SII-SWORD/CoKE huggingface dataset:
Pfam PF17340: Family of unknown function (DUF5370) (family)
This is a family of unknown function found in Bacillaceae.
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 PF22627: AglB core domain (domain)
This entry represents the C-terminal core domain of archaeal oligosaccharyltransferase AglB that transfers oligosaccharide chain from a lipid-linked oligosaccharide (LLO) donor to the asparagine residues in the N-glycosylation sequon, Asn-X-Ser/Thr (X=Pro). In the archaea AlgB, it occurs alone, rather than in complex as the eukaryotic homologue STT3. This domain adopts a mixed alpha/beta fold and contains a highly conserved WWDYG motif that may be of functional relevance.
Pfam PF16949: Putative ATP-binding cassette (family)
This is a family of putative two component ABC exporters. This is the membrane protein of approximately 573 residues and twelve transmembrane domains. It is encoded adjacent to an ATPase.
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF08689: Mediator complex subunit Med5 (family)
The mediator complex is required for the expression of nearly all RNA pol II dependent genes in Saccharomyces cerevisiae. Deletion of the MED5 gene leads to increased transcription of nuclear genes encoding components of the oxidative phosphorylation machinery, and decreased transcription of mitochondrial genes encoding components of the same machinery. There is no orthologue from pombe, and this subunit appears to be fungal specific.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.
Pfam PF03398: Regulator of Vps4 activity in the MVB pathway (family)
ESCRT-I, -II, and -III are endosomal sorting complexes required for transporting proteins and carry out cargo sorting and vesicle formation in the multivesicular bodies, MVBs, pathway. These complexes are transiently recruited from the cytoplasm to the endosomal membrane where they bind transmembrane proteins previously marked for degradation by mono-ubiquitination. Assembly of ESCRT-III, a complex composed of at least four subunits (Vps2, Vps24, Vps20, Snf7), is intimately linked with MVB vesicle formation, its disassembly being an essential step in the MVB vesicle formation, a reaction that is carried out by Vps4, an AAA-type ATPase. The family Ist1 is a regulator of Vps4 activity; by interacting with Did2 and Vps4, Ist1 appears to regulate the recruitment and oligomerisation of Vps4. Together Ist1, Did2, and Vta1 form a network of interconnected regulatory proteins that modulate Vps4 activity, thereby regulating the flow of cargo through the MVB pathway.
Pfam PF03615: GCM motif protein (family)
GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologues . In GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved.

The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' . The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues . The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding . The GCM domain is a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain . The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five-and three-stranded Î²-sheets, respectively, with three small helical segments packed against the same side of the two Î²-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded Î²-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the Î²-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site.
Wikipedia: In molecular biology, the GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologues. In GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 amino acids. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved.
Pfam PF13403: Hint domain (domain)
This domain is found in inteins.
Pfam PF02198: Sterile alpha motif (SAM)/Pointed domain (domain)
The highly conserved PNT (or Pointed) domain is found within a subset of the Ets transcription factors, including mammalian Ets-1, Ets-2, Erg, Fli-1, GABPalpha, and Tel, as well as Drosophila Pnt-P2 and Yan. The PNT domain is structurally related to the larger group of SAM domains through a common tertiary arrangement of four Î±-helices. A role in protein-protein association has been established for the PNT domain .
Pfam PF10758: Protein of unknown function (DUF2586) (family)
This bacterial family of proteins is a component of a contractile injection system related to phage sheath 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 PF03726: Polyribonucleotide nucleotidyltransferase, RNA binding domain (domain)
This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction.
Pfam PF02605: Photosystem I reaction centre subunit XI (family)
This family consists of the photosystem I reaction centre subunit XI, PsaL, from plants and bacteria.  PsaL is one of the smaller subunits in photosystem I with only two transmembrane alpha helices and interacts closely with PsaI.
Pfam PF19063: Family of unknown function (DUF5759) (family)
This is a family of uncharacterised proteins of unknown function found in viruses.
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 PF18374: Enolase N-terminal domain-like (domain)
This is the N-terminal domain found in o-succinylbenzoate synthase (OSBS) enzymes ([ec:4.2.1.113]). Like other members of the enolase superfamily, OSBS enzymes are composed of a C-terminal catalytic (beta/alpha)7beta-barrel domain [pfam:PF00113] and an N-terminal capping domain with an alpha+beta fold that is found in the enolase superfamily. This domain is different from other enolase super family N-terminal domains such as [pfam:PF03952]. This actino-bacterial N-terminal domain lacks the prototypical first two helices of the enolase capping domains. Structural analysis of T. fusca OSBS reveals that this is compensated for with an extra helix appended to the C-terminus.
Wikipedia: Phosphopyruvate hydratase, usually known as enolase, is a metalloenzyme (EC 4.2.1.11) that catalyses the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The chemical reaction is:2-phospho-D-glycerate  phosphoenolpyruvate + H2O
Pfam PF17866: AAA lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.
Pfam PF22057: BACOVA_00961-like (family)
This family represents BACOVA_00961 from Bacteroides ovatus ([swissprot:A7LT22]) and similar sequences mainly found in bacteroidetes. This protein shows an alpha-beta configuration.
Pfam PF05486: Signal recognition particle 9 kDa protein (SRP9) (domain)
This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the "Alu domain" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP. This family also contains the homologous fungal SRP21.
Pfam PF14836: Ubiquitin-like domain (domain)
This ubiquitin-like domain is found in several ubiquitin carboxyl-terminal hydrolases and in gametogenetin-binding protein.
Pfam PF19318: Family of unknown function (DUF5918) (family)
This family represents the N-terminal domain of the RING finger protein 37 (RNF37), an  U-box domain-containing protein. This is a variable region that probably has a role in function regulation.
