SII-SWORD/CoKE huggingface dataset:
Pfam PF01839: FG-GAP repeat (repeat)
This family contains the extracellular repeat that is found in up to seven copies in alpha integrins.  This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat.  The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats.
Pfam PF19165: Family of unknown function (DUF5847) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF05052: MerE protein (family)
The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon. The protein is thought not to have any direct role in conferring mercury resistance to the organism but may be a mercury resistance transposon.
Pfam PF04013: Putative SAM-dependent RNA methyltransferase (family)
This family is likely to be an S-adenosyl-L-methionine (SAM)-dependent RNA methyltransferase. It is responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs.
Pfam PF16400: Domain of unknown function (DUF5008) (family)
This small family of proteins is functionally uncharacterised. This family is found in Bacteroides, Paraprevotella, and Sphingobacterium. The members in this family are around 550 residues 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 PF17918: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in a number of different TetR transcription regulator proteins including SlmA proteins found in E. coli. Unlike other TetR proteins, SlmA functions not as a transcription regulator but rather as an NO (nucleoid occlusion) factor. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain.
Pfam PF20917: Asparaginal-tRNA synthetase, N-terminal domain (domain)
This domain is found at the N-terminal domain of the eukaryotic protein Asparaginal-tRNA synthetase (AsnRS, also known as NARS1). AsnRS is essential for protein translation and has been related to autoimmune and neurological diseases. Unlike its bacterial homologs, this protein has a conserved N-terminal extension (this entry) connected by an unstructured tether to the part of the enzyme that has homologues within eukaryotes and prokaryotes: an anticodon-binding domain ([pfam:PF01336]), a hinge region (HR), and a catalytic domain ([pfam:PF00152]). This domain folds into two alpha-helices and three beta-strands form a parallel/antiparallel  mixed beta-sheet and has a characteristic lysine-rich helical motif that interacts with tRNA. It also shows chemokine activity through its interaction with C-C chemokine receptor 3 (CCR3) and the promotion of NRS-CCR3-mediated proinflammatory signaling.
Pfam PF05470: Eukaryotic translation initiation factor 3 subunit 8 N-terminus (repeat)
The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA.
Pfam PF07393: Exocyst complex component Sec10-like, alpha-helical bundle (repeat)
This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion. It is also involved in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis. The exocyst is a member of the Complex Associated with Tethering Containing Helical Rods (CATCHRs) which also includes DSL1, COG and GARP complexes, evolutionary related. They share structural features comprising alpha-helical bundles towards the C-terminal and coiled-coil regions at the N-terminal. This entry represents the alpha-helical bundles of Sec10 and related proteins, like Recyclin-1 which is involved in recycling plasma membrane proteins internalised by endocytosis and Pof6, that together with skp1, is essential for septum processing and cell separation.
Pfam PF07843: Protein of unknown function (DUF1634) (family)
This family contains many hypothetical bacterial and archaeal proteins. A few members of this family are annotated as being putative transmembrane proteins, and the region in question in fact contains many  hydrophobic residues.
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 PF16458: Beta-prism lectin (repeat)
This beta-prism fold lectin is the C-terminal domain of the Vibrio cholerae cytolytic pore-forming toxin hemolysin. It binds to N-glycans with a heptasaccharide GlcNAc4Man3 core (NGA2).
Pfam PF14175: YaaC-like Protein (family)
The YaaC-like protein family includes the B. subtilis YaaC protein [swissprot:P37526], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 320 and 333 amino acids in length. AlphaFold shows that typical proteins in this family contain a largely alpha helical domain with a beta sheet domain nested within a loop. However, there also exist shorter homologues such as [swissprot:L5N9K9] which lack the inserted domain.
Pfam PF06578: YOP proteins translocation protein K (YscK) (family)
This family consists of several YscK proteins. The function of this protein is unknown but it belongs to an operon involved in the secretion of Yop proteins across bacterial membranes.
Pfam PF05844: YopD protein (family)
This family consists of several bacterial YopD like proteins. Virulent Yersinia species harbour a common plasmid that encodes essential virulence determinants (Yersinia outer proteins [Yops]), which are regulated by the extracellular stimuli Ca2+ and temperature. YopD is thought to be a possible transmembrane protein and contains an amphipathic alpha-helix in its carboxy terminus.
Pfam PF11200: Protein of unknown function (DUF2981) (family)
This eukaryotic family of 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 PF16590: Exocrine gland-secreting peptide (family)
ESP is a family of largely rodent exocrine gland-secreting peptides that are produced by the male extraorbital lacrimal gland to be secreted into the tear fluid. Other mice including females detect these peptides through receptors in the vomeronasal organ, and the receptors report information on mouse-strain, sex and species.  The peptides are short, all carrying an N-terminal signal-peptide to indicate they are for secretion which accounts for much of the common conservation.
