SII-SWORD/CoKE huggingface dataset:
Pfam PF11635: Mediator complex subunit 16, N-terminal (repeat)
Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression. This entry represents the N-terminal beta-propeller domain.
Wikipedia: Mediator of RNA polymerase II transcription subunit 16 is an enzyme that in humans is encoded by the MED16 gene.
Pfam PF00420: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (family)
This entry includes NADH:ubiquinone oxidoreductase, chain 4L and bacterial Mnh complex subunit C. They share significant protein sequence similarity .
ADH:ubiquinone oxidoreductase (complex I) (1.6.5.3) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) . In eukaryotes, NADH:ubiquinone oxidoreductase, chain 4L is usually found in either mitochondria or chloroplasts as part of the respiratory-chain NADH dehydrogenase (also known as complex I or NADH-ubiquinone oxidoreductase), an oligomeric enzymatic complex . However, it is also found in bacteria  and archaea  where it is annotated as NuoK subunit.
Mnh subunit C1 is a cation antiporter, involved in K(+) and Na(+) excretion .
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF24249: Domain of unknown function (DUF7452) (domain)
This entry represents a presumed domain found in a group of uncharacterised proteins from bacteria. This domain may adopt an all-beta configuration.
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 PF04425: Bul1 N terminus (family)
This family contains the N terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in [swissprot:P48524]).  The complex containing Bul1 and Rsp5 is involved in  intracellular trafficking of the general amino acid permease Gap1, degradation of Rog1 in cooperation with Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may contain HEAT repeats.
Pfam PF20008: Domain of unknown function (DUF6429) (domain)
This domain of unknown function is found in uncharacterised bacterial proteins. This domain is about 70 amino acids in length and contains the conserved sequence motifs WK, RS and TxxG.
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 PF02399: Origin of replication binding protein (family)
This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication.
Pfam PF07503: HypF finger (domain)
The HypF family of proteins are involved in the maturation and regulation of hydrogenase (). In the N-terminus they appear to have two Zinc finger domains, as modelled by this family.
Pfam PF05895: Siphovirus protein of unknown function (DUF859) (family)
This family consists of several uncharacterised proteins from the Siphoviruses and other bacterial viruses. Some members of this family are described as putative minor structural 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 PF12036: Protein of unknown function (DUF3522) (family)
This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 220 to 787 amino acids in length. This family belongs to the CREST superfamily, which are distant members of the GPCR superfamily.
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 PF06008: Laminin Domain I (coiled_coil)
coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure.
Wikipedia: Laminins are a family of glycoproteins of the extracellular matrix of all animals. They are major constituents of the basement membrane, namely the basal lamina. Laminins are vital to biological activity, influencing cell differentiation, migration, and adhesion.
Pfam PF21469: BH1974-like, central domain (domain)
This domain is located centrally in BH1974 protein from Alkalihalobacillus halodurans and similar bacterial proteins. It is found C-terminal to [pfam:PF02625] and N-terminal to [pfam:PF13478] and shows an alpha-beta structure.
Pfam PF01484: Nematode cuticle collagen N-terminal domain (family)
The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens, see [pfam:PF01391]. Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins.
Pfam PF02278: Polysaccharide lyase family 8, super-sandwich domain (family)
This family consists of a group of secreted bacterial lyase enzymes [ec:4.2.2.1] capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.
Pfam PF05724: Thiopurine S-methyltransferase (TPMT) (family)
This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyses S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines.
Pfam PF07830: Protein serine/threonine phosphatase 2C, C-terminal domain (domain)
Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It  consists of two domains: an N-terminal catalytic domain  and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices,  one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not  seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain.
Pfam PF02133: Permease for cytosine/purines, uracil, thiamine, allantoin (family)
This entry represents the purine-cytosine permease family, whose members include allantoin permease Dal4 , nicotinamide riboside transporter 1 (Nrt1) , purine-cytosine permease Fcy2/21/22 , thiamine transporter Thi7/Thi72 , uracil permease Fur4 , uridine permease Fui1  and vitamin B6 transporter Tpn1  from budding yeasts. This entry also includes cytosine permeases codB from E. coli  and purine-uracil permease AtNCS1 from Arabidopsis .
Wikipedia: The Nucleobase:Cation Symporter-1 (NCS1) Family (TC# 2.A.39) consists of over 1000 currently sequenced proteins derived from Gram-negative and Gram-positive bacteria, archaea, fungi and plants. These proteins function as transporters for nucleobases including purines and pyrimidines. Members of this family possess twelve transmembrane α-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport mechanism.
Pfam PF14053: Domain of unknown function (DUF4248) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 86 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 PF01765: Ribosome recycling factor (domain)
The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is  essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.
Wikipedia: Ribosome recycling factor or ribosome release factor (RRF) is a protein found in bacterial cells as well as eukaryotic organelles, specifically mitochondria and chloroplasts. It functions to recycle ribosomes after completion of protein synthesis. In humans, the mitochrondrial version is coded by the MRRF gene.
Pfam PF12897: Aspartate amino-transferase (domain)
These proteins catalyse the reversible transfer of an amino group from the amino acid substrate to an acceptor alpha-keto acid. They require pyridoxal 5'-phosphate (PLP) as a cofactor to catalyse this reaction. Trans-amination reactions are of central importance in amino acid metabolism and in links to carbohydrate and fat metabolism. This class of amino-transferases acts as dimers in a head-to-tail configuration. It has been demonstrated that these proteins are aspartate amino-transferases from Bacteria (Jansen, R.S. et al. Nat Commun 11, 1960 (2020)).
