SII-SWORD/CoKE huggingface dataset:
Pfam PF16165: Ferlin C-terminus (family)
This domain is found at the C-terminus of proteins belonging to the ferlin family, including dysferlin, myoferlin, otoferlin and fer-1-like proteins.
Pfam PF02599: Global regulator protein family (family)
This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay.  In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes. RmsA binds to RmsB regulatory RNA.
Wikipedia: Carbon storage regulator A (CsrA) is an RNA binding protein. The CsrA homologs are found in most bacterial species, in the pseudomonads they are called repressor of secondary metabolites. The CsrA proteins generally bind to the Shine–Dalgarno sequence of messenger RNAs and either inhibit translation or facilitate mRNA decay.
Pfam PF22921: Fukutin-related protein stem domain (domain)
This entry represents the N-terminal domain of the fukutin-related protein. Alpha-Dystroglycan (alpha-DG) is a highly-glycosylated surface membrane protein. Defects in the O-mannosyl glycan of alpha-DG cause dystroglycanopathy, a group of congenital muscular dystrophies. The core M3 O-mannosyl glycan contains tandem ribitol-phosphate (RboP), a characteristic feature first found in mammals. Fukutin and fukutin-related protein (FKRP), whose mutated genes underlie dystroglycanopathy, sequentially transfer RboP from cytidine diphosphate-ribitol (CDP-Rbo) to form a tandem RboP unit in the core M3 glycan. FKRP is composed of two domains, the N-terminal stem domain and the C-terminal catalytic domains. The overall structure of the stem domain is similar to that of the catalytic domain of polypeptide GalNAc transferase 10 (ppGalNAcT-10). However, the HxD motif of ppGalNAcT-10, which is critical to its catalytic reaction, was not conserved. Therefore, the stem domain of FKRP would not have glycosyltransferase activity despite its overall structural similarity to ppGalNAcT-10.
Pfam PF18216: N-formyltransferase dimerization C-terminal domain (domain)
This is the C-terminal domain of N-formyltransferase found in Francisella tularensis. N-formylated sugars are observed on O-antigens of pathogenic Gram-negative bacteria. This C-terminal domain is responsible for dimerization. In particular, the beta hairpin motif present in the domain helps create a subunit-subunit interface. The dimeric interface is characterized by a hydrophobic patch formed by Ile 195, Leu 197, Val 201, Met 203, Ile 207, Phe 223, Val 231, Val 233, Leu 235, and Leu 237 from both monomers.
Pfam PF04643: Motilin/ghrelin-associated peptide (family)
This family represents a peptide sequence that lies C-terminal to motilin/ghrelin on the respective precursor peptide. Its function is unknown.
Pfam PF04478: Mid2 like cell wall stress sensor (family)
This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress.  The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway []1.
Pfam PF17887: Jak1 pleckstrin homology-like domain (domain)
This entry is for the pleckstrin homology-like (PHL) subdomain found in Jak1 proteins. JAK1 is a member of the Janus kinase (JAK) family of non-receptor tyrosine kinases that are activated in response to cytokines and interferons. PHL (residues 283-419) together with the N-terminal ubiquitin-like subdomain (residues 36-111) and an acyl-coenzyme A binding protein-like subdomain (residues 148-282), associate into a canonical tri-lobed FERM domain.
Pfam PF04795: PAPA-1-like conserved region (family)
Family of proteins with a conserved region found in PAPA-1, a PAP-1 binding protein.
Pfam PF13918: PLD-like domain (domain)
This domain is found in a subset of the phospholipase D family members, including 5'-3' exonuclease PLD3/4 from animals  and viral phospholipases such as envelope phospholipase F13 (also known as OPG057) and homologues .

Human PLD3 is a 5'->3' DNA exonuclease which digests single-stranded DNA and may regulate inflammatory cytokine responses via the degradation of nucleic acids. PLD3 was initially thought to have phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp and, therefore, its catalytic phospholipase D activity is still controversial . PLD4, its closest homologue, does not posses phospholipase activity.

Envelope phospholipase F13 from Vaccinia virus is the major envelope protein that plays a role in the biogenesis of the viral double membrane and in egress of virus from the host cell that produces the wrapped form of virus that is required for cell-to-cell spread . It has been shown to have broad-specificity lipase activity .
Pfam PF14183: YwpF-like protein (family)
The YwpF-like protein family includes the B. subtilis YwpF protein [swissprot:P94588], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 167 amino acids in length. There is a conserved IIN sequence motif.
Pfam PF05377: Flagella accessory protein C (FlaC) (coiled_coil)
Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ.  The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells).
Pfam PF03177: Non-repetitive/WGA-negative nucleoporin C-terminal (repeat)
This is the C-terminal half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterised by the FG repeat [pfam:PF03093]; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore. This region is composed of a long alpha solenoid repeat structure.
