SII-SWORD/CoKE huggingface dataset:
Pfam PF02675: S-adenosylmethionine decarboxylase (family)
This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesised as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity.
Wikipedia: The enzyme adenosylmethionine decarboxylase catalyzes the conversion of S-adenosyl methionine to S-adenosylmethioninamine.
Polyamines such as spermidine and spermine are essential for cellular growth under most conditions, being implicated in many cellular processes including DNA, RNA and protein synthesis. S-adenosylmethionine decarboxylase (AdoMetDC) plays an essential regulatory role in the polyamine biosynthetic pathway by generating the n-propylamine residue required for the synthesis of spermidine and spermine from putrescein. Unlike many amino acid decarboxylases AdoMetDC uses a covalently bound pyruvate residue as a cofactor rather than the more common pyridoxal 5'-phosphate. These proteins can be divided into two main groups which show little sequence similarity either to each other, or to other pyruvoyl-dependent amino acid decarboxylases: class I enzymes found in bacteria and archaea, and class II enzymes found in eukaryotes. In both groups the active enzyme is generated by the post-translational autocatalytic cleavage of a precursor protein. This cleavage generates the pyruvate precursor from an internal serine residue and results in the formation of two non-identical subunits termed alpha and beta which form the active enzyme.
Pfam PF12701: Scd6-like Sm domain (domain)
The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi,  animals, plants and apicomplexans. The domain is also found in  Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the  the Rossmanoid YjeF-N domain. In addition both EDC3 and Scd6p are found fused to the FDF domain.
Pfam PF10287: Cell wall protein YJL171C/Tos1, C-terminal (domain)
This entry represents a domain found in a group of fungal cell wall proteins, including Tos1 and YJL171C from budding yeasts. They contain 5 highly conserved cysteines, two of which form a characteristic CGC sequence motif. Their function is not clear. It has been shown that these proteins are related to known glycosyl hydrolases.
Pfam PF11077: Protein of unknown function (DUF2616) (family)
This cysteine-rich family is expressed by the double-stranded Nucleopolyhedrovirus, a member of the Baculoviridae family of dsDNA viruses.  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 PF15882: Domain of unknown function (DUF4735) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 288 and 410 amino acids in length. There are two completely conserved C residues that may be functionally important. In mammals this protein family is thyroid-specific.
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 PF08785: Ku C terminal domain like (domain)
The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ.  Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs).  This domain is found at the C terminal of Ku which binds to DNA-PKcs.
Wikipedia: Ku is a dimeric protein complex that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to humans. The ancestral bacterial Ku is a homodimer. Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end. Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK. Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind, orienting the double-strand break for ligation.
Pfam PF22787: Tag1 middle barrel-like domain (domain)
This entry represents the middle barrel-like domain of Tag1. Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins. It was proposed that Tag1 is composed of 3 tandemly repeated LEA-2 domains.
Pfam PF24833: Rhabdovirus spike glycoprotein G central domain (domain)
This entry includes the glycoprotein G from Rhabdoviruses, such as rabies virus (RABV), Mokola virus (MOKV) and European bat lyssavirus 1 (EBLV), which attaches the virus to host cellular receptor, and induces endocytosis of the virion. It forms the glycoprotein spike that is made up of a trimer of G proteins. Each protomer of the trimer is composed of three domains: a membrane-distal pleckstrin homology domain (PH),  a membrane-proximal fusion domain (FD) and a laterally positioned central domain (CD). This entry represents the CD (which consists of domains I (beta-sheet rich) and II (alpha-helical) from).
Pfam PF04892: VanZ like family (family)
This family contains several examples of the VanZ protein, but also contains examples of phosphotransbutyrylases.
Pfam PF18011: C-terminal domain found in long catalases (domain)
This domain is found at the C-terminus of a variety of large catalase enzymes from bacteria. Structurally it is related to class I glutamine amidotransferase domains. The precise molecular function of this domain is uncertain.
Pfam PF23303: NUP120/160 Tetratricopeptide-like repeat (repeat)
This entry represents the tetratricopeptide-like repeat found in the C-terminal region of a set of Nucleoporin NUP120 proteins from fungi, including Chaetomium thermophilum, as well as Nucleoporin NUP160 from animals and plants. NUP120 is part of a Nuclear Pore Complex (NPC) as a component of the ctNup87 complex. NUP160 plays a role in regulating inflammatory response.
Pfam PF10750: Protein of unknown function (DUF2536) (family)
This family of proteins with unknown function appears to be restricted to Bacillus spp. Structural modelling suggests this domain may bind nucleic acids.
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 PF10298: WhiA N-terminal LAGLIDADG-like domain (domain)
This domain is found at the N terminal of sporulation factor WhiA. This domain is related to the LAGLIDADG Homing endonuclease domain while the C terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain.