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 PF24999: Laminin subunit beta-4-like domain (domain)
This domain is found in human Laminin subunit beta-4 (LAMB4) and in similar animal proteins. LAMB4 is thought to mediate the attachment, migration and organisation of cells into tissues during embryonic development by interacting with other extracellular matrix components. This domain is found associated with several copies of [pfam:PF00053]. It is predicted to adopt an all-alpha configuration.
Pfam PF18053: DNA gyrase B subunit insert domain (domain)
This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.
Pfam PF09654: Protein of unknown function (DUF2396) (family)
These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N-terminus.
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 PF04278: Tic22-like family (family)
The preprotein translocation at the inner envelope membrane of chloroplasts so far involves five proteins: Tic110, Tic55, Tic40, Tic22 (this family) and Tic20. The molecular function of these proteins has not yet been established.
Pfam PF09179: TilS substrate binding domain (domain)
This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.
Pfam PF18376: Mevalonate 5-diphosphate decarboxylase C-terminal domain (domain)
Mevalonate diphosphate decarboxylase ([ec:4.1.1.33]) catalyzes the ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) to form isopentenyl 5-diphosphate. The reaction is required for production of polyisoprenoids and sterols from acetyl-CoA.  This entry represents the C-terminal domain of the mevalonate 5-diphosphate decarboxylase enzyme which is a member of the GHMP kinase superfamily.
Pfam PF01568: Molydopterin dinucleotide binding domain (domain)
This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a  molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both  molybdopterin guanine dinucleotide molecules.
Pfam PF19522: Family of unknown function (DUF6052) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001397) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the lidamycin  biosynthetic gene cluster from Streptomyces globisporus C-1027 and appears to be predominantly present 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 PF09781: NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit (family)
Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF08163: DNA-dependent protein kinase catalytic subunit, CC3 (repeat)
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ), which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand breaks (DSBs) repair. DNA-PKcs phosphorylates a number of protein substrates, including the heat shock protein 90 (HSP90), the transcription factors p53, specificity protein 1 (Sp1), among others. It folds into three well-defined large structural units, consisting of a N-terminal region (arranged in four supersecondary alpha-helical structures, N1-N4), the Circular Cradle (consisting of five supersecondary alpha-helical structures CC1-CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. This domain represents a region of the Circular Cradle segment (CC) from DNA-PKcs that covers the complete CC3 and part of CC4. This domain contains the Ku-binding site A and a the highly conserved region (HCR) II.
Pfam PF08213: Mitochondrial mRNA-processing protein COX24, C-terminal (domain)
This domain of unknown function is found at the C terminal end of  Mitochondrial small ribosomal subunit protein mS38, also known as Mitochondrial mRNA-processing protein COX24 in yeast which is involved in the splicing of the COX1 mRNA. COX24 is a component of the mitochondrial ribosome (mitoribosome), responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. This domain is also found in COX24 mammalian homologue Aurora kinase A-interacting protein. This entry also includes uncharacterised proteins from bacteria.
Pfam PF06393: BH3 interacting domain (BID) (domain)
BID is a member of the BCL-2 superfamily of proteins are  key regulators of programmed cell death, hence this family is related to [pfam:PF00452] .  BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing  the BH3 domain and significantly changing the surface  charge and hydrophobicity, which causes a change of cellular localisation.
Wikipedia: The BH3 interacting-domain death agonist, or BID, gene is a pro-apoptotic member of the Bcl-2 protein family. Bcl-2 family members share one or more of the four characteristic domains of homology entitled the Bcl-2 homology (BH) domains, and can form hetero- or homodimers. Bcl-2 proteins act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities.
Pfam PF11784: Protein of unknown function (DUF3320) (family)
This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-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 PF20322: Family of unknown function (DUF6617) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 315 and 341 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 PF12015: Bud3, N-terminal (domain)
This domain is found in the N-terminal of the yeast Bud3 protein. Bud3 is involved in bud-site selection in budding yeasts. This domain has a conserved ENL sequence motif.
Pfam PF18203: IPTL-CTERM motif (conserved_site)
This entry represents a predicted C-terminal sorting motif.
Pfam PF03945: delta endotoxin, N-terminal domain (domain)
This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding.
Wikipedia: Delta endotoxins (δ-endotoxins) are a family of pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action and are the primary toxin produced by the genetically modified (GM) Bt maize/corn and other GM crops. During spore formation the bacteria produce crystals of such proteins that are also known as parasporal bodies, next to the endospores; as a result some members are known as a parasporin. The Cyt (cytolytic) toxin group is another group of delta-endotoxins formed in the cytoplasm. VIP toxins are formed at other stages of the life cycle.
Pfam PF14585: CagY type 1 repeat (repeat)
This repeat is found at the N-terminus of the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells ().
Pfam PF08170: POPLD (NUC188) domain (domain)
This domain is found in POP1-like nucleolar proteins.
Pfam PF04433: SWIRM domain (domain)
This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins.  It contains a helix-turn helix motif and binds to DNA.
Pfam PF16444: Domain of unknown function (DUF5041) (family)
This family consists of several uncharacterized proteins around 230 residues in length and is mainly found in various Bacteroidales 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 PF14621: RFX5 DNA-binding domain (domain)
RFX5 and RFXAP reveals molecular details associated with MHCII gene expression.
Pfam PF13758: Prefoldin subunit (coiled_coil)
This family includes prefoldin subunits that are not detected by [pfam:PF02996].
Pfam PF05943: EvpB/VC_A0108, tail sheath N-terminal domain (domain)
EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell.
Pfam PF09488: Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth) (family)
This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together with mannosyl-3-phosphoglycerate phosphatase (MPGP) [ec:2.4.1.217], comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase.