SII-SWORD/CoKE huggingface dataset:
Pfam PF22774: DNAJC11, beta-barrel domain (domain)
This entry represents a beta-barrel domain found in the central region of DNAJC11 from humans and its orthologues. DNAJC11 is a mitochondrial outer membrane protein involved in mitochondrial biogenesis and in the response to microenvironment changes and requirements. The J-domain mediates its mitochondrial localization, while the C-terminal domain is critical for protein-protein interactions. The function of this domain is believed to be involved in protein-protein interactions. However, its exact function is unknown.
Pfam PF16211: C-terminus of histone H2A (family)
Histone H2A is a small, highly conserved nuclear protein that, together with two molecules each of histones H2B, H3 and H4, forms the eukaryotic nucleosome core ; the nucleosome octamer winds ~146 DNA base-pairs. In the mouse, histone H2A can be replaced by histone H2A-like 1 .
This entry represents the C-terminal domain of Histone H2A.
Pfam PF17325: Stationary phase protein 4 (family)
Saccharomyces cerevisiae respond and cope to starvation by ceasing growth and entering a non-proliferating state referred to as stationary phase. Expression of SPG4 has been shown to be higher in stressed cells, and stationary phase cells compared to active cells. It is not required for growth on non-fermentable carbon sources.
Pfam PF21180: Topoisomerase 6 subunit A/Spo11, Toprim domain (domain)
This topoisomerase-primase (Toprim) nucleotidyl transferase/hydrolase domain is found in the type II topoisomerase VIA and Spo11, which structurally related. Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Topoisomerase VI is a type IIB enzyme that breaks double-stranded DNA and assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis.
Pfam PF12617: Iron-Sulfur binding protein C terminal (family)
This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with [pfam:PF00037]. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs.
Pfam PF02994: L1 transposable element RBD-like domain (domain)
This entry represents the RBD-like domain.
Pfam PF19729: F-box/LRR-repeat protein 18, LRR (repeat)
This entry represents the leucine-rich repeats (LRR) from F-box/LRR repeat protein 18 (also known as F-box and leucine-rich repeat protein 18, FBXL18), associated with F-box domains. This protein is the substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex through its F-box and the LRR motifs mediate the protein-protein interactions required for the binding of the specific substrates by SCFs complexes.
Pfam PF18037: Ubiquitin-like domain (domain)
This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster protein.
Pfam PF10094: Uncharacterized protein conserved in bacteria (DUF2332) (family)
Members of this family of hypothetical bacterial proteins have 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 PF01529: DHHC palmitoyltransferase (family)
This entry refers to the DHHC domain, found in DHHC proteins which  are palmitoyltransferases. Palmitoylation or, more specifically  S-acylation, plays important roles in the regulation of protein  localization, stability, and activity. It is a post-translational  protein modification that involves the attachment of palmitic acid  to Cys residues through a thioester linkage. Protein  acyltransferases (PATs), also known as palmitoyltransferases,  catalyze this reaction by transferring the palmitoyl group from  palmitoyl-CoA to the thiol group of Cys residues. They are  characterized by the presence of a 50-residue-long domain called  the DHHC domain, which in most but not all cases is also  cysteine-rich and gets its name from a highly conserved DHHC  signature tetrapeptide (Asp-His-His-Cys). The Cys residue within  the DHHC domain forms a stable acyl intermediate and transfers the  acyl chain to the Cys residues of a target protein. Some  proteins containing a DHHC domain include Drosophila DNZ1 protein, Mouse Abl-philin 2 (Aph2) protein, Mammalian ZDHHC9, Yeast ankyrin repeat-containing protein AKR1, Yeast Erf2 protein, and Arabidopsis thaliana tip growth defective 1.
Wikipedia: In molecular biology the DHHC domain is a protein domain that acts as an enzyme, which adds a palmitoyl chemical group to proteins in order to anchor them to cell membranes. The DHHC domain was discovered in 1999 and named after a conserved sequence motif found in its protein sequence. Roth and colleagues showed that the yeast Akr1p protein could palmitoylate Yck2p in vitro and inferred that the DHHC domain defined a large family of palmitoyltransferases. In mammals twenty three members of this family have been identified and their substrate specificities investigated. Some members of the family such as ZDHHC3 and ZDHHC7 enhance palmitoylation of proteins such as PSD-95, SNAP-25, GAP43, Gαs. Others such as ZDHHC9 showed specificity only toward the H-Ras protein. However, a recent study questions the involvement of classical enzyme-substrate recognition and specificity in the palmitoylation reaction. Several members of the family have been implicated in human diseases.