Wikipedia: Nucleoporins are a family of proteins which are the constituent building blocks of the nuclear pore complex (NPC). The nuclear pore complex is a massive structure embedded in the nuclear envelope at sites where the inner and outer nuclear membranes fuse, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm. Nuclear pores enable the passive and facilitated transport of molecules across the nuclear envelope. Nucleoporins, a family of around 30 proteins, are the main components of the nuclear pore complex in eukaryotic cells. Nucleoporin 62 is the most abundant member of this family. Nucleoporins are able to transport molecules across the nuclear envelope at a very high rate. A single NPC is able to transport 60,000 protein molecules across the nuclear envelope every minute.
Pfam PF11533: AtzH-like (domain)
This bacterial family of proteins includes AtzH from Pseudomonas sp. sp. AtzH is thought to be an amidase responsible for converting 1,3-dicarboxyurea to allophanate. This protein, which adopts a dimeric assembly, shows a seven-stranded anti-parallel beta- sheet and three helices.
Pfam PF20116: Family of unknown function (DUF6506) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 100 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 PF22287: TraI-like C-terminal domain (domain)
This entry represents the C-terminal domain of TraI proteins, which adopts an OB fold-like structure. TraI is a plasmid-specific component required for the initiation process of transfer DNA synthesis, as part of a specialised nucleoprotein complex - the relaxosome, together with TraH, I, and J. Site- and strand-specific cleavage at the transfer origin is dependent of TraI and TraJ.
Pfam PF04159: NB glycoprotein (family)
The NB glycoprotein is found in Influenza type B virus.  Its function is unknown.
Pfam PF23876: Family of unknown function (DUF7230) (family)
This entry represents a family of uncharacterized proteins found in phage and bacterial species, particularly in the Gammaproteobacteria class. Members of this family are typically short proteins, ranging from 32 to 85 amino acids in length. Many members are predicted to contain disordered regions and AlphaFold predictions show a non-globular structure.
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 PF10257: Retinoic acid induced 16-like protein (repeat)
This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans.
Pfam PF19977: xRRM domain (domain)
This entry represents the xRRM domain, which is an atypical RRM domain.
Pfam PF07678: A-macroglobulin TED domain (repeat)
This entry corresponds to the TED domain of the complement components such as C3, C4 and C5. This domain contains a short highly conserved region of proteinase-binding alpha-macro-globulins contains the cysteine and a glutamine of a thiol-ester bond that is cleaved at the moment of proteinase binding, and mediates the covalent binding of the alpha-macro-globulin to the proteinase. The GCGEQ motif is highly conserved.
Pfam PF23941: Domain of unknown function (DUF7276) (domain)
This entry represents the C-terminal domain from a large family of uncharacterised phage proteins that typically contain three domains.
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 PF06591: T4-like phage nuclear disruption protein (Ndd) (family)
This family consists of several nuclear disruption (Ndd) proteins from T4-like phages. Early in a bacteriophage T4 infection, the phage ndd gene causes the rapid destruction of the structure of the Escherichia coli nucleoid.  The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid.
Pfam PF19983: Family of unknown function (DUF6419) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000299) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the alterochromide A biosynthetic gene cluster from  Pseudoalteromonas piscicida JCM 20779.
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 PF01365: RIH domain (repeat)
The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels.  This region is found in the ryanodine receptor [swissprot:P21817] and the inositol-1,4,5- trisphosphate receptor [swissprot:Q14571]. This domain may form a binding site for IP3.
Pfam PF20093: Domain of unknown function (DUF6484) (domain)
This domain of unknown function is found in uncharacterised proteins from Proteobacteria. This domain is approximately 80 amino acids in length and exhibits overlaps with [pfam:PF04717], which suggests that it has an OB fold and, thus, it  belongs to the same clan. Many proteins containing this domain are related to the Type VI secretion system and to Phage-related baseplate 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 PF13721: SecD export protein N-terminal TM region (family)
This domain appears to be the fist transmembrane region of the SecD export protein. SecD is directly involved in protein secretion and important for the release of proteins that have been translocated across the cytoplasmic membrane.
Pfam PF24008: Domain of unknown function (DUF7322) (domain)
This domain is found in uncharacterised archaeal proteins. It is predicted to fold into an alpha-helical hairpin and it is likely associated with the membrane.
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 PF14570: RING/Ubox like zinc-binding domain (domain)
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF20456: Family of unknown function (DUF6709) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 340 and 435 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 PF17907: AWS domain (domain)
This entry represents the AWS (associated with SET domain) domain. This is a zinc binding domain. The full AWS domain contains 8 cysteines. This entry represents the N-terminal part of the domain, with the C-terminal part interwoven with the SET domain.
Pfam PF17133: Domain of unknown function (DUF5108) (family)
This is a family of Bacteroidetes proteins. The domain lies upstream of a Fasciclin family, [pfam:PF02469].
