SII-SWORD/CoKE huggingface dataset:
Pfam PF01249: Ribosomal protein S21e (family)
This entry represents the small ribosomal subunit protein eS21 found in eukaryotes.
A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts .
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 PF22896: Ribonuclease R, OB first domain, N-terminal (domain)
This entry represents a N-terminal OB (oligonucleotide/ oligosaccharide binding) domain found in a set of bacterial Ribonuclease R proteins. Ribonuclease R proteins are 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs.
Pfam PF10108: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB (family)
This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Pfam PF14952: Putative treble-clef, zinc-finger, Zn-binding (domain)
This domain resembles the zinc-binding domain of prokaryotic topoisomerases, family DNA_ligase_ZBD [pfam:PF03119]. The function of the eukaryotic proteins it is carried on is not known.
Pfam PF13255: Protein of unknown function (DUF4046) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 64 and 331 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 PF19626: Family of unknown function (DUF6131) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 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 PF07857: Transmembrane family, TMEM144 of transporters (family)
Members of this family fall in to the drug/metabolite transporter (dmt) superfamily. They carry 10xTM domains arranged as 5+5. Although these two sets may originally have arisen by gene-duplication the divergence now is such that the similarity between the two halves is no longer detectable by sequence.
Pfam PF15405: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF08154: NLE (NUC135) domain (domain)
This domain is located N terminal to WD40 repeats.  It is found in  the microtubule-associated protein [swissprot:Q12024].
Pfam PF17298: Family of unknown function (DUF5349) (family)
This is a family of unknown function found in Saccharomycetaceae.
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 PF20546: Family of unknown function (DUF6760) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically 89 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 PF06751: Ethanolamine ammonia lyase large subunit (EutB) (domain)
This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins ([ec:4.3.1.7]). Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC).
Pfam PF19529: Family of unknown function (DUF6057) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found primarily in Bacteroidetes bacteria. Proteins in this family are typically between 379 and 586 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 PF08321: PPP5 TPR repeat region (repeat)
This region is specific to the PPP5 subfamily of serine/threonine phosphatases and contains TPR repeats.
Pfam PF03849: Transcription factor Tfb2 (family)
This entry represents the p52/Tfb2 subunit in the TFIIH complex, which is not only required for transcription but also plays a central role in DNA repair. The TFIIH multiprotein complex consists of a 7-subunit core (XPB, p62, p52, p44, p34, and TTDA) that is associated with a 3-subunit CDK-activating kinase module (MAT1, cyclin H and Cdk7) . The p52 subunit interacts with subunit XPB, which is an ATP-dependent 3'-5' DNA helicase, and stimulates its ATPase activity .
Pfam PF19685: Family of unknown function (DUF6187) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from  the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. This family appears to be predominantly found in  Actinobacteria.
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 PF09762: CCDC93 coiled-coil domain (coiled_coil)
This is a coiled-coil domain found in CCDC93. Human CCDC93 is part of the COMMD/CCDC22/CCDC93 (CCC) complex that interacts with the multisubunit WASH complex, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. The CCC complex controls Notch activation by modulating its intracellular trafficking.
Pfam PF18210: Knl1 RWD C-terminal domain (domain)
This domain is found in Knl1, a sub-unit of the KMN network, present in Homo sapiens. The KMN network is the core of the outer kinetochore which is responsible for microtubule binding/stabilization and controls the spindle assembly checkpoint. This domain is the second of two RING finger, WD repeat, DEAD-like helicase (RWD) domains. The tandem RWD domains mediate kinetochore targeting of the microtubule-binding subunits by interacting with the Mis12 complex.  The Mis12 complex is a KMN sub-complex that tethers directly onto the underlying chromatin layer.