Pfam PF17675: Apg6 coiled-coil region (coiled_coil)
In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in  eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway.
Pfam PF16922: DNA replication complex GINS protein SLD5 C-terminus (domain)
The C-terminal domain of DNA replication complex GINS protein SLD5 is important in the assembly of the GINS complex, a complex which is involved in initiation of DNA replication and progression of DNA replication forks.
Pfam PF22939: GPI inositol-deacylase, winged helix domain (domain)
This winged helix domain (WHD) is found in a number of putative GPI inositol-deacylases. It has detectable sequence similarity to WHDs found in various ATPases. The function of this domain is unknown.
Pfam PF16926: Archaeal 4TM region of histidine kinase (family)
This N-terminal region of histidine-kinases consists of 4xTMs and is found in Archaea.
Pfam PF17891: Mu-like prophage FluMu N-terminal domain (domain)
Structural analysis of HI1506 (also known as Mu-like prophage FluMu protein gp35) from Haemophilus influenzae show that HI1506 consists of two structured domains connected by an unstructured 30 amino acid loop. This entry is the N-terminal domain which comprises a three-stranded antiparallel beta-sheet packed against an alpha-helix.
Pfam PF12041: Transcriptional regulator DELLA protein N terminal (domain)
Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins.
Pfam PF24297: Family of unknown function (DUF7481) (repeat)
This entry represents a group of uncharacterised sequences from bacteria. They may consist on repeats with a novel fold which is organised in three units with twisted beta-strands each.
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 PF00769: Ezrin/radixin/moesin family C terminal (domain)
This entry represents the C-terminal domain of the ERM family of proteins which consists of three closely-related proteins, ezrin, radixin and moesin. These proteins link actin filaments of cell surface structures to the plasma membrane, using a C-terminal F-actin binding segment and an N-terminal FERM domain ([pfam:PF00373]), a common membrane binding module. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). This entry represents the C-terminal actin-binding tail domain. This entry also includes Ermin proteins, oligodendrocyte-specific proteins associated with the cytoskeleton whose C-terminal domain is similar to that in ERM family.
Wikipedia: The ERM protein family consists of three closely related proteins, ezrin, radixin and moesin. The three paralogs, ezrin, radixin and moesin, are present in vertebrates, whereas other species have only one ERM gene. Therefore, in vertebrates these paralogs likely arose by gene duplication.
Pfam PF16035: Chalcone isomerase like (domain)
Chalcone isomerase (CHI, 5.5.1.6; also known as chalcone-flavanone isomerase) is a plant enzyme responsible for the isomerisation of chalcone to naringenin, a key step in the biosynthesis of flavonoids. The Petunia hybrida (Petunia) genome contains two genes coding for very similar enzymes, ChiA and ChiB, but only the first seems to encode a functional chalcone isomerase. Chalcone isomerase has a core 2-layer Î±/Î² structure consisting of Î²(3)-Î±(2)-Î²-Î±(2)-Î²(3) .

Altered inheritance of mitochondria protein 18/46, mitochondrial (AIM18/16) are CHI-like proteins from Saccharomyces cerevisiae, which lacks other enzymes of the flavonoid pathway. They show a similar fold to CHI with an extra fungal-specific loop. Instead of the chalcone isomerase activity these proteins bind heme, and structural prediction suggest this domain might be related to bacterial cytochrome P460 .

This entry represents the chalcone isomerases domain found in proteins from plants, fungi and bacteria.
Pfam PF00946: Mononegavirales RNA dependent RNA polymerase (family)
Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P.        This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor.
Pfam PF18905: Protein of unknown function (DUF5661) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 89 and 148 amino acids in length.
Pfam PF10600: PDZ-associated domain of NMDA receptors (domain)
This domain is found in higher eukaryotes between the second and third PDZ domains, [pfam:PF00595], of glutamate receptor like proteins. Its exact function is not known.
Pfam PF01284: Membrane-associating domain (domain)
MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis.
Pfam PF08610: Peroxisomal membrane protein (Pex16) (family)
Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane.
Pfam PF25033: VPS13-like family middle region (repeat)
VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites. It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on  the carbon source and metabolic state. VPS13A, VPS13C and VPS13D from mammals localise at contacts at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localise to endosome-endosome contacts. Mutations in human VPS13 proteins cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia.
Pfam PF03222: Tryptophan/tyrosine permease family (family)
Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related .

