SII-SWORD/CoKE huggingface dataset:
Pfam PF17603: Family of unknown function (DUF5499) (family)
This is a family of unknown function found in Myoviridae.
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 PF21438: Switch activating protein 1, N-terminal (domain)
Sap1 binds to DNA origins during cell growth cycles, preferentially to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T)n -3' (n>1). This is the N-terminal DNA-binding domain.
Pfam PF02375: jmjN domain (family)
This entry represents the JmjN domain.
The JmjN and JmjC domains are two non-adjacent domains which have been identified in the jumonji family of transcription factors. Although it was originally suggested that the JmjN and JmjC domains always co-occur and might form a single functional unit within the folded protein, the JmjC domain was later found without the JmjN domain in organisms from bacteria to human .

JmJC domains are predicted to be metalloenzymes that adopt the cupin fold, and are candidates for enzymes that regulate chromatin remodelling. The cupin fold is a flattened Î²-barrel structure containing two sheets of five antiparallel Î²-strands that form the walls of a zinc-binding cleft. JmjC domains were identified in numerous eukaryotic proteins containing domains typical of transcription factors, such as PHD, C2H2, ARID/BRIGHT and zinc fingers . The JmjC has been shown to function in a histone demethylation mechanism that is conserved from yeast to human .
Pfam PF05162: Ribosomal protein L41 (family)
This entry represents the large ribosomal subunit protein eS32 (previously known as eL41), which associates with the ribonucleoprotein particles of the 60S subunit late in the ribosomal maturation process. eS32 is encoded by the smallest known open reading frame and in yeast is composed of only 24 amino acids, 17 of which are arginine or lysine.
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 PF22325: Interferon-gamma receptor, N-terminal domain (domain)
This domain is found at the N-terminal end of Interferon-gamma receptor from Ectromelia virus (C4R) and simiral viral sequences. CR4 consists of two fibronectin type III domains (FBNIII) containing seven conserved beta-strands each: this entry and [pfam:PF07140].
Pfam PF17222: Viral cysteine endopeptidase C107 (family)
This is a family of viral cysteine endopeptidases that process RNA  polyproteins. Site directed mutagenesis suggest that H1434 and C1539 form the catalytic dyad.
Pfam PF09128: Regulator of G protein signalling-like domain (domain)
Members of this family adopt a structure consisting of twelve helices that fold into a compact domain that contains the overall structural scaffold observed in other RGS proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS ([pfam:PF00615]) fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. Members of the family bind to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways.
Pfam PF23398: FAZ1, conserved domain (domain)
This entry represents a conserved repeated domain found twice in FAZ1 from Trypanosoma brucei and similar sequences from trypanosomatids. This domain is found near the central region and at the very C-terminal of FAZ1. At least 50%  of the T. cruzi genome is repetitive sequence, consisting mostly of large gene families of surface proteins, retrotransposons, and subtelomeric repeats.
Pfam PF07510: GmrSD restriction endonucleases, C-terminal domain (domain)
This entry (previously known as DUF1524) represents a domain found C-terminal in the GmrSD family of modification-dependent restriction endonucleases including SspE proteins. SspE is a dual-function protein that exerts both N-terminal NTPase and C-terminal DNA nicking nuclease activities to defend against phage infection. SspE has a phosphorothioate (PT) modification-binding preference and utilises epigenetic PT modification to accomplish self-nonself discrimination and to coordinate its NTPase and DNA nicking activities to fight against phages. The domain represented in this entry has a DNA nicking nuclease activity and belongs to HNH nuclease superfamily.
Pfam PF09662: Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma) (family)
Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologues.
Pfam PF02438: Late 100kD protein (family)
The late 100kD protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus.
Pfam PF14062: Domain of unknown function (DUF4253) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 110 amino acids in length.
Pfam PF07439: Protein of unknown function (DUF1515) (family)
This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium 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 PF24587: Domain of unknown function (DUF7612) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to fold into a beta-barrel with a PH-like topology.
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 PF00086: Thyroglobulin type-1 repeat (domain)
Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines.  These form three disulphide bridges.  Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.
Wikipedia: Thyroglobulin type-1 repeat is an evolutionary conserved protein domain.
Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6.
Pfam PF01093: Clusterin (family)
Clusterin (Clu), also known as apolipoprotein J, is a vertebrate glycoprotein . Clusterin expression is complex, appearing as different forms in different cell compartments. One set of proteins is directed for secretion, and other clusterin species are expressed in the cytoplasm and nucleus. The secretory form of the clusterin protein (sCLU) is targeted to the ER by an initial leader peptide. This ~60kDa pre-sCLU protein is proteolytically cleaved into alpha- and beta-subunits and further glycosylated to form mature disulfide-linked heterodimeric secretory CLU (sCLU). sCLU is an 80kDa protein and acts as a molecular chaperone, scavenging denatured proteins outside cells . sCLU possesses nonspecific binding activity to hydrophobic domains of various non-native proteins , binds to some bacteria and bacterial proteins , and interacts with different immune molecules .

