SII-SWORD/CoKE huggingface dataset:
Pfam PF04574: Protein of unknown function (DUF592) (family)
This region is found in some SIR2 family proteins ([pfam:PF02146]).
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 PF09257: BCMA, TALL-1 binding (domain)
Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1.
Wikipedia: B-cell maturation antigen, also known as tumor necrosis factor receptor superfamily member 17 (TNFRSF17), is a protein that in humans is encoded by the TNFRSF17 gene.
Pfam PF12369: Gonadotropin hormone receptor transmembrane region (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF00560], [pfam:PF00001]. There are two completely conserved C residues that may be functionally important. This family contains the transmembrane region of Follicular stimulating hormone and leutenizing hormone - the two major gonadotropin hormone receptors. These receptors are G protein coupled receptors involved in development and maturation of germ cells in both fecund genders. The transmembrane region is conserved between the two different receptors while the extracellular ligand binding domains are less well conserved.
Pfam PF18380: Holliday junction resolvase Gen1 C-terminal domain (domain)
This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the cleavage of Holliday junction recombination intermediates. Structural comparison indicates that the C-terminal domain is similar to a series of chromobox homology proteins. Functional analysis indicates that the chromodomain provides an additional DNA binding site necessary for efficient HJ cleavage, and its truncation severely hampers GEN1's catalytic activity.
Wikipedia: A chromodomain is a protein structural domain of about 40–50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved among both plants and animals, and is represented in a large number of different proteins in many genomes, such as that of the mouse. Some chromodomain-containing genes have multiple alternative splicing isoforms that omit the chromodomain entirely. In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions. Chromodomain-containing proteins also bind methylated histones and appear in the RNA-induced transcriptional silencing complex. In histone modifications, chromodomains are very conserved. They function by identifying and binding to methylated lysine residues that exist on the surface of chromatin proteins and thereby regulate gene transcription.
Pfam PF01881: CRISPR associated protein Cas6, C-terminal (domain)
This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 showed it adopts a tandem ferredoxin/RRM fold. This entry represents the C-terminal domain.
Pfam PF18975: Family of unknown function (DUF5711) (repeat)
This is a family of unknown function mostly found in bacteria and archea. Some members contain WD repeats.
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 PF01424: R3H domain (domain)
The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues.  The function of the domain is predicted to be binding ssDNA.
Pfam PF11982: Domain of unknown function (DUF3483) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 230 amino acids in length. This domain is found associated with [pfam:PF02754].
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 PF09481: CRISPR-associated protein Cse1 (CRISPR_cse1) (family)
Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry, represented by CT1972 from Chlorobaculum tepidum, is found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse1.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF00852: Glycosyltransferase family 10 (fucosyltransferase) C-term (domain)
This is the C-terminal domain of a family of fucosyltransferases. This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is known as glycosyltransferase family 10. The C-terminal domain is the likely binding-region for ADP (manuscript in publication).
Wikipedia: A fucosyltransferase is an enzyme that transfers an L-fucose sugar from a GDP-fucose donor substrate to an acceptor substrate. The acceptor substrate can be another sugar such as the transfer of a fucose to a core GlcNAc (N-acetylglucosamine) sugar as in the case of N-linked glycosylation, or to a protein, as in the case of O-linked glycosylation produced by O-fucosyltransferase. There are various fucosyltransferases in mammals, the vast majority of which, are located in the Golgi apparatus. The O-fucosyltransferases have recently been shown to localize to the endoplasmic reticulum (ER).
Pfam PF03968: LptA/(LptD N-terminal domain) LPS transport protein (domain)
This family of proteins are involved in lipopolysaccharide transport across the gram negative inner and outer membranes. The type examples for this family are E. coli LptA [swissprot:P0ADV1] and the N-terminal domain of LptD [swissprot:P31554].