Aromatic amino acids are concentrated in the cytoplasm of Escherichia coli by 4 distinct transport systems: a general aromatic amino acid permease, and a specific permease for each of the 3 types (Phe, Tyr and Trp) . It has been shown  that some permeases in E. coli and related bacteria are evolutionary related. These permeases are proteins of about 400 to 420 amino acids and are located in the cytoplasmic membrane and, like bacterial sugar/cation transporters, are thought to contain 12 transmembrane (TM) regions  - hydropathy analysis, however, is inconclusive, suggesting the possibility of 10 to 12 membrane-spanning domains . The best conserved domain is a stretch of 20 residues which seems to be located in a cytoplasmic loop between the first and second transmembrane region.

This entry represents permeases from the acid/polyamine transporter 2 family, which includes tryptophan/threonine/serine transporters such as Mtr , TdcC and SdaC .
Pfam PF19349: Family of unknown function (DUF5927) (domain)
This entry represents a presumed domain that is functionally uncharacterised. This domain family is primarily found in Rhodobacteria, and is approximately 300 amino acids in length. The family is found to the C-terminus of [pfam:PF02485] and so is likely to have a role in carbohydrate modification.
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 PF05702: Herpesvirus UL49.5 envelope/tegument protein (family)
UL49.5 protein consists of 98 amino acids with a calculated molecular mass of 10,155 Da. It contains putative signal peptide and transmembrane domains but lacks a consensus sequence for N glycosylation. UL49.5 protein is an O-glycosylated structural component of the viral envelope.
Pfam PF07813: LTXXQ motif family protein (family)
This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP ([swissprot:P32158]). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Another member of this family, Spy ([swissprot:P77754]) is also a periplasmic protein that may be involved in the response to stress. The homology between CpxP and Spy may indicate that these two proteins are functionally related.
Pfam PF09220: L-A virus, major coat protein (domain)
Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus.
Pfam PF20487: Family of unknown function (DUF6726) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved LTKVV sequence 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 PF00358: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 (domain)
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).
Pfam PF05033: Pre-SET motif (family)
This protein motif is a zinc binding motif.  It  contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.
Pfam PF17055: Viral matrix protein M2 (family)
Is a viral transmembrane protein which forms a proton-selective ion channel that is needed for the efficient release of the viral genome during virus entry. Once is attached to the cell surface, the virion enters the cells by endocytosis. Acidification of the endosome triggers M2 ion channel activity. Also plays a role in viral proteins secretory pathways. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network. It seems that M2 protein ion channel activity can affect the status of the conformational form of cleaved HA during intracellular transport.
Pfam PF04298: Putative neutral zinc metallopeptidase (family)
Zinc metallopeptidase zinc binding regions have been predicted in some family members by a pattern match (Prosite:PS00142), of the characteristic HEXXH motif.
Pfam PF15958: Domain of unknown function (DUF4761) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 110 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 PF12848: ABC transporter (domain)
This domain is an extension of some members of [pfam:PF00005] and other ABC-transporter families.
Wikipedia: In molecular biology, ATP-binding domain of ABC transporters  is a water-soluble domain of transmembrane ABC transporters.
Pfam PF10328: Serpentine type 7TM GPCR chemoreceptor Srx (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF02650: WhiA C-terminal HTH domain (domain)
This domain is found at the C-terminus of the sporulation regulator WhiA.  It is predicted to form a DNA-binding helix-turn-helix structure.  The WhiA protein also contains two N-terminal domains that are distant homologues of LAGLIDADG homing endonucleases.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF14267: Domain of unknown function (DUF4357) (family)
This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. There are two completely conserved residues (G and W) 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 PF13815: Iguana/Dzip1-like DAZ-interacting protein N-terminal (family)
The DAZ gene-product - Deleted in Azoospermia - and a closely related sequence are required early in germ-cell development in order to maintain germ-cell populations. This family is the N-terminal region that is the only part of the protein in some fungi and lower metazoa.
Pfam PF11680: Protein of unknown function (DUF3276) (family)
This bacterial 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 PF19557: Family of unknown function (DUF6079) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically around 1200 amino acids in length. This family includes a P-loop domain at the N-terminus.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06165: Glycosyltransferase family 36 (domain)
The glycosyltransferase family 36 includes cellobiose phosphorylase  ([ec:2.4.1.20]), cellodextrin phosphorylase ([ec:2.4.1.49]), chitobiose  phosphorylase ([ec:2.4.1.-]).  Many members of this family contain two copies of this domain.