Pfam PF11953: Domain of unknown function (DUF3470) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 50 amino acids in length. This domain is found associated with [pfam:PF00037]. This domain has a single completely conserved residue N that may be functionally important.
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 PF22251: Vacuolar membrane protease, transmembrane domain (domain)
This entry includes fungal vacuolar membrane proteases, such as PFF1 from yeast, which may be involved in vacuolar sorting and osmoregulation. It is the homologue of human ERMP1. According to AlphaFold structure prediction, these proteins consist of a M28 peptidase domain ([pfam:PF04389]) at the N-terminal, a central transmembrane domain (TM) and a C-terminal domain with an elongated beta-sandwich-like fold ([pfam:PF22250]), similar to the Mu homology domain (MHD) ([pfam:PF00928]). This entry represents the TM domain of PFF1 and fungal its homologues.
Pfam PF05308: Mitochondrial fission regulator (family)
In eukaryotes, this family of proteins induces mitochondrial fission.
Pfam PF24962: Domain of unknown function (DUF7767) (domain)
This is a domain of unknown function found at the C-terminal of fungal sequences. It may adopt a ubiquitin-like 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 PF20573: Putative metallopeptidase family (DUF6782) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 256 and 362 amino acids in length. There is a conserved HEXRH sequence motif which is characteristic of metallopeptidase enzymes.
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 PF21620: S-layer protein SlpA, beta-barrel domain (domain)
This entry represents the beta-barrel found at the C-terminal of S-layer protein SlpA and similar S-layer proteins. SlpA plays an important role in the structural organisation and integrity of the S-layer. In Deinococcus radiodurans, SlpA binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium suggested to be part of the first lane of defense against UV radiation, especially under desiccation.
Pfam PF22637: BppA domain 1 (domain)
This entry represents domain found in accessory protein BppA and related proteins. Given the structural similarity to carbohydrate binding domains, it is likely that this domain is a carbohydrate binding module. BppA is a virion's baseplate component. The precise role of this protein in absorption is elusive but the presence of a carbohydrate binding domain with an extended saccharidic binding site suggests that this protein probably participates in receptor binding together with the bona fide receptor binding proteins.
Pfam PF02527: rRNA small subunit methyltransferase G (family)
This is a family of bacterial glucose inhibited division proteins these are probably involved in the regulation of cell devision. GidB has been shown to be a methyltransferase G specific to the rRNA small subunit. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. GidB specifically methylates the N7 position of a guanosine in 16S rRNA.
Pfam PF19192: Response receiver domain (domain)
This is a receiver domain (REC) commonly found in the same gene-neighbourhood of its cognate HK. Together they comprise a Two-Component System (TCS). There is a high degree of specificity among REC and DHp domains in a cognate pair. This domain is related to the Response_reg ([pfam:PF00072]) domain. We found that [pfam:PF19191] and this domain show high degree of linkage in the same gene-neighbourhoods across several bacterial lineages. This implies that they comprise a TCS.
Pfam PF06060: Mesothelin (repeat)
This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, which participates in cell adhesion, tumour progression, metastasis, and drug resistance. Due to its overexpression in various tumours, it constitutes a diagnostic an therapy target. This protein is predicted have superhelical structures with ARM-type repeats.
Pfam PF15814: Protein family FAM199X (family)
This family of proteins is found in eukaryotes. The function of FAM199X is not known.
Pfam PF19135: Protein of unknown function (DUF5818) (family)
This is a family of uncharacterised proteins.
Pfam PF15878: Protein Frey (family)
This family represents Frey proteins, which are key regulators for male fertility expressed transiently in round spermatids where it recruits IZUMO1 at the endoplasmic reticulum (ER) membrane and coordinates the oolemmal binding multimeric complex (IZUMO1 complex) assembly. Upon complete assembly of the IZUMO1 complex, its ER retention is released, facilitating IZUMO1 complex export to the acrosome. Frey interacts with SPPL2C, which inhibits its intramembrane protease activity directly accessing the catalytic centre of an I-CLiP.
Pfam PF18872: Daz repeat (repeat)
This short repeat is found in the Daz proteins is a varying number of copies. The molecular function of these repeats in unknown.
Pfam PF04021: Class III signal peptide (conserved_site)
This family of archaeal proteins contains.  an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase.
