SII-SWORD/CoKE huggingface dataset:
Pfam PF11212: Protein of unknown function (DUF2999) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF12777: Microtubule-binding stalk of dynein motor (domain)
the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component.
Pfam PF21390: Thiazolinyl imine reductase Irp3-like, C-terminal (domain)
Thiazolinyl imine reductases catalyse the NADPH-dependent reduction of a thiazoline to a thiazolidine, a step involved in formation of the siderophores yersiniabactin (Yersinia spp.) and pyochelin (Pseudomonas aeruginosa). These proteins consist of two domains, an N-terminal dinucleotide-binding domain ([pfam:PF01408]) and a C-terminal alpha/beta domain, involved in substrate binding and oligomerisation. This entry represents the C-terminal domain of Thiazolinyl imine reductase Irp3 from Yersinia enterocolitica and PchG from Pseudomonas aeruginosa.
Pfam PF21647: Domain of unknown function (DUF6857) (domain)
This is a domain of unknown function found at the C-terminal of uncharacterised plant proteins. These sequences have an OB fold at the N-terminal ([pfam:PF06075]). This domain may consist of 5-6 alpha helices.
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 PF13676: TIR domain (domain)
This is a family of Toll-like receptors.
Pfam PF17983: Trypsin inhibitors 1,2 and 3 (domain)
This is domain is found in trypsin inhibitor 1, 2 and 3 found in Chenopodiaceae. Structure analysis of S. oleracea trypsin inhibitor III (SOTI-III), in complex with bovine pancreatic trypsin, shows a knottin-like cystine-bridge topology.
Pfam PF11576: FeGP cofactor biosynthesis protein HcgB, guanylyltransferase (domain)
This entry represents the guanylyltransferase component of the Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgB. This family of proteins with unknown function appears to be restricted to Methanobacteria.
Pfam PF20921: Domain of unknown function DUF1846, C-terminal (domain)
This is the C-terminal domain found in the uncharacterised protein family UPF0371. It has a cytidine deaminase-like fold (pdbe:3bh1).
Pfam PF19172: Family of unknown function (DUF5854) (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 PF01264: Chorismate synthase (family)
Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows a high degree of sequence conservation . It is a protein of about 360 to 400 amino-acid residues.

Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two groups: enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctional, while those that can generate reduced FMN at the expense of NADPH, such as found in fungi and the ciliated protozoan Euglena gracilis, are bifunctional, having an additional NADPH:FMN oxidoreductase activity. Recently, bifunctionality of the Mycobacterium tuberculosis enzyme (MtCS) was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. Since shikimate pathway enzymes are present in bacteria, fungi and apicomplexan parasites (such as Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum) but absent in mammals, they are potentially attractive targets for the development of new therapy against infectious diseases such as tuberculosis (TB) .
Wikipedia: The enzyme chorismate synthase catalyzes the chemical reaction5-O-(1-carboxyvinyl)-3-phosphoshikimate  chorismate + phosphate
Pfam PF05303: GSKIP domain (domain)
This domain is found in GSK3-beta interaction protein (GSKIP), which binds to GSK3beta. It is also found as a short domain towards the N terminus in clustered mitochondria protein, also known as clueless in Drosophila, which is involved in proper cytoplasmic distribution of mitochondria.
Pfam PF11465: Natural killer cell receptor 2B4 (domain)
2B4 is a transmembrane receptor which is expressed primarily on natural killer cells. It plays a role in activating NK-mediated cytotoxicity through its interaction with CD48 on target cells in a subset of CD8 T cells. The structure of 2B4 consists of an immunoglobulin variable domain fold and contains two beta-sheets. One of the beta-sheets, the six-stranded sheet, contains structural features that may have a role in ligand recognition and receptor function.
Pfam PF21356: Vacuolar protein sorting-associated protein 27, GAT-like domain (domain)
This domain is found in Vacuolar protein sorting-associated protein 27 from Saccharomyces cerevisiae (Vps27) and similar sequences predominantly found in yeast. Vps27 binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. Besides the GAT domain (this entry), Vps27 contains VHS ([pfam:PF00790]) and FYVE domains ([pfam:PF01363]). This domain forms a three-helix bundle that resemble closely the structure of a GAT domain.
Pfam PF19648: Family of unknown function (DUF6151) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 185 and 201 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 PF15378: Domain of unknown function (DUF4605) (family)
This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 82 and 137 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 PF00793: DAHP synthetase I family (domain)
Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, [ec:2.5.1.54].