Pfam PF09329: Primase zinc finger (domain)
This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases.
Pfam PF02606: Tetraacyldisaccharide-1-P 4'-kinase (family)
This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, [ec:2.7.1.130].   This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl  beta-phosphate  ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.  This enzyme is  involved in the synthesis of lipid A portion of the bacterial  lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus.
Wikipedia: Tetraacyldisaccharide 4'-kinase is an enzyme that phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipopolysaccharide lipid A. This lipid forms outer membranes of Gram-negative bacteria. This enzyme catalyzes the chemical reactionATP + [2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl]-(1-&gt;6)-[2- N,3-O-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl phosphate]  ADP + [2-N,3-O-bis(3-hydroxytetradecanoyl)-4-O-phosphono-beta-D- glucosaminyl]-(1-&gt;6)-[2-N,3-O-bis(3-hydroxytetradecanoyl)-beta-D- glucosaminyl phosphate]
Pfam PF04034: Ribosome biogenesis protein, C-terminal (domain)
This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the  eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis.
Pfam PF00626: Gelsolin repeat (domain)
Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) . It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing.

Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin . Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues .

This gelsolin-like domain can also be found in the C-terminal of the members of Sec23/Sec24 family. They are components of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER).
Wikipedia: Gelsolin is an actin-binding protein that is a key regulator of actin filament assembly and disassembly. Gelsolin is one of the most potent members of the actin-severing gelsolin/villin superfamily, as it severs with nearly 100% efficiency.
Pfam PF17195: Protein of unknown function (DUF5132) (family)
Proteins in this family are uncharacterised, but have been identified as members of a gene cluster for the synthesis of Ansamitocin.
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 PF09694: Bacterial protein of unknown function (Gcw_chp) (family)
This entry represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis and Ralstonia solanacearum, usually as part of a paralogous family. The function is unknown.
Pfam PF00275: EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) (family)
This entry represents the core domain of 3-phosphoshikimate 1-carboxyvinyltransferase and UDP-N-acetylglucosamine 1-carboxyvinyltransferase. These proteins transfer enolpryruvate from phosphoenolpyruvate to 3-phosphoshikimate and UDP-N-acetyl-alpha-D-glucosamine respectively .

The domain can also be found in the fungal Pentafunctional AROM polypeptide (also known as 3-dehydroquinate synthase), although is this case it does not cover the whole protein but appears in association with other domains such as IPR030960. This protein catalyses 5 consecutive enzymatic reactions in prechorismate polyaromatic amino acid biosynthesis .
Wikipedia: 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an enzyme produced by plants and microorganisms. EPSPS catalyzes the chemical reaction:phosphoenolpyruvate (PEP) + 3-phospho shikimate (S3P) ⇌ phosphate + 5-enolpyruvylshikimate-3-phosphate (EPSP)
Pfam PF00073: picornavirus capsid protein (domain)
CAUTION: This alignment is very weak.  It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised.  The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.
Pfam PF15828: Required for drug-induced death protein 1 (family)
This family of proteins is found in eukaryotes and includes Required for drug-induced death protein 1 (RDD1) which regulates drug efflux through modulation of ABCB1 localization and activity.
Pfam PF18330: Ligase Pab1020 C-terminal region (domain)
This is the C-terminal region of RNA ligase Pab1020 present in Pyrococcus abyssi. Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction. This region contains both a dimerization domain and a C-terminal domain.
Pfam PF16851: Stomagen (domain)
Stomagen (epidermal patterning factor-like protein 9) acts as a positive regulator of stomatal development.
Pfam PF03472: Autoinducer binding domain (domain)
This domain is found a a large family of transcriptional regulators.  This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF18873: Sgo0707 N-terminal domain (domain)
This domain found at the N-terminus of the cell surface Sgo0707 protein. This domain is called the N1 domain and is involved in host colonisation.The largest domain, N1, comprises a putative binding cleft with a single cysteine located in its centre and exhibits an unexpected structural similarity to the variable domains of the streptococcal Antigen I/II adhesins.
Pfam PF06694: Plant nuclear matrix protein 1 (NMP1) (family)
This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm.
Pfam PF23086: Coilin, C-terminal Tudor domain (domain)
This domain is found in the homologues of Coilin. Coilin was initially discovered in sera from patients suffering from autoimmune disease. Its primary role is to serve as an assembly center in Cajal bodies, nuclear suborganelles that typically occur near histone gene clusters and the nucleolus, and are involved in the modification and assembly of nucleoplasmic snRNPs. This entry represents the C-terminal atypical Tudor domain of Coilin that contains large unstructured loops.
Pfam PF05960: Bacterial protein of unknown function (DUF885) (family)
This family consists of several hypothetical bacterial proteins several of which are putative membrane 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 PF00959: Phage lysozyme (domain)
This family includes lambda phage lysozyme and E. coli endolysin.
