SII-SWORD/CoKE huggingface dataset:
Pfam PF18529: Mitochondrial membrane-anchored proteins (repeat)
MIX forms an all alpha-helical fold comprising seven alpha-helices that fold into a single domain. The distribution of helices is similar to a number of scaffold proteins, namely HEAT repeats, 14-3-3, and tetratricopeptide repeat proteins, suggesting that MIX mediates protein-protein interactions.
Pfam PF20385: Family of unknown function (DUF6680) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 120 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 PF09763: Exocyst complex component Sec3, coiled-coil (repeat)
Sec3 (also known as ExoC1) is a component of the 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. The exocyst is also involved in other cell processes such as cell polarisation, primary ciliogenesis, cytokinesis, and tumourigenesis and metastasis. This complex has an elongated shape consisting of packed long rods, a structure that is shared among the Complex Associated with Tethering Containing Helical Rods (CATCHRs) proteins from related complexes such as Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP). Subunits of these complexes, apart of helical bundles, they usually have a coiled-coil (CC) region at the N-terminal. Sec3 is described as a membrane-anchoring component which serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. This entry represents the middle coiled-coil region (known as the 'CorEx motif') of Sec3 which forms an antiparallel 'zipper' with Sec5 subunit to assemble with Sec6-Sec8 zipper and form a four-helical bundle.
Pfam PF07997: Protein of unknown function (DUF1694) (family)
This family contains many hypothetical 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 PF12091: Protein of unknown function (DUF3567) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK 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 PF10375: GRAB domain (domain)
The GRAB (GRIP-related Arf-binding) domain is towards the C-terminus of Rud3 type proteins. This domain is related to the GRIP domain, but the conserved tyrosine residue found at position 4 in all GRIP domains is replaced by a leucine residue. The Arf small GTPase is localised to the cis-Golgi where it recruits proteins via their GRAB domain, as part of the transport of cargo from the endoplasmic reticulum to the plasma membrane.
Pfam PF21015: Ybfg C-terminal (domain)
This is the presumed C-terminal domain found the uncharacterized protein YbfG from Bacillus subtilis. This domain may adopt an alpha/beta structure. YbfG has a peptidoglycan-binding domain at the N-terminal ([pfam:PF01471]) and a central catalytic glycosyl hydrolase family 25 (GH25) domain ([pfam:PF08924]). YbfG has a significant degree of homology to BacA from E. faecalis, which together with BacL1, show cell wall lytic activity.
Pfam PF23884: Family of unknown function (DUF7237) (family)
This entry represents a protein of unknown function found in phage proteins. The domain contains approximately 77 residues and may contain a single transmembrane helix near 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 PF23146: IFT121, first zinc finger domain (domain)
This domain is found in the homologues of Intraflagellar transport protein 121 (IFT121). IFT121 is a component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors. This protein plays a role in cilia assembly and maintenance. IFT121 is predicted to contain a tandem of zinc fingers with rubredoxin-like fold. This entry represents the first rubredoxin-like zinc finger.
Pfam PF18017: SAM domain (Sterile alpha motif) (domain)
This entry corresponds to a SAM domain that is found at the N-terminus of the human C19orf47 protein.
Wikipedia: In molecular biology, the protein domain Sterile alpha motif is a putative protein interaction module present in a wide variety of proteins involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins, nevertheless with a low affinity constant.
Pfam PF00502: Phycobilisome protein (domain)
Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane . These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane.

