SII-SWORD/CoKE huggingface dataset:
Pfam PF17692: Family of unknown function (DUF5538) (family)
This is a family of unknown function found in primates.
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 PF08488: Wall-associated kinase (family)
This domain is found together with the eukaryotic protein kinase domain [pfam:PF00069] in plant wall-associated kinases (WAKs) and related proteins. WAKs are serine-threonine kinases which might be involved in signalling to the cytoplasm and are required for cell expansion.
Wikipedia: Wall-associated kinases (WAKs) are one of many classes of plant proteins known to serve as a medium between the extracellular matrix (ECM) and cytoplasm of cell walls. They are serine-threonine kinases that contain epidermal growth factor (EGF) repeats, a cytoplasmic kinase and are located in the cell walls. They provide a linkage between the inner and outer surroundings of cell walls. WAKs are under a group of receptor-like kinases (RLK) that are actively involved in sensory and signal transduction pathways especially in response to foreign attacks by pathogens and in cell development. On the other hand, pectins are an abundant group of complex carbohydrates present in the primary cell wall that play roles in cell growth and development, protection, plant structure and water holding capacity.
Pfam PF01092: Ribosomal protein S6e (family)
A number of eukaryotic and archaeal ribosomal proteins have been grouped on the basis of sequence similarities. Small ribosomal subunit protein eS6, previously known as Ribosomal protein S6 is the major substrate of protein kinases in eukaryotic ribosomes  and may play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.
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 PF14191: YodL-like (family)
The YodL-like protein family includes the B. subtilis YodL protein [swissprot:O30472], which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 100 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important.
Pfam PF06157: Protein of unknown function (DUF973) (family)
This family consists of several hypothetical archaeal proteins 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 PF06977: SdiA-regulated (repeat)
This family represents a conserved region approximately within a number of hypothetical bacterial proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. Some family members contain the [pfam:PF01436] repeat.
Pfam PF21623: Bacterial histidine kinase, sensor domain (domain)
This sensor domain is found in Histidine kinase from Vibrio parahaemolyticus. This domain shows an alpha-beta structure that folds into a double-PDC. It is found associated with [pfam:PF13426] and [pfam:PF00990].
Pfam PF13881: Ubiquitin-2 like Rad60 SUMO-like (domain)
This entry represents the ubiquitin domain found in ubiquitin-like protein 3 (UBL3)  and related proteins, such as MUB1-6 from Arabidopsis . The AtMUB proteins localize a specific subset of ubiquitin-conjugating (E2) enzymes to the plasma membrane .
Pfam PF15652: HNH/Endo VII superfamily toxin with a SHH signature (family)
A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6 or type 7 secretion system.
Pfam PF12437: Glutamine synthetase type III N terminal (family)
This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. The family is found in association with [pfam:PF00120]. This family is the N terminal region of glutamine synthetase type III which is one of the enzymes responsible for generation of glutamine through conversion glutamate to glutamine by the incorporation of ammonia (NH3).
Pfam PF10647: Lipoprotein LpqB beta-propeller domain (repeat)
The Gmad1 domain is found associated with the GerMN family, [pfam:PF10646], in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues.
Pfam PF21890: Lin-28A-like, second zinc knuckle (domain)
This domain is found at the C-terminal end of human Protein lin-28 homolog A (Lin-28A), an RNA-binding protein that inhibits processing of pre-let-7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabolism. This interaction requires the zinc-knuckle domains of Lin-28A. This entry represents the second of these domains.
Pfam PF21799: Mur ligase MurD-like, N-terminal domain (domain)
This domain is found at the N-terminal end of Mur ligases predominantly from proteobacteria, including UDP-N -acetylmuramoylalanine--D-glutamate ligase from Escherichia coli (MurD). Proteins in this family play a crucial role in the intracellular steps leading to the synthesis of bacterial peptidoglycan. MurD shows a three-domain topology, with the N-terminal (this entry) responsible for binding the UDP-precursor. This domain shows a Rossmann fold.
Pfam PF24582: Domain of unknown function (DUF7609) (domain)
This entry represents a domain found in a family of uncharacterised phage proteins. Structure prediction suggests that this protein may homodimerise (A0A377YTN9 ipTM=0.68).
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 PF06194: Phage Conserved Open Reading Frame 51 (family)
Family of conserved bacteriophage open reading frames.