Wikipedia: In molecular biology, glycoside hydrolase family 24 is a family of glycoside hydrolases.
Pfam PF03878: YIF1 (family)
YIF1 (Yip1 interacting factor) is an integral membrane protein that is required for membrane fusion of ER derived vesicles. It also plays a role in the biogenesis of ER derived COPII transport vesicles.
Pfam PF19531: Family of unknown function (DUF6058) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the formicamycins A-M biosynthetic gene cluster from  Streptomyces sp. KY5.
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 PF16727: DNA repair protein REV1 C-terminal domain (domain)
This is the C-terminal domain of DNA repair protein REV1. It interacts with REV7, POLN, POLK and POLI.
Pfam PF08016: Polycystin cation channel (family)
This family contains the cation channel region from group II of Transient receptor potential (TRP) channels, the TRPP subfamily, including PKD1, PKD2, PKD2L and mucolipin proteins.
Wikipedia: The Polycystin Cation Channel (PCC) Family consists of several transporters ranging in size from 500 to over 4000 amino acyl residues (aas) in length and exhibiting between 5 and 18 transmembrane segments (TMSs). This family is a constituent of the Voltage-Gated Ion Channel (VIC) Superfamily. These transporters generally catalyze the export of cations. A representative list of proteins belonging to the PCC family can be found in the Transporter Classification Database.
Pfam PF00756: Putative esterase (domain)
This family contains Esterase D [swissprot:P10768]. However it is not clear if all members of the family have the same function.  This family is related to the [pfam:PF00135] family.
Pfam PF11143: Protein of unknown function (DUF2919) (family)
This bacterial family of proteins has no known function. Some members are annotated as YfeZ 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 PF04527: Drosophila Retinin like protein (family)
Family of Drosophila proteins related to the C-terminal region of the Drosophila Retinin protein. Conserved region is found towards the C-terminus of the member proteins.
Pfam PF23093: Teneurin-3-like, galactose-binding domain-like (domain)
This domain is found in Teneurin-3 from Mus musculus (Tenm3), which is involved in neural development and plays a key role in the development of the visual pathway.
Pfam PF23813: Family of unknown function (DUF7184) (family)
This entry represents a family of phage proteins including Enterobacteria phage T4. The family is found in various phages that infect Escherichia coli and Shigella. The function of this protein family is currently 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 PF17851: Beta xylosidase C-terminal Concanavalin A-like domain (domain)
This domain is found to the C-terminus of the [pfam:PF04616] domain. This domain adopts a concanavalin A-like fold.
Pfam PF24876: PA4575-like protein (domain)
This entry represents a family of proteins that includes the Pseudomonas aeruginosa protein PA4575. The function of these proteins is unknown.
Pfam PF09136: Glucodextranase, domain B (domain)
Members of this family adopt a structure consisting of seven/eight-strand antiparallel beta-sheets, in a Greek-key topology, similar to the immunoglobulin beta-sandwich fold. They act as cell wall anchors, where they interact with the S-layer present in the cell wall of Gram-positive bacteria by hydrophobic interactions. In glucodextranase, Domain B is buried in the S-layer, and a flexible linker located between domain B and the catalytic unit confers motion to the catalytic unit, which is capable of efficient hydrolysis of the substrates located close to the cell surface.
Pfam PF10521: Tti2 family (family)
This family includes budding yeast Tel2-interacting protein 2 (Tti2) and similar proteins from animals and fungi. Tti2 is a component of the tel2-tti1-tti2 (TTT) complex, which is involved in the cellular resistance to DNA damage stresses, like ionizing radiation (IR), ultraviolet (UV) and mitomycin C (MMC). Its homologue from humans, together with the TTT complex and HSP90, may participate in the proper folding of newly synthesised phosphatidylinositol 3-kinase-related protein kinase (PIKK) proteins.
Pfam PF20967: MASE7 (domain)
This entry represents a predicted integral membrane sensor domain (MASE7), which is found in association with GGDEF domain ([pfam:PF00990]), histidine sensor kinases and adenylate cyclase output domain ([pfam:PF00211]).
Pfam PF16187: Middle or third domain of peptidase_M16 (family)
Peptidase_M16_M is the third domain of peptidase_M16 in eukaryotes of the insulin-degrading-enzyme type. Insulin-degrading enzymes - insulysin - are zinc metallopeptidases that metabolise several bioactive peptides, including insulin and the amyloid-beta-peptide.  The tertiary structure of insulin-degrading enzymes resembles a clamshell composed of four structurally similar domains arranged to enclose a large central chamber. Substrates must enter the chamber, and it is likely that a hinge-like conformational change allows substrate binding and product release. Triphosphates are found to dock between the inner surfaces of the non-catalytic domains three and four.