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 PF11350: Protein of unknown function (DUF3152) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is 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 PF01540: Adhesin lipoprotein (family)
This family consists of the p50 and variable adherence-associated antigen (Vaa) adhesins from Mycoplasma hominis. M. hominis is a mycoplasma associated with human urogenital diseases, pneumonia, and septic arthritis. An adhesin is a cell surface molecule that mediates adhesion to other cells or to the surrounding surface or substrate. The Vaa antigen is a 50-kDa surface lipoprotein that has four tandem repetitive DNA sequences encoding a periodic peptide structure, and is highly immunogenic in the human host. p50 is also a 50-kDa lipoprotein, having three repeats A,B and C, that may be a tetramer of 191-kDa in its native environment.
Pfam PF09471: IgA Peptidase M64 (family)
This is a family of highly selective metallo-endopeptidases. The primary structure of the Clostridium ramosum IgA proteinase shows no significant overall similarity to any other known metallo-endopeptidase.
Pfam PF00624: Flocculin repeat (repeat)
This short repeat is rich in serine and threonine residues.
Pfam PF08973: Domain of unknown function (DUF1893) (domain)
A member of the deaminase fold that binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate. Contextual analysis suggests that the domain  is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase.
Pfam PF24967: TR130 NTS domain (repeat)
This domain is found in the yeast Trafficking protein particle complex II-specific subunit 130 (TR130) and related proteins. TRS130 plays a role in the YPT GEF activity of TRAPP II in concert with the two other TRAPP II-specific subunits TRS65 and TRS120. This protein contains an N-terminal alpha-solenoid domain, known as NTS domain, followed by four Ig-like domains arranged in tandem. This entry represents the NTS domain.
Pfam PF00450: Serine carboxypeptidase (domain)
This group of serine peptidases belong to MEROPS peptidase family S10 (clan SC). The type example is carboxypeptidase Y from Saccharomyces cerevisiae (Baker's yeast) .

All known carboxypeptidases are either metallo carboxypeptidases or serine carboxypeptidases (3.4.16.5 and 3.4.16.6). The catalytic activity of the serine carboxypeptidases, like that of the trypsin family serine proteases, is provided by a charge relay system involving an aspartic acid residue hydrogen-bonded to a histidine, which is itself hydrogen-bonded to a serine . The sequences surrounding the active site serine and histidine residues are highly conserved in all the serine carboxypeptidases.
Pfam PF04106: Autophagy protein ATG5, UblB domain (domain)
ATG5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway. ATG5 is conjugated to ATG12; this conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 family, and therefore autophagosome formation. ATG5 comprises N- and C-terminal ubiquitin-like domains (UblA and UblB) that flank the helical-rich region (HBR). This is the UblB domain, found at the C-terminal.
Pfam PF18887: MBG domain (domain)
This entry corresponds to an MBG (mirror beta grasp) domain. It is found in a variety of bacterial cell surface proteins.
Pfam PF22419: Human bocavirus Nonstructural protein 1-like, N-terminal domain (domain)
This entry represents the Human bocavirus 1 (HBoV1) nonstructural protein 1 (NS1) N-terminal domain. HBoV-NS1 is a member of the histidine-hydrophobic-histidine (HUH) superfamily of endonucleases.
Pfam PF18071: HMW1C N-terminal (repeat)
This is the N-terminal domain found in Actinobacillus pleuropneumoniae HMW1C (ApHMW1C). HMW1 adhesin is an N-linked glycoprotein that mediates adherence to respiratory epithelium through N-glycosylation of protein acceptor sites an O-glycosylation of sugar acceptor sites. The N-terminal domain forms an all alpha domain (AAD) when combined with the domain spanning from residue 154 to residue 245. The AAD interacts extensively with the C-terminal GT-B fold in order to create unique groove with potential to accommodate the acceptor protein.
Pfam PF21359: TOPLESS, zinc finger domain (domain)
This is the zinc finger domain of TOPLESS and TOPLESS-related proteins, plant transcriptional co-repressors.
Pfam PF18195: GatD N-terminal domain (domain)
This is the N-terminal domain of GatD protein present in Pyrococcus abyssi. Two GatD and two GatE associate to form a tetramer complex. The tetramer complex is able to mature Glutamic acid-tRNA Glutamine into Glutamine-tRNA Glutamine, a necessary step in the translation of proteins. The N-terminal domain is involved in anchoring GatD to GatE in order to form the tetramer.
Pfam PF20237: Family of unknown function (DUF6594) (family)
This entry represents a group of uncharacterised proteins that contain a set of C-terminal transmembrane helices. The family may be related to [pfam:PF10267].
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 PF04028: Domain of unknown function (DUF374) (family)
Bacterial domain 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 PF12779: WXXGXW repeat (2 copies) (repeat)
This short repeat contains the motif WXXGXW where X can be any amino acid.  It is generally found in 2-5 copies in short secreted bacterial proteins. Its precise function is as yet unknown, but  evidence suggests that members of this family are important for the function of specific sub-types of two-partner secretion systems.