Wikipedia: 3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.
Pfam PF02920: DNA binding domain of tn916 integrase (domain)
The integrase family of site-specific recombinases catalyze a diverse array of DNA rearrangements in archaebacteria, eubacteria and yeast. The structure of the DNA binding domain of the the conjugative transposon Tn916 integrase protein was determined using NMR spectroscopy. The N-terminal domain was found to be structurally similar to the double stranded RNA binding domain (dsRBD). Experimental evidence suggests that the integrase protein interacts with DNA using residues located on the face of its three stranded Î²-sheet .
Pfam PF00253: Ribosomal protein S14p/S29e (family)
This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes.
Pfam PF09382: RQC domain (domain)
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure.  The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain.
Pfam PF07829: Alpha-A conotoxin PIVA-like protein (domain)
Alpha-A conotoxin PIVA ([swissprot:P55963]) is the major paralytic toxin found in the venom produced by the piscivorous snail Conus purpurascens. This peptide acts by blocking the acetylcholine binding site of the nicotinic acetylcholine receptor at the neuromuscular junction. The overall shape of the peptide is described as an "iron" with a highly charged hydrophilic loop of 15S-19R forming the "handle" domain that  is exposed to the exterior of the protein. The stability of  the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and  6Y is thought to constitute a "binding core" that is important in binding to the acetylcholine receptor.
Pfam PF05942: Archaeal PaREP1/PaREP8 family (family)
This family consists of several archaeal PaREP1 and PaREP8 proteins the function of this family is unknown.
Pfam PF11006: Protein of unknown function (DUF2845) (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 PF24802: Domain of unknown function (DUF7703) (domain)
This domain is found in a group of uncharacterised proteins mainly from fungi. It is predicted to contain seven transmembrane helices.
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 PF14189: Domain of unknown function (DUF4312) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 99 and 118 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 PF11091: Tail-tube assembly protein (family)
This tail tube protein is also referred to as Gp48. It is required for the assembly and length regulation of the tail tube of bacteriophage T4.
Pfam PF22424: HK620, Tail spike protein, C-terminal (domain)
This domain is found at the C-terminal end of Tail spike protein from Enterobacteria phage HK620 (9). This domain adopts a beta -sandwich configuration.
Pfam PF07175: Osteoregulin (disordered)
This family represents a conserved region approximately 180 residues long within osteoregulin, a bone-remodelling protein expressed highly in osteocytes within trabecular and cortical bone. A conserved RGD motif is found towards the C-terminal end of this region, and this is potentially involved in integrin recognition.
Wikipedia: Matrix extracellular phosphoglycoprotein is a protein that in humans is encoded by the MEPE gene. A conserved RGD motif is found in this protein, and this is potentially involved in integrin recognition.
Pfam PF13035: Protein of unknown function (DUF3896) (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.
Pfam PF04449: CS1 type fimbrial major subunit (family)
Fimbriae, also known as pili, form filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometres. They enable the cell to colonise host epithelia. This family constitutes the major subunits of CS1 like pili, including CS2 and CFA1 from Escherichia coli, and also the Cable type II pilin major subunit from Burkholderia cepacia. The major subunit of CS1 pili is called CooA.  Periplasmic CooA is mostly complexed with the assembly protein CooB.  In addition, a small pool of CooA multimers, and CooA-CooD complexes exists, but the functional significance is unknown. A member of this family has also been identified in Salmonella typhi and Salmonella enterica.
Pfam PF04840: Vps16, C-terminal region (repeat)
This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole.  It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport.  The role of VPS16 in this complex is not known.
Pfam PF22593: Sperm microtubule inner protein 11 (family)
This entry represents homologs of Sperm microtubule inner protein 11 (SPMIP11 also known as TEX49). SPMIP11 is a microtubule inner protein (MIP) part of the axonemal doublet microtubules (DMTs). It is likely involved in the stabilisation of the microtubule structure in the sperm flagella. SPMIP11 belongs to the sperm-specific MIPs and binds to protofilament A07 in the sperm DMTs.
Pfam PF21353: Period circadian protein homolog 3-like, PAS-A domain (domain)
This domain is found in Period circadian protein homolog 3 from Mus musculus (Per3) and similar proteins predominantly found in vertebrates. Per3 is involved in the day-time dependent (circadian) regulation of many physiological, behavioural, and biochemical processes. This entry represents the first PAS domain (PAS-A) present in this protein. This domain shows a five-stranded antiparallel beta- sheet covered on one face by alpha-helices.
