SII-SWORD/CoKE huggingface dataset:
Pfam PF07792: Docking domain of Afi1 for Arf3 in vesicle trafficking (domain)
This domain occurs at the N-terminal of Afi1, an Arf3p-interacting protein, is a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3, the highly conserved small GTPases (ADP-ribosylation factors). Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalization. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.
Pfam PF02325: YGGT family (family)
This family includes subunit CCB3 of cofactor assembly complex C, involved in c-type cytochrome maturation in photosynthetic organisms. This family also includes uncharacterised protein YggT, associated with bacteria outside the cyanobacteria.
Pfam PF16371: N terminal of Calcineurin-like phosphoesterase (family)
This is the N-terminal of Calcineurin-like phosphoesterases. It is around 150 residues in length from various Bacteroides species. The function of this family is unknown.
Pfam PF01974: tRNA intron endonuclease, catalytic C-terminal domain (domain)
Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron [ec:3.1.27.9].
Pfam PF23682: ORF28 (family)
This protein family includes ORF28 from Fowl aviadenovirus 4, a 97-residues long protein sequence.
Pfam PF06048: Domain of unknown function (DUF927) (domain)
This entry represents a domain found in bacterial proteins of unknown  function. The crystal structure has been solved for a protein containing this domain SWISS:Q0WXP6.
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 PF09551: Stage II sporulation protein R (spore_II_R) (family)
SpoIIR is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation.
Pfam PF16275: Splicing factor 1 helix-hairpin domain (domain)
This domain, approximately 100 residues in length, is  mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA  complex. In this domain, it contains a highly conserved SPSP  motif in its C terminal and phophorylation of SPSP motif induces a  disorder-to-order transition within a novel SF1/U2AF65 interface,  indicating a phosphorylation-dependent control of pre-mRNA splicing factors.
Pfam PF16126: Domain of unknown function (DUF4838) (family)
This family consists of several uncharacterized proteins found in various Bacteroides and Chloroflexus species. The function of this family is unknown.
Pfam PF23387: IFT80/172/WDR35/WDR19 TRP domain (repeat)
This entry describes the tetratricopeptide-like repeat (TPR) domain found in proteins comprising the intraflagellar transport (IFT) complexes B2 and A, which are found in nematodes and mammals, including IFT80, IF172, WDR35, WDR19, and DYF2. The IFT complex is required for retrograde ciliary transport and entry of G protein-coupled receptors (GPCRs) into cilia, and it is involved in ciliogenesis.
Pfam PF14652: Domain of unknown function (DUF4457) (family)
This family of proteins is found in eukaryotes. It is found repeated several times in the vertebrate KIAA0556 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 PF03796: DnaB-like helicase C terminal domain (domain)
The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Wikipedia: DnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. Initially when DnaB binds to dnaA, it is associated with dnaC, a negative regulator. After DnaC dissociates, DnaB binds dnaG.
Pfam PF14257: Domain of unknown function (DUF4349) (family)
This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 282 and 353 amino acids in length.  There is a single completely conserved residue D that may be functionally important. The N-terminus contains a lipoprotein signal peptide sequence.
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 PF07334: Interferon-induced 35 kDa protein (IFP 35) N-terminus (family)
This family represents the N-terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration. This family also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Pfam PF21551: Exosome complex component CSL4, N-terminal domain (domain)
This domain is found at the N-terminal end of Exosome complex component CSL4 from Saccharomyces cerevisiae, a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events.
Pfam PF07129: Protein of unknown function (DUF1381) (family)
This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus bacteriophage proteins of around 65 residues in length. 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 PF09641: Protein of unknown function (DUF2026) (domain)
This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. It is cited as a major prophage head protein, so might generally be of viral origin.
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 PF05189: RNA 3'-terminal phosphate cyclase (RTC), insert domain (domain)
RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of  RNA, in a reaction involving formation of the covalent AMP-cyclase  intermediate. The structure of RTC demonstrates that RTCs are  comprised two domain.  The larger domain contains an insert domain of approximately 100 amino acids.
Pfam PF09893: Uncharacterized protein conserved in archaea (DUF2120) (family)
This domain, found in various hypothetical archaeal 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 PF16583: Zinc-regulated secreted antivirulence protein C-terminal domain (family)
ZirS_C is the C-terminal domain of ZirS, zinc-regulated secreted protein, that is part of a type V-like secretion system. The domain adopts a bacterial Ig-like fold. This domain interacts with its transporter ZirT, and ZirS also interacts directly with ZirU, the third component of this antivirulence complex.  ZirT is the zinc-regulated transporter through which ZirS is secreted.
Pfam PF20176: Family of unknown function (DUF6541) (family)
This family is composed of a group of large bacterial integral membrane proteins that likely have a transporter 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 PF09569: ScaI restriction endonuclease (family)
This family includes the ScaI (recognises and cleaves AGT^ACT) restriction endonuclease.
Pfam PF22065: Cep192 domain 7 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the seventh domain found in the metazoan Cep192 homologs.
Pfam PF03610: PTS system fructose IIA component (family)
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS)  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.

