SII-SWORD/CoKE huggingface dataset:
Pfam PF19357: Family of unknown function (DUF5934) (family)
This presumed domain found in type IV secretion system proteins is functionally uncharacterised. This domain family is found in proteobacteria, and is approximately 170 amino acids in length. The family is found in association with [pfam:PF11130]. There are two conserved sequence motifs: GWDL and QGEY.
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 PF02454: Sigma 1s protein (family)
The reoviral gene S1 encodes for haemagglutinin (sigma 1 protein), an outer capsid protein and a major factor in determining virus-host cell interactions. Sigma 1s is one of two translation products of the S1 gene.
Pfam PF17767: Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain (domain)
Nicotinate phosphoribosyltransferase ([ec:2.4.2.11]) is the rate limiting enzyme that catalyses the first reaction in  the NAD salvage synthesis. This is the N-terminal domain of the enzyme.
Pfam PF18911: PKD domain (domain)
This entry is composed of PKD domains found in bacterial surface proteins.
Pfam PF03280: Proteobacterial lipase chaperone protein (family)
The proteobacterial lipase chaperone is a lipase helper protein which may be involved in the folding of extracellular lipase during its passage through the periplasm .
Pfam PF21566: Beta-N-acetylglucosaminidase, C-terminal domain (domain)
This domain is found at the C-terminal end of Beta-N- acetylglucosaminidase from Thermotoga maritima (NagA), which hydrolyses chitooligomers into monomer beta-N-acetylglucosamine. NagA forms a dimer structure in which the monomer structure is organised into an N- and a C-terminal domain ([pfam:PF00933] and this entry, respectively). This domain shows an alpha-beta- alpha-sandwich fold, which comprises six beta-strands with two alpha-helices on either side of the sheet.
Pfam PF00335: Tetraspanin family (family)
Tetraspanins are a distinct family of proteins, containing four transmembrane domains: a small outer loop (EC1), a larger outer loop (EC2), a small inner loop (IL) and short cytoplasmic tails. They contain characteristic structural features, including 4-6 conserved extracellular cysteine residues, and polar residues within transmembrane domains. A fundamental role of tetraspanins appears to be organizing other proteins into a network of multimolecular membrane microdomains, sometimes called the 'tetraspanin web'.

This entry represents tetraspanin proteins. It also recognises a number of peripherins. These are related retinal-specific members of the tetraspanin family which are located at the rims of the photoreceptor disks, where they may act jointly in disk morphogenesis .
Wikipedia: Tetraspanins are a family of membrane proteins found in all multicellular eukaryotes also referred to as the transmembrane 4 superfamily (TM4SF) proteins. These proteins have four transmembrane alpha-helices and two extracellular domains, one short and one longer, typically 100 amino acid residues. Although several protein families have four transmembrane alpha-helices, tetraspanins are defined by conserved amino acid sequences including four or more cysteine residues in the EC2 domain, with two in a highly conserved 'CCG' motif. Tetraspanins are often thought to act as scaffolding proteins, anchoring multiple proteins to one area of the cell membrane.
Pfam PF00032: Cytochrome b(C-terminal)/b6/petD (domain)
In the mitochondrion of eukaryotes and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III (1.10.2.2) - also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a analogous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase (1.10.99.1), also known as the b6f complex.

Cytochrome b/b6  is an integral membrane protein of approximately 400 amino acid residues that probably has 8 transmembrane segments. In plants and cyanobacteria, cytochrome b6 consists of two subunits encoded by the petB and petD genes. The sequence of petB is colinear with the N-terminal part of mitochondrial cytochrome b, while petD corresponds to the C-terminal part. Cytochrome b/b6 non-covalently binds two haem groups, known as b562 and b566. Four conserved histidine residues are postulated to be the ligands of the iron atoms of these two haem groups.

Apart from regions around some of the histidine haem ligands, there are a few conserved regions in the sequence of b/b6. The best conserved of these regions includes an invariant P-E-W triplet which lies in the loop that separates the fifth and sixth transmembrane segments. It seems to be important for electron transfer at the ubiquinone redox site - called Qz or Qo (where o stands for outside) - located on the outer side of the membrane. This entry is the C terminus of these proteins.
Wikipedia: Cytochrome b is a protein found in the membranes of aerobic cells. In eukaryotic mitochondria and in aerobic prokaryotes, cytochrome b is a component of respiratory chain complex III — also known as the bc1 complex or ubiquinol-cytochrome c reductase. In plant chloroplasts and cyanobacteria, there is a homologous protein, cytochrome b6, a component of the plastoquinone-plastocyanin reductase, also known as the b6f complex. These complexes are involved in electron transport, the pumping of protons to create a proton-motive force (PMF). This proton gradient is used for the generation of ATP. These complexes play a vital role in cells.
