SII-SWORD/CoKE huggingface dataset:
Pfam PF24327: Domain of unknown function (DUF7497) (domain)
This domain is found in a group of uncharacterised eukaryotic proteins. It contains two highly conserved cysteines. This domain is predicted to fold into Ig-like beta-sandwich.
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 PF16793: RepB DNA-primase N-terminal domain (domain)
RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication.  RepBprime primases such as in this family recognise both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesise primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode.
Pfam PF04860: Phage portal protein (family)
Bacteriophage portal proteins form a dodecamer and is located at a  five-fold vertex of the viral capsid.  The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during  infection.  The portal protein is though to rotate during DNA packaging. Portal proteins from different phage show little sequence homology, so  this family does not represent all portal proteins.
Pfam PF08323: Starch synthase catalytic domain (domain)
This region represents the catalytic domain of glycogen (or starch) synthases that use ADP-glucose (2.4.1.21), rather than UDP-glucose (2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate.
Pfam PF22764: Tail fiber protein gp32 (family)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Stacked hexamers of the tail tube protein gp32 form the central tube of the E217 tail. The tail tube protein is structurally conserved and homologous to the tail tube protein found in non-contractile tails, bacterial pyocins, and type VI secretion systems. Gp32 consists of a classical beta-sandwich that contains two four-stranded sheets facing each other and surrounded by a long alpha-helix and an extended beta-turn.
Pfam PF20018: vWA-MoxR associated protein middle region (VMAP-M) 14 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF11033: Competence protein J (ComJ) (family)
ComJ is a competence specific protein.
Pfam PF23244: Von Willebrand factor-like domain (domain)
This domain is found in human von Willebrand factor (vWF) and similar proteins mainly found in animals. vWF is important in the maintenance of hemostasis and acts as a chaperone for coagulation factor VIII, delivering it to the site of injury. This domain adopts an all-beta structure. It is often found associated to [pfam:PF00094].
Pfam PF00937: Coronavirus nucleocapsid (family)
Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organisations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which  phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA),,. It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).
Pfam PF12898: Stc1 domain (domain)
The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe this protein acts as a protein linker which links the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. The region is reported as a LIM domain here, but has a slightly different arrangement of its CxxC pairs from the Pfam LIM domain [pfam:PF00412], hence why it is not part of that family. The tandem zinc-finger structure could mediate protein-protein interactions.
Pfam PF19926: Family of unknown function (DUF6389) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650.
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 PF02623: FliW protein (family)
The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterised as being a flagellar assembly factor. Experimental characterisation was also carried out in Treponema pallidum (TP0658).  In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogues in Helicobacter pylori (HP1154 and HP1377) were found to be able to bind to flagellin. FliW proteins are involved in flagellar assembly. FliW is part of a three-part feedback loop: in Bacillus subtilis FliW inhibits CsrA (an RNA-binding protein) which inhibits FliC translation; hence FliW is required for FliC (flagellin) production.
Pfam PF23432: Domain of unknown function (DUF7118) (family)
This family represents a group of proteins from halobacteria. Members are predicted to adopt an all-alpha 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 PF19920: MoxR-vWA-beta-propeller ternary system domain bpX4 (domain)
Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF19235: Family of unknown function (DUF5888) (family)
This is a family of uncharacterised proteins of unknown function found in viruses. This family also includes proteins found in Bacteria and Fungi that are thought to contain WD40 repeats.
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 PF00588: SpoU rRNA Methylase family (family)
This family of proteins probably use S-AdoMet.
Pfam PF05821: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) (family)
This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF03853: YjeF-related protein N-terminus (domain)
YjeF-N domain is a novel version of the Rossmann fold with a set of  catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to  Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and  FLJ21128), where they may be involved in decapping and catalyze  hydrolytic RNA-processing reactions.
Wikipedia: In molecular biology, the YjeF N terminal is a protein domain found in the N-terminal of the protein, EDC3. The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes. They help assemble the processing body (P-body) in preparation for mRNAdecay. Structural homology indicated it may have some similarity to the enzyme family, hydrolase.
Pfam PF11213: Protein of unknown function (DUF3006) (family)
This 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 PF10324: Serpentine type 7TM GPCR chemoreceptor Srw (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. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz.
Pfam PF15879: NADH-ubiquinone oxidoreductase MWFE subunit (family)
MWFE is a short subunit of NADH-ubiquinone oxidoreductase found in eukaryotes. It is necessary for the activity of NADH-ubiquinone oxidoreductase complex I in mitochondria. This subunit is essential for the assembly and function of the enzyme. MWFE is found to be phosphorylated, eg in rat heart mitochondria. The short family includes much of a signal peptide.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF24344: PH domain (domain)
This domain is found in uncharacterised fungal proteins. It shares significant sequence similarity to known Pleckstrin homology domains (PH-domains) and it is predicted to adopt similar structure. Proteins containing this domain also contain a DH-domain located downstream the PH-domain and are likely members of the Dbl family of guanine nucleotide exchange factors.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF21479: Dickkopf-related protein 1/2/4, C-terminal subdomain 2 (domain)
Dickkopf-related proteins are cysteine-rich secretory proteins and highly conserved inhibitors of the canonical Wnt signaling pathway, which play key roles in many essential biological processes. The C-terminal domain is described as two subdomains, each consisting of three anti-parallel beta-strands that are connected by a long loop which contains a short alpha-helix. This domain is strongly conserved in Dkk1, Dkk2 and Dkk4, and directly contacts LRP6. This entry represents the second subdomain. In Dkk3 these residues differ and is consistent with studies indicating that Dkk3 is a divergent family member that does not inhibit Wnt signalling. This domain share significant sequence similarity to the colipase fold.