Pfam PF06400: Alpha-2-macroglobulin RAP, N-terminal domain (domain)
The alpha-2-macroglobulin receptor-associated protein (RAP)  is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of  all currently known ligands of these receptors.  The N-terminal domain is predominately alpha helical. Two different studies have provided conflicted domain boundaries.
Wikipedia: Low density lipoprotein receptor-related protein-associated protein 1 also known as LRPAP1 or RAP is a chaperone protein which in humans is encoded by the LRPAP1 gene.
Pfam PF13882: Bravo-like intracellular region (domain)
This is the very C-terminal intracellular region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY.  The function is not known.
Pfam PF12695: Alpha/beta hydrolase family (domain)
This family contains a diverse range of alpha/beta hydrolase enzymes.
Wikipedia: The alpha/beta hydrolase superfamily is a superfamily of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function that share a common fold. The core of each enzyme is an alpha/beta-sheet, containing 8 beta strands connected by 6 alpha helices. The enzymes are believed to have diverged from a common ancestor, retaining little obvious sequence similarity, but preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best-conserved structural features of the fold.
Pfam PF18362: Tri-helix bundle domain (domain)
This domain can be found in the myosin-binding motif (m-domain) region present in myosin-binding protein C (MyBP-C). MyBP-C is a sarcomeric assembly protein necessary for the regulation of sarcomere structure and function. The MyBP-C family of proteins consists mainly of modules with immunoglobulin (Ig) or fibronectin folds. This domain exhibits a three-helix bundle fold and there is a known actin-binding motif, LK(R/K)XK positioned in the third helix (alpha3), similar to that found in villin and related proteins.
Pfam PF21505: 26S proteasome subunit RPN2, N-terminal domain (repeat)
This entry represents the N-terminal helical domain of 26S proteasome regulatory subunit RPN2 and 26S proteasome non-ATPase regulatory subunit 1 (PSMD1). It adopts a rod-like structure.
Pfam PF20063: Family of unknown function (DUF6462) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly in Firmicutes. Proteins in this family are typically between 62 and 78 amino acids in length. Some of the members are probably transcriptional regulators. This family has overlaps with families in clan CL0123, which suggests that they share the helix-turn-helix motif.
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 PF01370: NAD dependent epimerase/dehydratase family (family)
This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.
Wikipedia: The enzyme UDP-glucose 4-epimerase, also known as UDP-galactose 4-epimerase or GALE, is a homodimeric epimerase found in bacterial, fungal, plant, and mammalian cells. This enzyme performs the final step in the Leloir pathway of galactose metabolism, catalyzing the reversible conversion of UDP-galactose to UDP-glucose. GALE tightly binds nicotinamide adenine dinucleotide (NAD+), a co-factor required for catalytic activity.
Pfam PF14430: Immunity protein Imm1 (family)
A predicted immunity protein, with an alpha+beta fold and a conserved C-terminal tryptophan residue. The protein is present in a wide range of bacteria in polymorphic toxin systems as an immediate gene  neighbour of the toxin gene.
Pfam PF06198: Protein of unknown function (DUF999) (family)
Family of conserved Schizosaccharomyces pombe proteins with 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 PF19385: Family of unknown function (DUF5960) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF05039: Agouti protein (domain)
The agouti protein regulates pigmentation in the mouse hair follicle producing a black hair with a subapical yellow band. A highly homologous protein agouti signal protein (ASIP)is present in humans and is expressed at highest levels in adipose tissue where it may play a role in energy homeostasis and possibly human pigmentation.
Wikipedia: Agouti-related protein (AgRP), also called agouti-related peptide, is a neuropeptide produced in the brain by the AgRP/NPY neuron. It is synthesized in neuropeptide Y (NPY)-containing cell bodies located in the ventromedial part of the arcuate nucleus in the hypothalamus. AgRP is co-expressed with NPY and acts to increase appetite and decrease metabolism and energy expenditure. It is one of the most potent and long-lasting of appetite stimulators. In humans, the agouti-related peptide is encoded by the AGRP gene.
Pfam PF07440: Caerin 1 protein (family)
This family consists of several caerin 1 proteins from Litoria species. The caerin 1 peptides are among the most powerful of the broad-spectrum antibiotic amphibian peptides.
Pfam PF00177: Ribosomal protein S7p/S5e (domain)
This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.
Pfam PF06683: Protein of unknown function (DUF1184) (family)
This family contains a number of hypothetical proteins of unknown function from Arabidopsis thaliana.
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 PF23050: N4BP1, first type I KH-domain (domain)
This domain is found in the N4BP1 family which includes the NEDD4-binding protein 1, KHNYN and NYNRIN and other related proteins. Members of this family contain two type I K homology (KH) domains. This entry represents the fist KH domain.