Pfam PF19775: Family of unknown function (DUF6261) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 246 and 334 amino acids in length. Some members are thought to be hemagglutinin-related 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 PF11056: Recombination, repair and ssDNA binding protein UvsY (family)
UvsY protein enhances the rate of single-stranded-DNA-dependant ATP hydrolysis by UvsX protein. The enhancement of ATP hydrolysis by UvsY protein is shown to result from the ability of UvsY protein to increase the affinity of UvsX protein for single-stranded DNA.
Pfam PF24865: Domain of unknown function (DUF7731) (domain)
This entry represents a domain found in uncharacterised plant proteins. It contains a set of conserved cysteines that are predicted to form disulfide bonds.
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 PF23150: CFAP61 dimerisation domain (domain)
This entry represents a domain found at the C-terminal of the FAD reductase domain of cilia and flagella associated protein 61 (CFAP61), according to structure prediction, which may be involved in dimerisation. CFAP61 is located at the midpiece of the sperm, where it apparently functions in flagellum formation.
Pfam PF08273: Zinc-binding domain of primase-helicase (domain)
This entry is represented by bacteriophage T7 DNA helicase/primase (also known as Gp4), an ATP-dependent DNA helicase and primase that is essential for viral DNA replication and recombination . Primase activity synthesizes short RNA primers at the sequence 5'-GTC-3' on the lagging strand that the polymerase elongates using dNTPs and providing the primase is still present .

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities .
Pfam PF13999: MarB protein (family)
The MarB protein is found in the multiple antibiotic resistance (mar) locus in Escherichia coli. The MarB protein is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved GSDKSD sequence motif.
Pfam PF17452: Uncharacterized YnfE-like (family)
This is a family of unknown function found in Bacillus.
Pfam PF21717: DTX3L, alpha/beta domain (domain)
DTX3L is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. This entry represents a domain found towards the N-terminal of DTX3L, whose function is unknown. According to structure predictions (AlphaFold), it may adopt a beta-alpha-beta-beta-alpha conformation, similar to Smr domains.
Pfam PF04153: NOT2/NOT3/NOT5 C-terminal (domain)
NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This entry represents the C-terminal SH3-like domain of NOT2, NOT3 and NOT5, which mediate heterodimerization and NOT-module assembly.
Pfam PF09822: ABC-type uncharacterized transport system (domain)
This domain is found in various prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins.
Pfam PF10460: Peptidase M30 (family)
This family contains the metallopeptidase hyicolysin. Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.
Pfam PF11547: E3 ubiquitin ligase EDD (domain)
EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins.
Pfam PF04008: Adenosine specific kinase (family)
The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation. In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein.
Pfam PF06406: Plasmid segregation protein ParM, N-terminal (domain)
This entry consists of several bacterial ParM/StbA plasmid stability proteins. ParM is involved in the control of plasmid partition and required for the accurate segregation of the plasmid, which forms filaments to drive partition. This protein is an actin homologue and consists of two domains (I and II) with the same conformation.  This is the N-terminal domain.
Wikipedia: ParM is a prokaryotic actin homologue which provides the force to drive copies of the R1 plasmid to opposite ends of rod shaped bacteria before cytokinesis.
Pfam PF14256: YwiC-like protein (family)
The YwiC-like protein family includes the B. subtilis YwiC protein [swissprot:P46909], which is functionally uncharacterised. This domain family is found in bacteria, and is approximately 130 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Pfam PF14584: Protein of unknown function (DUF4446) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 165 and 176 amino acids in length.
Pfam PF17192: MukF middle domain (domain)
The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid.
Pfam PF05923: APC repeat (conserved_site)
This short region is found repeated in the mid region of the adenomatous polyposis  proteins (APCs). In the human protein many cancer-linked SNPs are found near the first three occurrences of the motif. These repeats bind beta-catenin.
Pfam PF10734: Protein of unknown function (DUF2523) (family)
This is a family of phage related proteins whose function is uncharacterised.