Pfam PF14669: Putative aspartate racemase (family)
This is a small family of vertebrate putative aspartate racemases. The family lies on TOPAZ 1 proteins.
Pfam PF03769: Attacin, C-terminal region (family)
This family includes attacin, sarcotoxin and diptericin.  All members of this family are insect antibacterial proteins which are induced by the fat body and subsequently released into secreted into the hemolymph where they act synergistically to kill the invading microorganism.
Pfam PF10439: Bacteriocin class II with double-glycine leader peptide (family)
This is a family of bacteriocidal bacteriocins secreted by Streptococcal species in order to kill off closely-related competitor Gram-positives. The sequence includes the peptide precursor, this being cleaved off proteolytically at the double-glycine. The family does not carry the YGNGVXC motif characteristic of pediocin-like Bacteriocins, Bacteriocin_II [pfam:PF01721]. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, eg family EntA_Immun [pfam:PF08951]. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter. It seems likely that this whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins. and the same bacteriocins can be produced by different species.
Pfam PF10234: Clusterin-associated protein-1 (family)
This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell.
Pfam PF01785: Closterovirus coat protein (family)
This family consist of coat proteins from closteroviruses a member of the closteroviridae.  The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript.  Members of the closteroviridae include Sugar beet  yellow virus and Grapevine leafroll-associated virus, closteroviruses have a positive strand ssRNA genome with no DNA stage during replication.
Pfam PF11772: DNA-directed RNA polymerase subunit beta (family)
This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be [ec:2.7.7.6]. It is membrane-bound and is referred to by the name EpuA.
Pfam PF19520: Dipeptidyl peptidase 8 and 9 N-terminal (repeat)
Dipeptidyl peptidase (DPP) family members 8 and 9 are similar to DPP4, consisting of one N-terminal beta-propeller and a C-terminal alpha/beta hydrolase domain, which form a functional homodimer. This entry represents the N-terminal beta-propeller of DPP8 and 9 which consists of eight blades and enlaces a central round pore. It provides the key arginine residue fundamental for substrate fixation which is located in the R-segment, at the interconnecting loop between blades 1 and 2. Ligand binding to DPP8/9 induces a rearrangement at the active site through a disorder-order transition in a loop segment which includes the key arginine residue and partially folds in an alpha-helix (R-helix). DPP8 and DPP9 play a role in the immune system and in preadipocyte differentiation. DPP9 is also essential for neonatal survival and plays a role in antigen maturation, cell migration, and cell adhesion.
Pfam PF10589: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (domain)
This entry represents the iron-sulphur binding domain of NADH-ubiquinone oxidoreductase 51kDa subunit from NADH:ubiquinone oxidoreductase.
Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 51kDa (in mammals), which is the second largest subunit of complex I . The 51kDa subunit, as the corresponding bacterial subunit (Nqo1 in Thermus and NuoF in E. coli) , contains the NADH-binding site, the primary electron acceptor FMN-binding site, and a 4Fe-4S cluster .
Pfam PF20555: Domain of unknown function (DUF6767) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 59 and 74 amino acids in length. There are two conserved sequence motifs: VTGP and DPE. The proteins contain four conserved cysteines. Proteins in this family are found in actinobacteria.
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 PF18497: Ribonuclease III N-terminal domain (domain)
This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, [ec:3.1.26.3]). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity.
Pfam PF01620: Ribonuclease (pollen allergen) (family)
This family contains grass pollen proteins of group V. [swissprot:Q40963] has been shown to possess ribonuclease activity.
Pfam PF04688: SPP1 phage holin (family)
This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes.
Pfam PF03279: Bacterial lipid A biosynthesis acyltransferase (family)
Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS molecules are variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A . The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS . The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids . These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units.

The bacterial lipid A biosynthesis protein, or lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase 2.3.1, transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA during lipopolysaccharide core biosynthesis .
Pfam PF04076: Bacterial OB fold (BOF) protein (domain)
Proteins in this family form an OB-fold.  Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties.  They contain an predicted N-terminal signal peptide which indicates that they localise in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.
Pfam PF15804: Coiled-coil domain-containing protein 168 (repeat)
CCDC168_N is the N-terminal region of eukaryotic coiled-coil proteins 168 family. There are up to 17, on average 6, copies of this repeat in most members.