Wikipedia: A kinetochore is a disc-shaped protein structure associated with duplicated chromatids in eukaryotic cells where the spindle fibers attach during cell division to pull sister chromatids apart. The kinetochore assembles on the centromere and links the chromosome to microtubule polymers from the mitotic spindle during mitosis and meiosis. The term kinetochore was first used in a footnote in a 1934 Cytology book by Lester W. Sharp and commonly accepted in 1936. Sharp's footnote reads: "The convenient term kinetochore has been suggested to the author by J. A. Moore", likely referring to John Alexander Moore who had joined Columbia University as a freshman in 1932.
Pfam PF16713: Enriched in aromatic and glycine Residues box (domain)
The Enriched in Aromatic and Glycine Residues (EAGR) box is found in proteins from Mycoplasma, often tandemly repeated, and may have a role in cell motility.
Pfam PF23395: SAM-like domain (domain)
This entry represents a SAM-like domain found close to the C-terminus of a variety of long proteins.  This domain is often associated with [pfam:PF23394]. The function of this domain unknown.
Pfam PF23091: ELAPOR1-like, TNF receptor-like (domain)
This domain is found in Endosome/lysosome-associated apoptosis and autophagy regulator family member 2 from humans (ELAPOR1), which may protect cells from cell death by inducing cytosolic vacuolisation and up-regulating the autophagy pathway and may play a role in apoptosis and cell proliferation. This domain, which contain several conserved cysteines, is predicted to adopt a TNF-receptor (TNFR) fold.
Pfam PF01167: Tub family (domain)
Tubby, an autosomal recessive mutation, mapping to mouse chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This mutation maps to the tub gene . The mouse tubby mutation is the cause of maturity-onset obesity, insulin resistance and sensory deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member , although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development .

Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal (IPR005398) portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed Î²-barrel that surrounds a central Î± helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors .
Wikipedia: The tubby protein is encoded by the TUB gene. It is an upstream cell signaling protein common to multicellular eukaryotes. The first tubby gene was identified in mice, and proteins that are homologous to tubby are known as "tubby-like proteins" (TULPs). They share a common and characteristic tertiary structure that consists of a beta barrel packed around an alpha helix in the central pore. The gene derives its name from its role in metabolism; mice with a mutated tubby gene develop delayed-onset obesity, sensorineural hearing loss, and retinal degeneration.
Pfam PF11847: Alpha-(1->3)-arabinofuranosyltransferase, N-terminal GT-C domain (family)
This domain is found at the N-terminal end of alpha-(1->3)- arabinofuranosyltransferase from Mycolicibacterium smegmatis (AftD, [ec:2.4.2.47]), which is involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan -peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. It catalyses the addition of an arabinofuranosyl (Araf) residue from the sugar donor decaprenyl-phospho-arabinose (DPA) on the C-3 of an alpha-(1->5)-linked Araf from the arabinan backbone of AG. This domain shows mixed alpha/beta folds homologous to other solved GT-C glycosyltransferase structures.
Pfam PF18946: GpV Apex motif (conserved_site)
This entry represents a short motif found at the C-terminus of Phage gpV proteins. These proteins act as a spike for piercing the host membrane. The apex motif contains a conserved HXH motif that coordinates an iron ion.
Pfam PF22028: Family of unknown function (DUF6934) (family)
This is a family of uncharacterised bacterial proteins. They are predicted to adopt an alpha/beta structure consisting of a central mixed beta-sheet packed on both sides with alpha-helices that is reminiscent to the common structural core of N-acetyltransferases (NAT).
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 PF07941: Potassium channel Kv1.4 tandem inactivation domain (family)
This family features the tandem inactivation domain found at the N-terminus of the Kv1.4 potassium channel. It is composed of two subdomains. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N-terminus anchored at a 5-turn helix, and is thought to work by occluding the ion pathway, as is the case with a classical ball domain. Inactivation domain 2 (ID2, residues 40-50) is a 2.5 turn helix with a high proportion of hydrophobic residues that probably serves to attach ID1 to the cytoplasmic face of the channel. In this way, it can promote rapid access of ID1 to the receptor site in the open channel. ID1 and ID2 function together to being about fast inactivation of the Kv1.4 channel, which is important for the channel's role in short-term plasticity.
