SII-SWORD/CoKE huggingface dataset:
Pfam PF19916: vWA-MoxR associated protein middle region 0 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF03354: Terminase large subunit, ATPase domain (domain)
Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the "Lid subdomain" with reference to analogous lid subdomains found in other ATPases. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyses ATP hydrolysis. This entry also includes bacterial proteins of unknown function.
Pfam PF08234: Chromosome segregation protein Spc25 (family)
This is a family of chromosome segregation proteins.  It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex, and in vertebrates it forms part of the Ndc80 complex.
Pfam PF13051: Protein of unknown function (DUF3912) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length.
Pfam PF02678: Pirin (family)
This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homologue of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily.
Pfam PF24613: Cadherin-related hmr-1, EGF domain (domain)
This domain is foud towards the C-terminal end of Cadherin -related hmr-1 from Caenorhabditis elegans, a calcium-dependent cell adhesion protein required for adherens junction assembly and connecting adherens junctions to the cytoskeleton.
Pfam PF15023: Protein of unknown function (DUF4523) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in mammals.
Pfam PF20005: FtsH ternary system domain X7 (domain)
Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF21781: Family of unknown function (DUF6876) (domain)
This entry represents a family of uncharacterised proteins that show structural similarity to [pfam:PF06124].
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 PF21630: Hypothetical protein Q4D059-like (family)
This protein family represents a group of proteins from related kinetoplastid parasites found in Trypanosomatidae, including the functionally uncharacterised [swissprot:Q4D059] from Trypanosoma cruzi, which is predicted to be a 4-oxalocrotonate tautomerase. Q4D059 shows a parallel/ anti-parallel three-stranded beta-sheet packed against four helical regions.
Pfam PF06123: Inner membrane protein CreD (family)
This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with an Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA.
Pfam PF06489: Orthopoxvirus A49R protein (family)
This family consists of several Orthopoxvirus A49R proteins. The function of this family is unknown.
Pfam PF16428: Domain of unknown function (DUF5025) (family)
This family consists of several uncharacterized proteins around 200 in length and is mainly found in various Parabacteroides species. 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 PF11080: Endoribonuclease GhoS (family)
GhoS is part of the GhoT-GhoS type V toxin-antitoxin (TA) system. GhoT is inhibited by antitoxin GhoS, which specifically cleaves its  mRNA.
Pfam PF18405: Mitochondrial SLC25 homolog (family)
This family includes distant homologs of mitochondrial carrier proteins (MCs, also known in mammals as solute carrier family 25, SLC25). Sequence analysis suggest that it is likely that Lpg1137 forms a standard MC structure with a pseudo-threefold symmetry with six transmembrane helices. Furthermore, sequence logos of the repeats in homologues of Lpg1137, compared to sequence logo of the eukaryotic mitochondrial carriers support the structural similarity by highlighting the conservation of structurally important Pro and Gly residues (e.g., Pro at positions 15 and 239 in the logos or the YxG motif at positions 45-47. It was previously thought that members of this family are serine proteases that target the mitochondria-associated ER membrane (MAM) and degrades STX17 (syntaxin 17), a SNARE implicated in macroautophagy/autophagy as well as mitochondria dynamics and membrane trafficking in fed cells.
Pfam PF00116: Cytochrome C oxidase subunit II, periplasmic domain (domain)
Cytochrome c oxidase (7.1.1.9)  is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals). In Archaea, a cytochrome-c-type oxidase from Natronobacterium (cytochrome ba3) has been shown to consists of four subunits .

Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.

It has been shown  that nitrous oxide reductase (gene nosZ) of Pseudomonas has sequence similarity in its C terminus to CO II. This enzyme is part of the bacterial respiratory system which is activated under anaerobic conditions in the presence of nitrate or nitrous oxide. NosZ is a periplasmic homodimer that contains a dinuclear copper centre, probably located in a 3-dimensional fold similar to the cupredoxin-like fold that has been suggested for the copper-binding site of CO II .
Wikipedia: Cytochrome c oxidase II is a protein in eukaryotes that is encoded by the MT-CO2 gene. Cytochrome c oxidase subunit II, abbreviated COXII, COX2, COII, or MT-CO2, is the second subunit of cytochrome c oxidase. It is also one of the three mitochondrial DNA (mtDNA) encoded subunits of respiratory complex IV.
Pfam PF10554: Ash protein family (family)
This family was identified by Iyer and colleagues. It includes the Ash protein from bacteriophage P4.
Pfam PF23016: RsmI C-terminal HTH domain (domain)
This entry represents a small helical domain at the C-terminus of RsmI that folds into a typical three helical DNA/RNA binding bundle containing HTH motif. This domain is found in Ribosomal RNA small subunit methyltransferase I (RsmI) and related proteins. RsmI is an S-adenosyl-L-methionine-dependent methyltransferase that catalyses the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. It may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity. In vitro, active on the assembled 30S subunit, but not naked 16S rRNA or 70S ribosomes.