A specific nuclear form of CLU (nCLU) acts as a pro-death signal, inhibiting cell growth and survival. The nCLU protein has two coiled-coil domains, one at its N terminus that is unable to bind Ku70, and a C-terminal coiled-coil domain that is uniquely able to associate with Ku70 and is minimally required for cell death. The sCLU protein is cytoprotective and anti-apoptotic, whereas the nCLU protein is pro-apoptotic .
This family also includes clusterin-like protein 1 (CLUL1), which is expressed specifically in cone photoreceptor cells  and is likely to be necessary for normal cone function .
Pfam PF06491: Disulphide isomerase (family)
This family of proteins has disulphide isomerase activity, [ec:5.3.4.1]. It has a similar fold to thioredoxin, with an alpha-beta-alpha-beta-alpha-beta-beta-alpha topology. It has a conserved CGC motif in the loop immediately downstream of the first beta strand. This motif is essential for activity.
Pfam PF14188: Domain of unknown function (DUF4311) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13229: Right handed beta helix region (repeat)
This region contains a parallel beta helix region that shares some similarity with Pectate lyases.
Pfam PF24581: Domain of unknown function (DUF7608) (domain)
This domain is found in uncharacterised fungal proteins. It is predicted to adopt an alpha-helical structure consisting of four helices.
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 PF17158: Membrane-associated sensor, integral membrane domain (family)
MASE4 (Membrane-Associated SEnsor) is an integral membrane sensor domain found in various GGDEF domain proteins, including a functional diguanylate cyclase DgcT (YcdT) and the enzymatically inactive CdgI (YeaI) of Escherichia coli. In the Shiga toxin-producing enteroaggregative E. coli O104:H4, which caused the outbreak of the haemolytic uraemic syndrome in Germany in 2011, MASE4-containing diguanylate cyclase DgcX, UniProtKB:B7LBD9_ECO55, was highly expressed, ensuring strong biofilm formation.
Pfam PF04882: Peroxin-3 (family)
Peroxin-3 is a peroxisomal protein. It is thought to be involve in membrane vesicle assembly prior to the translocation of matrix proteins.
Pfam PF00554: Rel homology DNA-binding domain (domain)
Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains.  This is the N-terminal DNA-binding domain that is similar to that found in P53.  The C-terminal domain has an immunoglobulin-like fold (See [pfam:PF16179]) that functions as a dimerisation domain.
Wikipedia: The Rel homology domain (RHD) is a protein domain found in a family of eukaryotic transcription factors, including both NF-κB and NFAT, among others. Some of these transcription factors appear to form multi-protein DNA-bound complexes. Phosphorylation of the RHD appears to play a role in the regulation of some of these transcription factors, acting to modulate the expression of their target genes.
Pfam PF10275: Peptidase C65 Otubain (family)
This family of proteins conserved from plants to humans is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryote being a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif.
Pfam PF15788: Domain of unknown function (DUF4705) (repeat)
DUF4705 is a family of repeated domains that is found in eukaryotes. It can occur up to 10 times in any one sequence. The repeat is rich in glycine and proline residues.
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 PF10905: Protein of unknown function (DUF2695) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18704: Chromatin organization modifier domain 2 (domain)
Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired.  The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5.  Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa).
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 PF24009: Domain of unknown function (DUF7323) (domain)
This entry represents a small beta barrel domain found at the N-terminus of some phage 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 PF16268: Domain of unknown function (DUF4921) (family)
This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various Corynebacterium species.  Several proteins are predicted as galactose-1-phosphate  uridylytransferases. The function of this family is unknown.
Pfam PF08953: Domain of unknown function (DUF1899) (repeat)
This set of domains is found in various eukaryotic proteins. Function 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 PF19142: Family of unknown function (DUF5825) (family)
This is a family of uncharacterised 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 PF05291: Bystin (family)
Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy. This family also includes the yeast protein ENP1. ENP1 is an essential protein in Saccharomyces cerevisiae and is localised in the nucleus. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective yeast cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits.
Pfam PF05096: Glutamine cyclotransferase (repeat)
This family of enzymes [ec:2.3.2.5] catalyse the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively. This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes.
Pfam PF23812: Phage tail assembly chaperone (domain)
This entry represents a putative phage tail assembly chaperone protein domain found primarily in viruses that infect bacteria. The domain is typically around 100 amino acids in length. Tail assembly chaperones are known to assist in forming and attaching phage tails. This entry is found in caudoviruses of several families including Myoviridae, Podoviridae and Siphoviridae, but is not universal in phages.
Pfam PF15910: ICOS V-set domain (domain)
This family contains divergent V-set ig domains found in the ICOS protein.
Wikipedia: V-set domains are Ig-like domains resembling the antibody variable domain. V-set domains are found in diverse protein families, including immunoglobulin light and heavy chains; in several T-cell receptors such as CD2, CD4, CD80, and CD86; in myelin membrane adhesion molecules; in junctional adhesion molecules (JAM); in tyrosine-protein kinase receptors; and in the programmed cell death protein 1 (PD1).
Pfam PF07868: Protein of unknown function (DUF1655) (family)
This protein is found in some prophages found in Lactobacillales lactis ().
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 PF21832: Family of unknown function (DUF6892) (family)
This entry represents a family of uncharacterised bacterial 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.