SII-SWORD/CoKE huggingface dataset:
Pfam PF17342: Family of unknown function (DUF5372) (family)
This family of unknown function is found in Bacteria.
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 PF14280: Domain of unknown function (DUF4365) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 182 and 530 amino acids in length. There is a single completely conserved residue D that may be functionally important.
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 PF13275: S4 domain (domain)
The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4.
Pfam PF01233: Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain (domain)
The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold.
Wikipedia: In enzymology, a glycylpeptide N-tetradecanoyltransferase is an enzyme that catalyzes the chemical reactiontetradecanoyl-CoA + glycylpeptide  CoA + N-tetradecanoylglycylpeptide
Pfam PF01343: Peptidase family S49 (family)
This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain.
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
Pfam PF17932: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in family members such as HTH-type transcriptional repressor KstR2 as well as fatty acid metabolism regulator proteins. In Mycobacterium smegmatis, KstR2 is involved in involved in cholesterol catabolism, while YsiA in Bacillus subtilis is involved in fatty acid degradation.
Pfam PF15983: Domain of unknown function (DUF4767) (family)
This domain family is found in bacteria, and is approximately 140 amino acids in length. There is a single completely conserved residue Q that may be functionally important.
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 PF16356: Domain of unknown function (DUF4983) (family)
This family consists of uncharacterised proteins around 600 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF18847: Large polyvalent protein associated domain 29 (domain)
This is an alpha and beta fold domain with conserved polar residues that is found in polyvalent proteins of conjugative elements.
Pfam PF13107: Protein of unknown function (DUF3964) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: FYF and AFW.
Pfam PF09819: ABC-type cobalt transport system, permease component (family)
Members of this family of prokaryotic proteins include various hypothetical proteins as well as ABC-type cobalt transport systems.
Pfam PF02924: Bacteriophage lambda head decoration protein D (domain)
Bacteriophage lambda head decoration protein D stabilises the head shell after the rearrangement of GP7 subunits of the head shell lattice that accompanies expansion of the head. There are approximately 420 copies of protein D per mature phage.
Pfam PF21483: Toxin CdiA-like, helical domain (domain)
This entry represents the helical domain of  EC869 CdiA toxin, a toxin of the Contact-dependent growth inhibition (CDI) system. EC869 appears to function as a Zn2+-dependent DNAse degrading the genome of target cells.
Pfam PF03292: Poxvirus P4B major core protein (family)
This family includes the major core protein 4b from Vaccinia virus, also known as Major core protein OPG129. It is a major component of the virion core that undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition. It is essential for the formation of a structurally normal core .
Pfam PF00063: Myosin head (motor domain) (domain)
Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril. Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains , 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family . Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy . The 3-D structure of the head portion of myosin has been determined  and a model for actin-myosin complex has been constructed .

The globular head is well conserved, some highly-conserved regions possibly relating to functional and structural domains . The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. Although the sequence of the tail is not well conserved, the chemical character is, hydrophobic, charged and skip residues occuring in a highly ordered and repeated fashion .

This domain is also found in chitinases present in filamentous fungi, enzymes that play a critical role in promoting the synthesis of chitin at the hyphal tip, thus influencing fungal growth and the architecture of fungal infection structures .
Wikipedia: The myosin head is the part of the thick myofilament made up of myosin that acts in muscle contraction, by sliding over thin myofilaments of actin. Myosin is the major component of the thick filaments and most myosin molecules are composed of a head, neck, and tail domain; the myosin head binds to thin filamentous actin, and uses ATP hydrolysis to generate force and "walk" along the thin filament. Myosin exists as a hexamer of two heavy chains, two alkali light chains, and two regulatory light chains. The heavy chain can be subdivided into the globular head at the N-terminal and the coiled-coil rod-like tail at the C-terminal, although some forms have a globular region in their C-terminal.