Pfam PF03259: Roadblock/LC7 domain (domain)
This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes [swissprot:Q9Y2Q5] Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus [swissprot:Q50883], a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.
Wikipedia: Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport; thus, they are called "minus-end directed motors". In contrast, most kinesin motor proteins move toward the microtubules' plus-end, in what is called anterograde transport.
Pfam PF13796: Putative sensor (family)
This family is often found at the N-terminus of proteins containing [pfam:PF07730] and [pfam:PF02518]. The N-termini of proteins containing these two domains often function in stimulus sensing.
Pfam PF15465: Domain of unknown function (DUF4634) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 98 and 133 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 PF07762: Protein of unknown function (DUF1618) (repeat)
The members of this family are mainly hypothetical proteins expressed by grasses.
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 PF15916: Domain of unknown function (DUF4743) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with [pfam:PF00293].
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 PF09221: Bacteriocin class IId cyclical uberolysin-like (domain)
Members of this family are membrane-interacting peptides, produced by Firmicutes that display a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. They adopt a helical structure, with four or five alpha helices forming a Saposin-like fold.  The structure has been found to be cyclical. It should be pointed out that one reference implies that both circularin A and gassericin A are class V or IIc-type bacteriocins; however we find that these two proteins fall into different Pfam families families, this one and BacteriocIIc_cy, [pfam:PF12173].
Wikipedia: Bacteriocin AS-48 is a cyclic peptide antibiotic produced by the eubacteria Enterococcus faecalis that shows a broad antimicrobial spectrum against both Gram-positive and Gram-negative bacteria. Bacteriocin AS-48 is encoded by the pheromone-responsive plasmid pMB2, and acts on the plasma membrane in which it opens pores leading to ion leakage and cell death. The globular structure of bacteriocin AS-48 is composed of five alpha helices enclosing a hydrophobic core. The mammalian NK-lysin effector protein of T and natural killer cells has a similar structure, though it lacks sequence homology with bacteriocins AS-48.
Pfam PF11347: Protein CHLORORESPIRATORY REDUCTION 42-like (family)
This family includes includes Protein CHLORORESPIRATORY REDUCTION 42 (CRR42) from Arabidopsis thaliana, which is required for both formation and activity of the chloroplast NAD(P)H dehydrogenase (NDH) complex of the photosynthetic electron transport chain. CRR42 functions in assembly or stabilization of the NDH complex and it is likely involved, together with CRR1 and CRR6 in the incorporation of NdhJ, NdhM, NdhK and NdhI into the NDH subcomplex A assembly intermediate (NAI500) to produce the complex NAI400. This family also includes uncharacterised proteins from cyanobacteria.
Pfam PF06745: KaiC (domain)
This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
Wikipedia: In molecular biology, the cyanobacterial clock proteins are the main circadian regulator in cyanobacteria. The cyanobacterial clock proteins comprise three proteins: KaiA, KaiB and KaiC. The kaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction. This complex is expressed from a KaiABC operon.
Pfam PF02794: RTX toxin acyltransferase family (family)
Members of this family are enzymes [ec:2.3.1.-]. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor.  This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in [swissprot:P06736] resulted in complete inactivation of the enzyme.
Pfam PF12626: Polymerase A arginine-rich C-terminus (domain)
The C-terminus of polymerase A in E coli is arginine-rich and is necessary for full functioning of the enzyme.
Pfam PF18167: SMODS-associated NUDIX domain (domain)
NUDIX domain with distinctive features in the substrate-interacting region observed associating with SMODS domain synthetases. Predicted to cleave nucleotide diphosphate bonds, potentially to regulate flux through the pore formed by fused 2TM module.
Pfam PF10431: C-terminal, D2-small domain, of ClpB protein (domain)
This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, [pfam:PF00004]) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N, [pfam:PF02861], at the N-terminus as well as AAA, [pfam:PF00004] and AAA_2, [pfam:PF07724].
Pfam PF06122: Conjugative relaxosome accessory transposon protein (family)
The TraH protein is thought to be a relaxosome accessory component, also necessary for transfer but not for H-pilus synthesis within the conjugative transposon.
Pfam PF04965: Baseplate wedge protein gp25 (domain)
This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerisation, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologues from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologues of T4 gp6 and gp7 proteins in contractile injection systems.
Pfam PF20957: GxGYxYP_N second domain (domain)
This entry represents a domain that is found repeated in three copies per protein and is likely to be involved in binding the bacterial cell wall. This domain is found in association with [pfam:PF14323].
Pfam PF06508: Queuosine biosynthesis protein QueC (domain)
This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyse the conversion of 7-deaza-7-carboxyguanine to preQ0.
Pfam PF07465: Photosystem I protein M (PsaM) (family)
This family consists of several plant and cyanobacterial photosystem I protein M (PsaM) sequences. PsaM forms part of the photosystem I complex and its binding is stabilised by PsaI.