This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits . The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.
Wikipedia: Phycobilisomes are light-harvesting antennae that transmit the energy of harvested photons to photosystem II and photosystem I in cyanobacteria and in the chloroplasts of red algae and glaucophytes. They were lost during the evolution of the chloroplasts of green algae and plants.
Pfam PF13238: AAA domain (domain)
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF16023: DUF4784 WD40-like domain (repeat)
This is a family of uncharacterised proteins from Bacteroidetes. This entry adopts a 6-bladed beta propeller 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 PF23905: Domain of unknown function (DUF7247) (domain)
This entry represents an uncharacterised phage domain composed of a seven stranded beta sheet with a C-terminal alpha helix. Structure prediction suggests this protein may form a homodimer.
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 PF05090: HTTM domain (domain)
This entry represents the HTTM (for horizontally transferred transmembrane) domain found at the N-terminal in metazoan Vitamin K-dependent gamma-carboxylase and in diverse domain architectures in bacterial proteins. This domain shows four transmembrane regions.
Pfam PF00532: Periplasmic binding proteins and sugar binding domain of LacI family (domain)
This family includes the periplasmic binding proteins, and the LacI  family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes.  The LacI family of proteins consist of  transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain ([pfam:PF00356]).
Pfam PF21607: [Acyl-carrier-protein] S-malonyltransferase, inserted helical domain (domain)
This domain is found in the C-terminal region of [Acyl-carrier-protein] S-malonyltransferase from Bacillus velezensis (FabD) and similar bacterial proteins. FabD, a marine polyunsaturated fatty acid (PUFA) synthase involved in difficidin A biosynthesis, is is organised into two domains: anacetyl-transferase (AT) domain ([pfam:PF00698]) and an enoyl reductase (ER) domain that consists of a TIM-barrel domain ([pfam:PF03060]) and an inserted alpha-helical substrate-binding domain (this entry).
Pfam PF10999: Protein of unknown function (DUF2839) (family)
This bacterial family of unknown function appear to be restricted to Cyanobacteria.
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 PF24068: Tapetum determinant 1, C-terminal (domain)
This domain is found at the C-terminal end of Protein TAPETUM DETERMINANT 1 from Arabidopsis thaliana (TPD1) and similar proteins from plants. TPD1 is involved in cell specification during anther and pollen development. This domain is predicted to adopt a beta-sandwich structure.
Pfam PF19994: GTPase-associated system helical domain (domain)
This entry represents a Helical domain observed in the GAP1-N1 type of GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. GASH is one component of the GTPase-activated complex in these systems, potentially involved in the sensing of invasive elements.
Pfam PF10717: Occlusion-derived virus envelope protein ODV-E18 (family)
This family of occlusion-derived viral envelope proteins are detected in viral-induced intranuclear microvesicles and are not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. The ODV-E18 protein is encoded by baculovirus late genes with transcription initiating from a TAAG motif. It exists as a dimer in the ODV envelope and contains a hydrophobic domain which is putatively acting as a target or retention signal for intranuclear microvesicles.
Pfam PF17531: Spanin, outer lipoprotein subunit T7-like virus (family)
This family contains members of the outer membrane spanin subunit protein (o-spanin), found in  Bacteriophage T7. Spanins are lytic proteins that act on bacterial outer membrane by disrupting it, allowing progeny virions to spread. O-spanin acts together with inner membrane spanin subunit (i-spanin) to form the spanin complex necessary for function. The gene encoding this protein (Rz1-like o-spanin) is completely embedded in the longer gene for the Rz-like i-spanin subunit.
Pfam PF06662: D-glucuronyl C5-epimerase C-terminus (repeat)
This family represents the C-terminus of D-glucuronyl C5-epimerase ([ec:5.1.3.-]). Glucuronyl C5-epimerases catalyse the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans.
Pfam PF18459: Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain (domain)
This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1). PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function). The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds.
Pfam PF03262: Coronavirus 6B/7B protein (family)
The function of the Coronavirus 6B and 7B proteins is not known.
Pfam PF15781: ParE-like toxin of type II bacterial toxin-antitoxin system (domain)
ParE is the toxin family of a type II toxin-antitoxin family. This family consists of proteins of unknown function related to ParE, but does not include ParE.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF01174: SNO glutamine amidotransferase family (domain)
This family and its amidotransferase domain was first described in. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of [pfam:PF01174] and [pfam:PF01680].
Pfam PF03597: Cytochrome oxidase maturation protein cbb3-type (family)
Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation .

Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Pfam PF22783: BapA, prefix-like domain (domain)
This entry represents the N-terminal domain of two largely unrelated repetitive proteins, both named Biofilm-associated protein BapA (from Salmonella enterica and from Paracoccus denitrificans), which share common domains at the two ends. The conserved prefix (N-terminal) domain is shared by a number of other large, repetitive proteins from proteobacteria and are thought to be associated with adhesion or biofilm formation.
Pfam PF02148: Zn-finger in ubiquitin-hydrolases and other protein (domain)
This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) , All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties.

Some of the proteins containing an UBP zinc finger include:


 * Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD)
 * Human deubiquitinating enzyme 5 (UBP5)
 * Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA)
 * Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8)
 * Yeast deubiquitinating enzyme 14 (UBP14)

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Pfam PF08867: FRG domain (domain)
This presumed domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised.
Pfam PF11277: Mediator complex subunit 24 N-terminal (family)
This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish.  Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14.
Wikipedia: Mediator of RNA polymerase II transcription subunit 24 is an enzyme that in humans is encoded by the MED24 gene.
Pfam PF01663: Type I phosphodiesterase / nucleotide pyrophosphatase (family)
This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyse the cleavage of phosphodiester and phosphosulfate bonds in NAD,  deoxynucleotides and nucleotide sugars. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which  exhibits type I phosphodiesterases activity. The alignment encompasses the active site. Also present with in this family is 60-kDa Ca2+-ATPase form  F. odoratum.
Pfam PF14934: Transmembrane protein 254 (family)
This family contains proteins found in eukaryotes, including human Transmembrane protein TMEM254 (C10orf57). The exact function of this protein is still unknown, however it is thought to be an integral membrane protein. The protein sequence is 123 amino acids in length and has a mass of approximately 14.2 kDa. The family also includes some longer proteins that possess an N-terminal dehydrogenase domain, [pfam:PF01073].
Pfam PF14392: Zinc knuckle (domain)
The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins.
Pfam PF12181: DNA binding domain of the motility gene repressor (MogR) (domain)
This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in repression of transcription of the flagellar gene in Listeria bacteria. This allows a phenotypical switch from an extracellular bacterium to an intracellular pathogen. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR.
Pfam PF14149: YhfH-like protein (family)
The YhfH-like protein family includes the B. subtilis YhfH protein [swissprot:O07606], which is functionally uncharacterised. Its expression is repressed by the Spx paralogue MgsR, which regulates genes involved in stress response.  This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 53 amino acids in length.
Pfam PF02884: Polysaccharide lyase family 8, C-terminal beta-sandwich domain (domain)
This family consists of a group of secreted bacterial lyase enzymes [ec:4.2.2.1] capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen.
Pfam PF19506: Family of unknown function (DUF6040) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Clostridia. Proteins in this family are typically between 203 and 265 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.