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 PF17646: Closterovirus 1a polyprotein central region (family)
This family represents an alignment of the Zemlya region of closteroviruses. The alignment of the 1a polyprotein of the Closteroviridae family members revealed that this region was not conserved in other genera. The homologs of the Zemlya region are not found in other viral or cellular proteins. This region is named the Zemlya region (zemlya is the Russian word for Earth), meaning that its conserved amino acid sequence represents a 'solid ground' within the highly variable central region of 1a polyporotein. It is composed of four predicted alpha-helices, alphaA to alphaD, and contains three conserved positions: i) a strictly conserved glutamate (E) in helix alphaA (E1291 in Beet yellows closterovirus (BYV)); ii) a strictly conserved proline (P1380) in alphaD; and iii) a conserved basic position (arginine or lysine; R1384 in BYV). The presence of a conserved proline in helix alphaD is noteworthy because prolines are strongly disfavoured in helices; this proline most probably induces a kink in the helix. Functional studies have suggested that most part of the Zemlya region, targets the ER and remodels the ER membranes. More specifically, deletion analysis and substitutions of the conserved hydrophobic amino acid residues suggest a role of the putative amphipathic helix (alphaD) in the formation of globules. Hence it was proposed that this specific region in 1a protein protein may be involved in the biogenesis of closterovirus.
Pfam PF22506: Cj1289-like, C-terminal domain (domain)
This domain is found at the C-terminal end of the possible periplasmic protein [swissprot:Q0P8W8] from Campylobacter jejuni (Cj1289) and similar sequences mainly found in epsilonproteobacteria. This domain is normally associated to [pfam:PF09312]. It shows an alpha-beta configuration. Its specific function is unknown.
Pfam PF03073: TspO/MBR family (family)
Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues.
Wikipedia: Translocator protein (TSPO) is an 18 kDa protein mainly found on the outer mitochondrial membrane. It was first described as peripheral benzodiazepine receptor (PBR), a secondary binding site for diazepam, but subsequent research has found the receptor to be expressed throughout the body and brain. In humans, the translocator protein is encoded by the TSPO gene. It belongs to a family of tryptophan-rich sensory proteins. Regarding intramitochondrial cholesterol transport, TSPO has been proposed to interact with StAR to transport cholesterol into mitochondria, though evidence is mixed.
Pfam PF04957: Ribosome modulation factor (family)
This protein associates with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia coli cells.
Pfam PF15811: Small VCP/p97-interacting protein (family)
SVIP, small VCP/p97-interacting protein, is a family of proteins found in eukaryotes. SVIP was identified by yeast two-hybrid screening to be an interactive partner of VCP/p97. Mammalian VCP/p97 and its yeast counterpart Cdc48p participate in the formation of organelles, including the endoplasmic reticulum (ER), Golgi apparatus, and nuclear envelope. Over-expression of SVIP caused the formation of large vacuoles that seemed to be derived from the ER. The family has two putative coiled-coil regions and contains proteins of approximately 80 amino acids in length.
Pfam PF24232: Family of unknown function (DUF7445) (family)
This entry represents an uncharacterized protein family found in mycobacteriophages. The function of this protein is currently unknown.  The family is approximately 147 amino acids long. These proteins contain two small domains. The most N-terminal one contains a CXXC and HXXC motif that likely bind to zinc.
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 PF06763: Prophage minor tail protein Z (GPZ) (family)
This family consists of several prophage minor tail protein Z like sequences from Escherichia coli, Salmonella typhimurium and Lambda-like bacteriophages.
Pfam PF01593: Flavin containing amine oxidoreductase (domain)
This family consists of various amine oxidases, including maze polyamine oxidase (PAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines.  Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.
Wikipedia: Flavin-containing amine oxidoreductases are a family of various amine oxidases, including maize polyamine oxidase (PAO), L-amino acid oxidases (LAO) and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. In vertebrates, MAO plays an important role in regulating the intracellular levels of amines via their oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidise spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid-binding proteins, and antibacterial glycoproteins.
Pfam PF02694: Uncharacterised BCR, YnfA/UPF0060 family (family)
Some members of this family have been proposed to function as a thallium-specific efflux pump.