Pfam PF01001: Hepatitis C virus non-structural protein NS4b (family)
No precise function has been assigned to NS4b.  However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.
Pfam PF07634: RtxA repeat (repeat)
This short repeat is found in the RtxA toxin family.
Pfam PF23411: Vps42 beta-propeller (repeat)
Vps41 is a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex. It is essential or membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport. It consists of a beta-propeller at the N-terminal, represented in this entry, followed by an alpha-solenoid (TPR-like) domain, a CHCR domain and a RING zinc finger.
Pfam PF15706: TMEM132 C-terminal (domain)
TMEM132 family of proteins includes TMEM132A-E, which are transmembrane proteins that regulate neuronal structure and function. In mammalian cells, they may regulate NAP1 in the WAVE regulatory complex (WRC) to finely modulate actin nucleation, cellular cytoskeletal and morphological changes. TMEM132D member has been associated with panic disorders, anxiety and major depressive disorders. TMEM132D is a single-pass transmembrane protein that is highly expressed in the cortical regions of the human and mouse brain. This entry represents the C-terminal region of these proteins which includes the transmembrane helix.
Pfam PF10518: TAT (twin-arginine translocation) pathway signal sequence (conserved_site)
The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes . Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria . In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state .

It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases . The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases .

In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength .

The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides .
Pfam PF20873: Primase chain A, C-terminal domain (domain)
This domain is found at the C-terminal end of the small subunit (PriS) of the core primase from the archaeon Sulfolobus solfataricus, an RNA polymerase that catalyzes the synthesis of the RNA primers required by the DNA polymerases. PriS is the catalytic subunit, with the active site located within an exposed groove in the concave side of two divergent beta-sheets, surrounded on the outside by alpha-helices This C-terminal domain, which is not found in other homologues, shows a mixed alpha-beta fold. It seems to support and position the elongated hairpin structure leading into the zinc-binding motif (PriS-Zn).
Pfam PF03960: ArsC family (family)
This family is related to glutaredoxins [pfam:PF00462].
Wikipedia: In molecular biology, the ars operon is an operon found in several bacterial taxon. It is required for the detoxification of arsenate, arsenite, and antimonite. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur.
Pfam PF09135: Alb1 (family)
Alb1 is a nuclear shuttling factor involved in ribosome biogenesis.
Pfam PF14487: ssDNA thymidine ADP-ribosyltransferase, DarT (family)
This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 201 and 230 amino acids in length. There is a single completely conserved residue E that may be functionally important. This family is distantly similar to [pfam:PF01885]. Studies in search for novel ADP-ribosylation systems in bacterial genomes have identified an operon that encodes a conserved protein containing a distinct type of macrodomain associated with this family. This led to the identification of a toxin-antitoxin (TA) system, with DarT acting as the toxin. It is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. This modification in turn can be removed by DarG, the antitoxin macrodomain protein. In addition, it was illustrated that substitution of the single completely conserved glutamate residue resulted in attenuation of function where DarT was non-toxic.
Pfam PF09378: HAS barrel domain (domain)
The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family.
Pfam PF00348: Polyprenyl synthetase (domain)
This entry includes a group of polyprenyl synthetase enzymes from all cellular organisms. It has been shown  that these enzymes share some regions of sequence similarity. From 3D structure analysis, it was revealed that they also share structure and reaction mechanisms, using similar strategies for substrate binding and catalysis .

This entry also includes Bifunctional sesterterpene synthases  and Bifunctional terpene synthase FUP1 from Fusarium proliferatum, which is involved in mycotoxin fusaproliferin biosynthesis .
A variety of isoprenoid compounds are synthesised by various organisms. For example in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyse a 1'4-condensation between 5 carbon isoprene units.
Wikipedia: Polyprenyl synthetases are a class of enzymes responsible for synthesis of isoprenoids. Isoprenoid compounds are synthesized by various organisms. For example, in eukaryotes the isoprenoid biosynthetic pathway is responsible for the synthesis of a variety of end products including cholesterol, dolichol, ubiquinone or coenzyme Q. In bacteria this pathway leads to the synthesis of isopentenyl tRNA, isoprenoid quinones, and sugar carrier lipids. Among the enzymes that participate in that pathway, are a number of polyprenyl synthetase enzymes which catalyze a 1'4-condensation between 5-carbon isoprene units. It has been shown that all the above enzymes share some regions of sequence similarity. Two of these regions are rich in aspartic-acid residues and could be involved in the catalytic mechanism and/or the binding of the substrates.