Pfam PF23503: Apicomplexa small protein domain (domain)
This domain is found in a group of uncharacterised small from apicomplexa, including [swissprot:A7AP47] from the parasite Babesia bovis, which is encoded by an small open reading frame (smORF). This domain, predicted to adopt an alpha- helical structure, is found twice in some longer members.
Pfam PF15366: Domain of unknown function (DUF4597) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 76 amino acids in length. There is a conserved TPPTPT 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.
Pfam PF08735: Putative pyruvate format-lyase activating enzyme (DUF1786) (family)
This family is annotated as pyruvate formate-lyase activating enzyme ([ec:1.97.1.4]) in UniProt. It is not clear where this annotation comes from.
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 PF11155: Domain of unknown function (DUF2935) (domain)
This family of proteins with unknown function appears to be restricted to Firmicutes. The structure of this protein has been solved and each domain is composed of four alpha helices. A metal cluster composed of iron and magnesium lies between the two domains.
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 PF22819: TcaA protein NTF2-like domain (domain)
This entry represents the C-terminal domain of the TcaA protein. This domain has an NTF2-like fold. This suggests this domain could have an enzymatic function.
Pfam PF04731: Caudal like protein activation region (family)
This family consists of the amino termini of proteins belonging to the caudal-related homeobox protein family.  This region is thought to mediate transcription activation.  The level of activation caused by mouse Cdx2  ([swissprot:P43241]) is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway.  Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain ([pfam:PF00046]).
Pfam PF01016: Ribosomal L27 protein (family)
Large ribosomal subunit protein bL27 (known as L27) is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below.

Bacterial L27           Nxxxxxxxxx
Algal L27               Nxxxxxxxxx
Plant L27          tttttNxxxxxxxxxxxxx
Yeast MRP7           tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

't': transit peptide.
'N': N-terminal of mature protein.
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 PF04686: Streptomyces sporulation and cell division protein, SsgA (family)
The precise function of SsgA is unknown. It has been found to be essential for spore formation, and to stimulate cell division.
Pfam PF00527: E7 protein, Early protein (family)
This family includes the E7 oncoprotein from various papillomaviruses . Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest .
Pfam PF16342: Domain of unknown function (DUF4972) (family)
This family consists of uncharacterized proteins around 490 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF19855: Family of unknown function (DUF6330) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are approximately 70 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 PF08358: Carlavirus coat (family)
This domain is found together with the viral coat protein domain ([pfam:PF00286]) in coat/capsid proteins of Carlaviruses infecting plants.
Pfam PF22337: Phage tail fiber repeats (repeat)
This entry represents a small repeat found in phage tail proteins from tailed bacteriophages and prophages mainly from flavobacteria.
Pfam PF07368: Protein of unknown function (DUF1487) (family)
This family consists of several uncharacterised proteins from Drosophila melanogaster. 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 PF07775: PaRep2b protein (family)
This is a family of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in  length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer  functional.
Pfam PF18119: RIG-I receptor C-terminal domain (domain)
This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA.
Pfam PF09948: Predicted metal-binding integral membrane protein (DUF2182) (family)
This domain, found in various hypothetical bacterial membrane proteins having predicted metal-binding properties, 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 PF20053: Wolframin cysteine-rich domain (family)
Located N-terminal to the wolframin OB-fold domain, this region could represent an extension to the core of the OB fold domain. The observed conserved cysteine residues could contribute to disulfide-bond-mediated cross-linking in calcium-stores regulation.
Pfam PF09252: Allergen Fel d I-B chain (domain)
Members of this family of cat allergens adopt a helical structure consisting of eight alpha helices, in a Uteroglobin-like fold. They are one of the most important causes of allergic asthma worldwide.
Wikipedia: Fel d 1 is a secretoglobin protein complex that, in cats, is encoded by the CH1 and CH2 genes.
Pfam PF24243: Phage tail tip domain (family)
This small region is found at the C-terminus of a variety of actinophage fiber proteins.  According to structure predictions these proteins form homotrimers. Presumably this domain mediates interaction with either the host cell or with another phage tail fiber protein. The structure of this region forms three beta strands and up to two small alpha helices, with one of the beta strands in the trimeric structure strand swapping between the monomers. In some phage we find this domain in isolation in rather short 60 residue proteins.
Pfam PF00632: HECT-domain (ubiquitin-transferase) (domain)
The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.
Wikipedia: In molecular biology, the HECT domain is a protein domain found in ubiquitin-protein ligases. The name HECT comes from 'Homologous to the E6-AP Carboxyl Terminus'. Proteins containing this domain at the C terminus include ubiquitin-protein ligase, which regulates ubiquitination of CDC25. Ubiquitin-protein ligase accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester, and then directly transfers the ubiquitin to targeted substrates. A cysteine residue is required for ubiquitin-thioester formation. Human thyroid receptor interacting protein 12 (TRIP12), which also contains this domain, is a component of an ATP-dependent multisubunit protein that interacts with the ligand binding domain of the thyroid hormone receptor. It could be an E3 ubiquitin-protein ligase. Human E6AP ubiquitin-protein ligase interacts with the E6 protein of the cancer-associated Human papillomavirus type 16 and Human papillomavirus type 18. The E6/E6-AP complex binds to and targets the p53 tumour-suppressor protein for ubiquitin-mediated proteolysis.
Pfam PF22567: UBA-like domain (domain)
This entry primarily represents the UBA domain found in the UBAP1 protein.