free fatty acids at alkaline pH (e.g. pH 9.5).
Pfam PF25090: Domain of unknown function (DUF7805) (domain)
This domain is found in a group of uncharacterised proteins from animals. Many proteins in this group also contain [pfam:PF00057].
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 PF15570: Immunity protein 43 (family)
A predicted immunity protein with an alpha+beta fold with conserved tryptophan, proline, aspartate, serine and arginine residues.  Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-AHH family of HNH/Endonuclease VII fold nucleases. The gene for this toxin is also found in heterogeneous poly-immunity loci.
Pfam PF20449: Family of unknown function (DUF6706) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 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 PF04017: Domain of unknown function (DUF366) (family)
Archaeal domain of unknown 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 PF10116: Protein required for attachment to host cells (family)
Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells. Furthermore, it has been reported that this family includes bacterial family of the archaeo-eukaryotic release factor superfamily, lacks fusions to N-terminal codon recognition domain and C-terminal Pelota domain. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pfam PF03981: Ubiquinol-cytochrome C chaperone (family)
Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone (CBP3) is required for assembly of coenzyme QF-2-cytochrome C reductase. This protein is organised into two domains: a variable N-terminal domain of unknown function present in mitochondrial Cbp3 homologues and a conserved C-terminal ubiquinol-cytochrome c chaperone domain (this entry). The crystal structure of this domain has been resolved in the homologue from the bacteria Brucella abortus, showing an all-helical fold . This domain is also found other proteins mainly from eukaryotes and Proteobacteria.

In vertebrates, CBP3 homologs are known as Ubiquinol-cytochrome c reductase complex assembly factors 1 (Uqcc1)

Some members of this group are annotated as part of the UPF0174 family.
Pfam PF22152: Permutotetravirus RNA-dependent RNA polymerase palm domain (domain)
This entry represents the palm domain of RdRp from Permutotetravirus, such as Thosea asigna virus (TaV) which is an insect virus that has a positive-sense ssRNA genome encoding a replicase and capsid proteins. The replicase has a non-canonical arrangement in the palm sub-domain of the RNA-dependent RNA polymerase (RdRP), with a sequence permutation where the active site is anchored that is also found in Birnaviridae.
Pfam PF09317: Acyl-CoA dehydrogenase, C-terminal, bacterial type (domain)
This C-terminal domain is functionally uncharacterised and is predominantly found in various prokaryotic acyl-coenzyme A dehydrogenases and seems to be essential for its function.
Pfam PF01186: Lysyl oxidase (family)
Lysyl oxidase (1.4.3.13) (LOX)  is an extracellular copper-dependent enzyme that catalyses the oxidative deamination of peptidyl lysine residues in precursors of various collagens and elastins, yielding alpha-aminoadipic-delta-semialdehyde. The deaminated lysines are then able to form semialdehyde cross-links, resulting in the formation of insoluble collagen and elastin fibres in the extracellular matrix .

The active site of LOX resides towards the C terminus: this region also binds a single copper atom in an octahedral coordination complex involving at least 3 His residues . Four histidine residues are clustered in a central region of the enzyme. This region is thought to be involved in cooper-binding and is called the 'copper-talon' .
Pfam PF17476: Clostridial binary toxin B/anthrax toxin PA domain 3 (domain)
This entry represents the beta-grasp domain in anthrax protective antigen.
Wikipedia: The AB toxins are two-component protein complexes secreted by a number of pathogenic bacteria, though there is a pore-forming AB toxin found in the eggs of a snail. They can be classified as Type III toxins because they interfere with internal cell function. They are named AB toxins due to their components: the "A" component is usually the "active" portion, and the "B" component is usually the "binding" portion. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit. T
Pfam PF12833: Helix-turn-helix domain (domain)
Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins  is related to the arabinose operon regulatory protein AraC [cite:PUB00004444], [cite:PUB00003566]. Except for celD , all of these proteins seem to be positive transcriptional factors.

Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerisation .

The known structure of MarA (P27246) shows that the AraC domain is Î± helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.

This entry representsthe full AraC domain containing the two HTH subdomains.
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 PF17098: WTAP/Mum2p family (family)
The Wtap family includes female-lethal(2)D from Drosophila and pre-mRNA-splicing regulator WTAP from mammals. The former is required for female-specific splicing of Sex-lethal RNA, and the latter is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. The family also includes the yeast Mum2p protein which is part of the Mis complex.
Pfam PF10795: Protein of unknown function (DUF2607) (family)
This family is conserved in Gammaproteobacteria. 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 PF20384: Family of unknown function (DUF6679) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved DQQRWIE sequence motif.
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.