Wikipedia: Potassium voltage-gated channel subfamily A member 4 also known as Kv1.4 is a protein that in humans is encoded by the KCNA4 gene. It contributes to the cardiac transient outward potassium current (Ito1), the main contributing current to the repolarizing phase 1 of the cardiac action potential.
Pfam PF18924: Protein of unknown function (DUF5674) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 110 amino acids in length.
Pfam PF08974: Domain of unknown function (DUF1877) (domain)
This domain is found in a set of hypothetical 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.
Pfam PF03167: Uracil DNA glycosylase superfamily (domain)
This entry represents various uracil-DNA glycosylases and related DNA glycosylases (3.2.2), such as uracil-DNA glycosylase , thermophilic uracil-DNA glycosylase , G:T/U mismatch-specific DNA glycosylase (Mug) , and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1) . These proteins have a 3-layer Î±/Î²/Î± structure.

Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosylic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs . These aberrant uracil residues are genotoxic . The sequence of uracil-DNA glycosylase is extremely well conserved  in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses .
Wikipedia: DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC 3.2.2. Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced. DNA glycosylases catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond.
Pfam PF11250: Fantastic Four meristem regulator (family)
FAF is a family of plant proteins that regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop. The proteins are expressed in the centre of the shoot meristem, overlapping with the site of WUS - the homeodomain transcription factor WUSCHEL- expression. FAF proteins are capable of modulating shoot growth by repressing WUS in the organising centre of the shoot meristem. The ability of plants to form new organs throughout their life cycle requires tight control of the meristems to avoid unregulated growth. Plants have evolved an elaborate genetic network that controls meristem size and maintenance. WUS and the CLAVATA (CLV) ligand-receptor system are at the core of the network that regulates the size of the stem cell population in the shoot meristem.
Pfam PF08069: Ribosomal S13/S15 N-terminal domain (domain)
This domain is found at the N-terminus of ribosomal S13 and S15 proteins.                      This domain is also identified as NUC021.
Pfam PF08195: TRI9 protein (family)
Putative gene of 129 bp in the Trichothecene gene cluster of Fusarium sporotrichioides and F. graminearum. Encoding a predicted protein of 43 amino acids which function is unknown.
Pfam PF08941: USP8 interacting (domain)
This domain interacts with the UBP deubiquitinating enzyme USP8.
Pfam PF04430: Protein of unknown function (DUF498/DUF598) (domain)
This is a large family of uncharacterised proteins found in all domains of life.  The structure shows a novel fold with three beta sheets.  A dimeric form is found in the crystal structure. It was suggested that the cleft in between the two monomers might bing nucleic acid.
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 PF12092: Protein of unknown function (DUF3568) (family)
This family of bacterial proteins includes the outer membrane lipoprotein Flpp3 from Francisella tularensis ([swissprot:Q5NF33]). Flpp3, a virulence determinant of tularemia, shows a six stranded  beta-sheet supported with two crossing alpha-helices. It has a  hydrophobic internal cavity that has been suggested to bind a small  organic molecule. However, its specific function is still 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 PF10145: Phage-related minor tail protein (family)
Members of this family are found in putative phage tail tape measure proteins.
Pfam PF23341: PEP5/VPS11 N-terminal (repeat)
This entry represents the beta-propeller domain found at the N-terminal of the Pep5-like zinc finger protein from Schizosaccharomyces pombe and its orthologues from human, mouse and A. thaliana Vacuolar protein sorting-associated protein 11. Vps11 aggregates with other Vps proteins to form the homotypic fusion and protein sorting complex (HOPS), which promotes the fusion of late endosomes and autophagosomes with lysosomes. Pep5 (also known as Vps11) was initially isolated as a protease deficient mutant and shown to be involved in protein trafficking and vacuole biogenesis pathways.