The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).
According to structural and sequence analyses, the PTS EIIA domain can be divided in different groups. The mannose class of EIIA consists of a single five-stranded mixed Î² sheet, flanked by helices on both sides . The phosphorylation site (His) is located at the end of the third Î² strand, in a shallow crevice lined with hydrophobic residues.

This entry represents the mannose-type EIIA domain. This type of domain can also be found in the multidomain protein dihydroxyacetone kinase DhaM from some bacteria .
Pfam PF06757: Insect allergen related repeat, nitrile-specifier detoxification (family)
This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the small white butterfly Pieris rapae. NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain.
Pfam PF02214: BTB/POZ domain (domain)
In voltage-gated K+ channels this domain is responsible for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. In KCTD1 ([swissprot:Q719H9]) this domain functions as a transcriptional repressor. It also mediates homomultimerisation of KCTD1 and interaction of KCTD1 with the transcription factor AP-2-alpha.
Wikipedia: K+ channel tetramerisation domain  is the N-terminal, cytoplasmic tetramerisation domain (T1) of voltage-gated K+ channels. It defines molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. It is distantly related to the BTB/POZ domain Pfam PF00651.
Pfam PF06934: Fatty acid cis/trans isomerase (CTI) (family)
This family consists of several fatty acid cis/trans isomerase proteins which appear to be found exclusively in bacteria of the orders Vibrionales and Pseudomonadales. Cis/trans isomerase (CTI) catalyses the cis-trans isomerisation of esterified unsaturated fatty acids in phospholipids, mainly palmitoleic acid (C16:1) and cis-vaccenic acid C(18:1), in response to toxic organic solvents, heat and osmotic stress, and heavy metals. The CTI protein is located in the periplasm and has been shown to be involved in solvent tolerance in Pseudomonas strains.
Pfam PF07915: Glucosidase II beta subunit-like protein (family)
The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II ([swissprot:P14314]), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown.  This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain.
Pfam PF11493: Thylakoid soluble phosphoprotein TSP9 (family)
The plant-specific protein, TSP9 is phosphorylated and released in response to changing light conditions from the photosynthetic membrane. The protein resembles the characteristics of transcription/translation regulatory factors. The structure of the protein is predicted to consist of a random coil.
Pfam PF13844: Glycosyl transferase family 41 (family)
This family of glycosyltransferases includes O-linked beta-N-acetylglucosamine (O-GlcNAc) transferase, an enzyme which catalyses the addition of O-GlcNAc to serine and threonine residues. In addition to its function as an O-GlcNAc transferase, human OGT, [swissprot:O15294], also appears to proteolytically cleave the epigenetic cell-cycle regulator HCF-1.
Wikipedia: N-glycosyltransferase is an enzyme in prokaryotes which transfers individual hexoses onto asparagine sidechains in substrate proteins, using a nucleotide-bound intermediary, within the cytoplasm. They are distinct from regular N-glycosylating enzymes, which are oligosaccharyltransferases that transfer pre-assembled oligosaccharides. Both enzyme families however target a shared amino acid sequence asparagine—-any amino acid except proline—serine or threonine (N–x–S/T), with some variations.
Pfam PF11443: Domain of unknown function (DUF2828) (domain)
This is a uncharacterised domain found in eukaryotes and viruses. According to structure predictions and comparison, this domain may have a alpha-helical fold closely related to the TROVE domain suggesting possible involvement in RNA binding.
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 PF17305: Family of unknown function (DUF5354) (family)
This family of unknown function is found mostly in Metazoa.
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 PF13471: Transglutaminase-like superfamily (domain)
This family includes uncharacterised proteins that are related to the transglutaminase like domain [pfam:PF01841].
Pfam PF08008: Viral cysteine rich (domain)
Members of this family are polydna viral proteins that contain a cysteine rich motif.  Some members of this family have multiple copies of this domain.
Pfam PF05414: Viral domain of unknown function (DUF1717) (domain)
This domain is found in viral proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12696: TraM recognition site of TraD and TraG (family)
This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation.  These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. This domain interacts with the relaxosome component TraM via the latter's tetramerisation domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore.
Pfam PF14593: PH domain (domain)
This entry represents the pleckstrin homology (PH) domain from 3-phosphoinositide-dependent protein kinase 1 (PDK1) type proteins.