Pfam PF04459: Protein of unknown function (DUF512) (family)
Family of uncharacterised prokaryotic 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 PF13479: AAA domain (domain)
This AAA domain is found in a wide variety of presumed phage proteins.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF09797: N-acetyltransferase B complex (NatB) non catalytic subunit (repeat)
This is the non-catalytic subunit of the N-terminal acetyltransferase B complex (NatB), NAA25. The NatB complex catalyses the acetylation of the amino-terminal methionine residue of all proteins beginning with Met-Asp or Met-Glu and of some proteins beginning with Met-Asn or Met-Met. In Saccharomyces cerevisiae this subunit is called MDM20 and in Schizosaccharomyces pombe it is called Arm1 NatB acetylates the Tpm1 protein and regulates and tropomyosin-actin interactions. This subunit is required by the NatB complex for the N-terminal acetylation of Tpm1.
Pfam PF24485: DHX34-like, C2H2-type zinc finger (domain)
This C2H2-type zinc finger domain is found at the C-terminal end of human Probable ATP-dependent RNA helicase DHX34 and similar animal proteins.
Pfam PF15424: Odontogenic ameloblast-associated family (family)
Odontogenic ameloblast-associated protein, also known as apin, is a tooth-associated epithelia protein that probably plays a role in odontogenesis, the complex process that results in the initiation and generation of the tooth. It may be incorporated in the enamel matrix at the end of mineralisation process .
Wikipedia: Odontogenic ameloblast-associated protein is a protein that in humans is encoded by the ODAM gene.
Pfam PF11746: Domain of unknown function (DUF3303) (domain)
Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
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 PF17550: Family of unknown function (family)
This is a family of unknown function found in Yersinia pestis.
Pfam PF14542: GCN5-related N-acetyl-transferase (domain)
This family of GCN5-related N-acetyl-transferases bind both CoA and acetyl-CoA. They are characterised by highly conserved glycine, a cysteine residue in the acetyl-CoA binding site near the acetyl group, their small size compared with other GNATs and a lack of of an obvious substrate-binding site.  It is proposed that they transfer an acetyl group from acetyl-CoA to one or more unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The substrate might be another macromolecule.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF22044: Sporulation protein 24 (family)
This family includes Sporulation protein 24 from Saccharomyces cerevisiae (SPO24) and similar sequences from yeasts. SPO24  is a 67-amino-acid protein required for efficient sporulation.
Pfam PF25000: Domain of unknown function (DUF7779) (domain)
This is a presumed domain found in uncharacterised sequences from fungi. It may be a winged helix domain according to structure predictions.
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 PF02460: Patched SSD (domain)
The transmembrane protein Patched [swissprot:P18502] is a receptor for the morphogenic Sonic Hedgehog. This protein associates with the smoothened protein (SMO) to transduce hedgehog signals. These proteins consist of twelve transmembrane segments and two extracellular domains (ECDs). This entry represents the Sterol-sensing domain (SSD) formed by some of the TM segments. This domain may play a role in the transport and/or regulation of the SMO ligand.
Pfam PF01219: Prokaryotic diacylglycerol kinase (family)
Prokaryotic diacylglycerol kinase (DAGK) and undecaprenol kinase (UDPK) constitute a family of multispan membrane enzymes that are very small, lack relationships to any other family of proteins and exhibit an unusual structure. Escherichia coli DAGK plays an important role in recycling diacylglycerol produced as a by-product of biosynthesis of molecules located in the periplasmic space. UDPK seems to play an analogous role in Gram-positive bacteria, where it is essential for biofilm formation by the oral pathogen Streptococcus mutans . In Bacillus subtilis, UDPK is an essential kinase in the diacylglycerol cycle involved in lipoteichoic acid production and seems to be indispensable for the maintenance of spore stability and viability .

Diacylglycerol kinase (2.7.1.107) (DAGK) is an enzyme that catalyses the formation of phosphatidic acid from diacylglycerol and ATP, an important step in phospholipid biosynthesis. In bacteria DAGK is a very small (13 to 15 kD) membrane protein which seems to contain three transmembrane domains .
Wikipedia: Diacylglycerol kinase is a family of enzymes that catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid (PA), utilizing ATP as a source of the phosphate. In non-stimulated cells, DGK activity is low, allowing DAG to be used for glycerophospholipid biosynthesis, but on receptor activation of the phosphoinositide pathway, DGK activity increases, driving the conversion of DAG to PA. As both lipids are thought to function as bioactive lipid signaling molecules with distinct cellular targets, DGK therefore occupies an important position, effectively serving as a switch by terminating the signalling of one lipid while simultaneously activating signalling by another.
Pfam PF11745: Protein of unknown function (DUF3304) (family)
This is a family of bacterial 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 PF00668: Condensation domain (family)
This domain is found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain ([pfam:PF00550]). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site.
Wikipedia: In molecular biology, the condensation domain is a protein domain found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non-ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pp-binding). It has been shown that mutations in the HHXXXDG sequence motif in this domain abolish activity suggesting this is part of the active site.
Pfam PF15693: Mediator complex subunit 26 C-terminal (domain)
Med26_C is the C-terminal domain of subunit 26 of the Mediator complex in eukaryotes. Med19 and Med26 act synergistically to mediate the interaction between REST (a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes) and Mediator. The C-terminal domain is critical and sufficient for its assembly into Mediator and its interaction with Pol II. The most highly conserved C-terminal amino acids are critical for these interactions because deletion of the last eight amino acids from the Med26 C terminus disrupted binding to Mediator and Pol II.
Wikipedia: Mediator of RNA polymerase II transcription subunit 26 is an enzyme that in humans is encoded by the MED26 gene. It forms part of the Mediator complex.
Pfam PF05649: Peptidase family M13 (family)
M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure  regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk.
Pfam PF03397: Rhabdovirus matrix protein (family)
The matrix (M) proteins of Rabies virus (RV) plays a key role in both assembly and budding of progeny virions. A PPPY motif (PY motif or late-budding domain) is conserved in the M proteins. These PY motifs are important for virus budding and for mediating interactions with specific cellular proteins containing WW domains.
Pfam PF18035: Bap31/Bap29 cytoplasmic coiled-coil domain (coiled_coil)
Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8.  Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31. This entry represents the cytoplasmic domain which forms a heterodimeric coiled-coil with Bap29. This Bap29 and Bap31 are homologous to each other and this entry includes both proteins.
Pfam PF23826: Domain of unknown function (DUF7196) (domain)
This entry represents an uncharacterized protein domain found in viruses and bacteria, including Mycobacteriophages, Nocardia, Streptomyces and Rhodococcus species. The domain is typically between 50-99 amino acids in length. In some proteins, the domain is found at the C-terminus. AlphaFold prediction shows a small domain composed of three beta strands in a sheet with a single alpha helix between strands 2 and 3.
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 PF10665: Minor capsid protein (family)
This is a putative tail-knob or minor capsid protein from bacteriophages.
Pfam PF15333: TATA box-binding protein-associated factor 1D (family)
TAF1D is a family of eukaryotic proteins that are members of the SL1 complex The SL1 complex includes TBP and TAF1A, TAF1B and TAF1C, and plays a role in RNA polymerase I transcription. Alternatives names have included 'JOSD3, Josephin domain containing 3'.
Pfam PF11608: MARF1, RNA recognition motif 1 (domain)
MARF1 (also known as Limkain-b1) is an essential protein for controlling meiosis and retrotransposon surveillance in mouse oocytes, first described as a human autoantigen localised to a subset of ABCD3 and PXF marked peroxisomes. It may function both as an adaptor to recruit specific RNA targets and an effector to catalyse the specific cleavages of target RNAs. MARF1 contains an N-terminal NYN domain, two central RRMs, and C-terminal OST-HTH/LOTUS domains. This domain represents the RNA recognition motif 1 (RRM1) of MARF1.
Pfam PF22134: DNA Mimic Protein Arn (domain)
This entry represents Arn (Anti-restriction nuclease) proteins found in Caudoviricetes phages. The structure of Arn consists of a three- stranded, anti-parallel beta-sheet on one side, while on the otherside, four alpha-helices are bundled together. Arn was identified as an inhibitor of the restriction enzyme McrBC. A structural analysis of Arn revealed that its shape and negative charge distribution are similar to dsDNA, suggesting that this protein could act as a DNA mimic.
Pfam PF18627: Peptidoglycan GlcNAc deacetylase N-terminal domain (domain)
This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a member of the family 4 carbohydrate esterases (CE-4).
Pfam PF01037: Lrp/AsnC ligand binding domain (domain)
The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold. This domain binds almost exclusively amino acids but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).