Pfam PF16716: Bone marrow stromal antigen 2 (domain)
Bone marrow stromal antigen 2, also known as tetherin, is an antiretroviral defence protein, that blocks release of enveloped virus from the cell surface . Bst2/tetherin contains two membrane anchors which are employed to retain some enveloped viruses, including HIV-1, tethered to the plasma membrane in the absence of virus encoded antagonists . Its expression is induced by interferon-alpha  and was originally linked to B cell development .
Wikipedia: Tetherin, also known as  bone marrow stromal antigen 2, is a lipid raft associated protein that in humans is encoded by the BST2 gene. In addition, tetherin has been designated as CD317. This protein is constitutively expressed in mature B cells, plasma cells and plasmacytoid dendritic cells, and in many other cells, it is only expressed as a response to stimuli from IFN pathway.
Pfam PF00540: gag gene protein p17 (matrix protein) (domain)
The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus.
Pfam PF10912: Protein of unknown function (DUF2700) (family)
This family of proteins with unknown function appears to be restricted to Caenorhabditis elegans.
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 PF15522: Novel toxin 14 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system.
Pfam PF21260: Lysosomal alpha-mannosidase-like, central domain (domain)
This domain is found in Lysosomal alpha-mannosidase from Bos taurus (Laman) and similar proteins from eukaryotes. This protein is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. Laman, which belongs to the glycoside hydrolase family 38 (GH38), is organised into four domains: the alpha-beta N-terminal [pfam:PF01074], a three-helix bundle domain [pfam:PF09261], and three mainly beta-sheet domains (covered by this entry, [pfam:PF07748] and [pfam:PF17677]).
Pfam PF18541: RuvC endonuclease subdomain 3 (domain)
Cas9 proteins are abundant across the bacterial kingdom, but vary widely in both sequence and size. All known Cas9 enzymes contain an HNH domain that cleaves the DNA strand complementary to the guide RNA sequence (target strand), and a RuvC nuclease domain required for cleaving the noncomplementary strand (non-target strand), yielding double-strand DNA breaks (DSBs). The crystal structures of type II-A and II-C Cas9 proteins highlight the features in Cas9 enzymes that support their function as RNA-guided endonucleases. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. The RuvC domain forms the structural core of the nuclease lobe, a six-stranded beta sheet surrounded by four alpha helices, with all three conserved subdomains (I, II, III) contributing catalytic residues to the active site.
Pfam PF15247: Histone RNA hairpin-binding protein RNA-binding domain (family)
This family represents the RNA-binding domain of histone RNA hairpin-binding protein.
Wikipedia: Histone RNA hairpin-binding protein or stem-loop binding protein (SLBP) is a protein that in humans is encoded by the SLBP gene.
Pfam PF03685: Uncharacterised protein family (UPF0147) (family)
This family of small proteins have no known function.
Pfam PF12461: Spiroplasma phage ORF1-like family (family)
This entry includes the ORF1 protein from spiroplasma phages.
Pfam PF16519: Tetramerisation domain of TRPM (domain)
TRPM7_tetra is a short anti-parallel coiled-coil tetramerisation domain of the transient receptor potential cation channel subfamily M member proteins 1-8. It is held together by extensive core packing and interstrand polar interactions. Transient receptor potential (TRP) channels comprise a large family of tetrameric cation-selective ion channels that respond to diverse forms of sensory input. The presence of cytoplasmic domains that direct channel assembly appears to be a feature of many voltage-gated ion channel superfamily members.
Pfam PF17936: Bacterial Ig domain (domain)
This domain is found in a wide variety of extracellular bacterial proteins often in multiple tandem copies.
Pfam PF24982: Domain of unknown function (DUF7773) (domain)
This domain is found in uncharacterised worm proteins mainly from clade Rhabditida. It contains a number of highly conserved cysteine residues that are predicted to form disulfide bonds. This domain is predicted to fold into a four-stranded antiparallel meander decorated with alpha-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 PF19797: Family of unknown function (DUF6281) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the  kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus.
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 PF20236: Family of unknown function (DUF6593) (domain)
This entry represents a large family of Uncharacterized fungal 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 PF24930: Domain of unknown function (DUF7750) (domain)
This is a domain of unknown function found in plant sequences. It may adopt a three-helical bundle fold.
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 PF00612: IQ calmodulin-binding motif (conserved_site)
Calmodulin-binding motif.
Wikipedia: The IQ calmodulin-binding motif is an amino acid sequence motif containing the following sequence:[FILV]Qxxx[RK]Gxxx[RK]xx[FILVWY]
Pfam PF22236: Telomere end-binding protein alpha subunit OB2 domain (domain)
This entry represents the second OB-fold domain (OB2) of the telomere end-binding protein (TEBP) alpha subunit. Similar to the first OB-fold domain (OB1), this domain binds to ssDNA.