Pfam PF19601: Family of unknown function (DUF6106) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. This protein is distantly related to [pfam:PF14256].
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 PF02091: Glycyl-tRNA synthetase alpha subunit (domain)
This entry represents the alpha subunit of glycine-tRNA ligase (also known as glycyl-tRNA synthetase alpha subunit). It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
In eubacteria, glycine-tRNA ligase (6.1.1.14) is an alpha2/beta2 tetramer composed of 2 different subunits . In some eubacteria, in archaea and eukaryota, glycine-tRNA ligase is an alpha2 dimer (see IPR002315). It belongs to class IIc and is one of the most complex ligases. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha and beta subunits also lack significant sequence similarity. However, they are translated from a single mRNA , and a single chain glycine-tRNA ligase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain .
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel Î²-sheet fold flanked by Î±-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an Î±-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Pfam PF14677: FANCI solenoid 3 (repeat)
This is the solenoid 3 (S3) domain of the Fanconi anemia group I protein.
Pfam PF12838: 4Fe-4S dicluster domain (domain)
Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
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 PF03567: Sulfotransferase family (domain)
This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyses the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST).  Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development.  Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate.
Wikipedia: In biochemistry, carbohydrate sulfotransferases are enzymes within the class of sulfotransferases which catalyze the transfer of the sulfate functional group to carbohydrate groups in glycoproteins and glycolipids. Carbohydrates are used by cells for a wide range of functions from structural purposes to extracellular communication. Carbohydrates are suitable for such a wide variety of functions due to the diversity in structure generated from monosaccharide composition, glycosidic linkage positions, chain branching, and covalent modification. Possible covalent modifications include acetylation, methylation, phosphorylation, and sulfation. Sulfation, performed by carbohydrate sulfotransferases, generates carbohydrate sulfate esters. These sulfate esters are only located extracellularly, whether through excretion into the extracellular matrix (ECM) or by presentation on the cell surface. As extracellular compounds, sulfated carbohydrates are mediators of intercellular communication, cellular adhesion, and ECM maintenance.
Pfam PF17617: Viral unique short region 10 (family)
This family contains US10 proteins found in HCMV Human cytomegalovirus. US10 is a unique short region trans-membrane glycoprotein found in the endoplasmic reticulum (ER). It down-regulates cell surface expression of HLA-G, but not that of classical class I MHC molecules. Despite of binding to classical class I MHC molecules and delaying their trafficking, it does not affect their steady-state cell surface levels. US10 contains a tri-leucine motif in the cytoplasmic tail which is responsible for down-regulation of HLA-G.
Pfam PF01197: Ribosomal protein L31 (family)
This entry groups large ribosomal subunit proteins bL31 classified as type A and type B.
Ribosomal protein bL31 is one of the proteins from the large ribosomal subunit. bL31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.
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 PF03573: outer membrane porin, OprD family (family)
This family includes outer membrane proteins related to OprD. OprD has been described as a serine type peptidase. However the proposed catalytic residues are not conserved suggesting that many of these proteins are not peptidases.
Wikipedia: Outer membrane porin D is a protein family containing bacterial outer membrane porins which are involved in transport of cationic amino acids, peptides, antibiotics and other compounds.
Pfam PF20021: vWA-MoxR associated protein middle region (VMAP-M) 18 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF12700: HlyD family secretion protein (family)
This family is related to [pfam:PF00529].
Pfam PF14935: Transmembrane protein 138 (family)
This family of proteins is found in eukaryotes and members are approximately 160 amino acids in length. There are two conserved sequence motifs: YYY and DPR. This transmembrane protein belongs to a family found in eukaryotes and is involved in the biogenesis and degradation of ciliated cells. Mutations in this protein cause the disease Joubert syndrome(JBTS) where the cilia becomes non-motile. Ciliopathy can be severe since cilia provide the cell with large amounts of information through signals. Ciliopathy can affect cell behaviour as the appropriate signals between the cell and its environment are not made, which can affect cell survival.
Pfam PF15724: TMEM119 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 283 amino acids in length.
Pfam PF08552: Inositolphosphorylceramide synthase subunit Kei1 (family)
Kei1 is a subunit of Saccharomyces cerevisiae inositol phosphorylceramide (IPC) synthase. It is localised to the Golgi and is cleaved by the late Golgi processing endopeptidase Kex2.  Kei1 is essential for both the activity and the Golgi localization of IPC synthase.
Pfam PF09258: Glycosyl transferase family 64 domain (domain)
Members of this family catalyse the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate.
Pfam PF07723: Leucine Rich Repeat (repeat)
This Pfam entry includes some LRRs that fail to be detected with the [pfam:PF00560] model.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF12997: Domain of unknown function, E. rectale Gene description (DUF3881) (family)
Based on Eubacterium rectale gene EUBREC_3695.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture.
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 PF16879: C-terminal domain of Sin3a protein (family)
Sin3a_C is a family of eukaryotic species.  It is found at the C-terminus of the co-repressor Sin3a, and downstream of family Sin3_corepress, [pfam:PF08295].