PDK1 plays an important role in insulin and growth factor signalling cascades. It phosphorylates and activates many AGC (cAMP-dependent, cGMP-dependent, protein kinase C (PKC)) family of protein kinases members, including protein kinase B (PKB, also known as Akt), p70 ribosomal S6-kinase (S6K), serum and glucocorticoid responsive kinase (SGK), p90 ribosomal S6 kinase (RSK), and PKC . PDK1 contains an N-terminal serine/threonine kinase domain followed by a PH domain. Following binding of the PH domain to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, PDK1 activates these enzymes by phosphorylating a Ser/Thr residue in their activation loop. .
This superfamily represents the PH domain and structurally related domains.

Pleckstrin homology (PH) domains are small modular domains that occur in a large variety of signalling proteins, where they serve as simple targeting domains that bind lipids .

PH domains have a partly opened Î²-barrel topology that is capped by an Î±-helix. The structure of PH domains is similar to the phosphotyrosine-binding domain (PTB) found in IRS-1 (insulin receptor substrate 1) , Shc adaptor and Numb ; to the Ran-binding domain, found in Nup nuclear pore complex and Ranbp1 ; to the Enabled/VASP homology domain 1 (EVH1 domain), found in Enabled, VASP (vasodilator-stimulated phosphoprotein), Homer and WASP actin regulatory protein ; and to the third domain of FERM, found in moesin, radixin, ezrin, merlin and talin .
Pfam PF14875: N-term cysteine-rich ER, FAM69 (domain)
The FAM69 family of cysteine-rich type II transmembrane proteins localise to the endoplasmic reticulum (ER) in cultured cells, probably via N-terminal di-arginine motifs. These proteins carry at least 14 luminal cysteines which are conserved in all FAM69s. There are currently few indications of the involvement of FAM69 members in human diseases. It would appear that FAM69 proteins are predicted to be have a protein kinase structure and function. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain, inserted within the structure of the kinase domain, suggests they function as Ca2+-dependent kinases (unpublished).
Pfam PF05989: Chordopoxvirus A35R protein (family)
This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown.
Pfam PF11004: 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase (family)
This is a family of 3-deoxy-D-manno-oct-2-ulosonic acid 3-hydroxylases, which catalyse the conversion of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) to D-glycero-D-talo-oct-2-ulosonic acid (Ko). It contains a potential iron-binding motif, HXDX(n)H (n>40). Hydroxylation activity is iron-dependent.