Pfam PF19490: Family of unknown function (DUF6025) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000938) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family  includes a protein from the fosfomycin biosynthetic gene cluster  from Streptomyces fradiae.
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 PF24945: Domain of unknown function (DUF7759) (domain)
This domain is found in uncharacterised proteins mainly from flagellate Discoba. It has detectable similarity to known PDZ domains and it is predicted to adopt similar structure. It is frequently found in multiple tandem copies.
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 PF23440: Broad-minded protein Rab TBC domain (domain)
The Broad-minded family proteins are essential for the proper response to Sonic hedgehog (Shh) signaling during neural tube development. Members of the Broad-minded family collaborate with cyclin-dependent kinase 20 (CDK20) to regulate the structure of the primary cilium. They are involved in the coordination of the ciliary membrane and axoneme assembly, which is crucial for the activation of the GLI2 transcription factor in response to Shh signaling.  This entry represents the C-terminal Rab TBC-like domain.
Pfam PF00249: Myb-like DNA-binding domain (domain)
This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
Wikipedia: Myb genes are part of a large gene family of transcription factors found in animals and plants. In humans, it includes Myb proto-oncogene like 1 and Myb-related protein B in addition to MYB proper. Members of the extended SANT/Myb family also include the SANT domain and other similar all-helical homeobox-like domains.
Pfam PF04989: Rhamnosyl O-methyltransferase/CmcI (family)
Members of this family are about 220 amino acids long. It includes Rhamnosyl O-methyltransferase which catalyses the O-methylation of the hydroxyl group located on C-2 of the first rhamnosyl residue linked to the phenolic group of glycosylated phenolphthiocerol dimycocerosates (PGL) and p-hydroxybenzoic acid derivatives (p-HBAD). This entry also includes CmcI protein [swissprot:O85726] which was previously presumed to represent the cephalosporin-7--hydroxylase. However, it is apparently a methyltransferase that works with hydroxylase CmcJ, and its most likely function is to catalyse the transfer of a methyl group from SAM to the 7alpha-hydroxy cephalosporin in the second catalytic reaction of cephamycin formation. Studies using recombinant proteins purified from E. coli suggest that the complex, but not the separate proteins, exhibits a strong interaction with SAM and cephalosporin C.
Pfam PF01075: Glycosyltransferase family 9 (heptosyltransferase) (family)
Members of this family belong to glycosyltransferase family 9.  Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core.
Pfam PF22428: DIS3-like exonuclease 2-like, C-terminal (domain)
This domain is found at the C-terminal end of DIS3-like exonuclease 2 from Schizosaccharomyces pombe (Dis32) and similar fungal proteins. Dis32, also known as Dis3l2, is a 3'-5'-exoribonuclease that specifically recognises RNAs polyuridylated at their 3' end and mediates their degradation. This domain shows three antiparallel beta -strands that show OB-fold characteristics.
Pfam PF22248: Endoplasmic reticulum metallopeptidase 1, C-terminal domain (domain)
Endoplasmic reticulum metallopeptidase 1 (ERMP1, also known as Felix-ina, FXNA or Fxna peptidase) is a multi-pass membrane protein located in the endoplasmic reticulum membrane. In humans, it may play a crucial role in processing proteins required for the organisation of somatic cells and oocytes into discrete follicular structures, although which proteins are hydrolysed has not yet been determined. According to AlphaFold structure predictions, these proteins consists of a M28 peptidase domain ([pfam:PF04389]), a TM domain and a C-terminal elongated banana-shaped all beta-sheet domain (represented in this entry), structurally similar to the Mu homology domain ([pfam:PF00928]), a protein-protein interaction module found in endocytic proteins involved in clathrin-mediated endocytosis.
Pfam PF23614: Domain of unknown function (DUF7141) (domain)
This domain is found in uncharacterised proteins mainly from Fungi. These proteins are likely involved in chromatin remodelling. The domain represented by this entry is predicted to fold into a globular structure with significant similarity to chromo domain ([pfam:PF00385]).
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 PF17765: MmyB-like transcription regulator ligand binding domain (domain)
This domain is found in a family of actinobacterial transcription factors. The structure shows it has a PAS domain like fold and it is bound to Myristic acid.