Pfam PF23423: Family of unknown function (DUF7111) (family)
This family represents a group of proteins from halobacteria. It has several conserved motifs AxYxET, ERxL/VxF and GYAMLK/RVR. Members are predicted to show a beta-sheet and an alpha-helix.
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 PF18657: YDG domain (domain)
This presumed domain is found in a wide variety of bacterial cell surface proteins. This domain has a highly conserved YDG motif near its N-terminus. This domain is likely related to the [pfam:PF17883] domain.
Pfam PF22584: Cilia- and flagella-associated protein 143 (family)
This family represents the homologues of Cilia- and flagella-associated protein 143 (CFAP143, also known as SPAG8). CFAP143 is one of the core microtubule inner proteins (MIPs) of the doublet microtubules (DMTs) in cilia and sperm axoneme. It binds to protofilaments A09-A13 in the sperm DMTs. CFAP143 was found to play a role in regulation of the cell cycle by controlling progression through the G2/M phase.
Pfam PF06904: Extensin-like protein C-terminus (family)
This family represents the C-terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress. Note that many family members of this family are hypothetical.
Pfam PF11759: Keratin-associated matrix (family)
The major structural proteins of mammalian hair are the hair keratin intermediate filaments (KIFs) and the keratin-associated proteins (KRTAPs). In the hair cortex, hair keratins are embedded in an inter-filamentous matrix consisting of KRTAPs which are essential for the formation of a rigid and resistant hair shaft as a result of disulfide bonds between cysteine residues. There are essentially three groups of KRTAPs, viz: the high-sulfur (HS) and ultra-high-sulfur (UHS) KRTAPs (cysteine content: 16-30 and >30 mol%, respectively) and the high-glycine/tyrosine (HGT: 35-60 mol% glycine and tyrosine) KRTAPs.
Pfam PF22773: Myosin-1, central acidic domain (domain)
This is the central acidic domain (CA) found at the C-terminal of myosin-1 from S.pombe and similar sequences. Myo-1 localizes to actin patches which assemble at sites of endocytosis. The CA domain binds and activates Arp2/3, however, this interaction is dispensable for endocytosis. Mammalian orthologues, such as the human Myo1e, do not contain CA domains.
Pfam PF08385: Dynein heavy chain, N-terminal region 1 (family)
Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.
Wikipedia: Dyneins are a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work. Dynein transports various cellular cargos, provides forces and displacements important in mitosis, and drives the beat of eukaryotic cilia and flagella. All of these functions rely on dynein's ability to move towards the minus-end of the microtubules, known as retrograde transport; thus, they are called "minus-end directed motors". In contrast, most kinesin motor proteins move toward the microtubules' plus-end, in what is called anterograde transport.
Pfam PF05927: Penaeidin (family)
This family consists of several isoforms of the penaeidin protein which is specific to shrimps. Penaeidins, a unique family of antimicrobial peptides (AMPs) with both proline and cysteine-rich domains, were initially identified in the hemolymph of the Pacific white shrimp, Litopenaeus vannamei.
Pfam PF16404: BT_2262-like, C-terminal domain (domain)
This domain found at the C-terminal end of proteins found in Bacteroidetes, including BT_2262 from Bacteroides thetaiotaomicron, a small outer membrane lipoprotein located on the periphery of the SusCD complex, which is essential for the import of oligosaccharides and for glycan degradation. This domain shows an eight-stranded beta-barrel with structural similarity to lipid binding domains. Its specific function remains unknown.
Pfam PF03618: Kinase/pyrophosphorylase (family)
This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity.
Pfam PF12334: Rickettsia outer membrane protein B, passenger domain (repeat)
This domain is found in Rickettsia and it is associated with [pfam:PF03797], an autotransporter domain. This entry includes the the outer membrane protein B, a surface-exposed major structural protein that is involved in adhesion and invasion of host cells, playing a role as a rickettsial virulence factor and immunogen during infection. It serves as a protective envelope. These proteins contain two structural segments, an N-terminal long passenger domain that serves as an adhesin and a C-terminal autotransporter domain. This entry represents the passenger domain which is composed of a beta-solenoid structural repeat. This domain is methylated at its lysine residues by PKMT1 and PKMT2, and this methylation appears to be associated with rickettsial pathogenicity and immunogenic response.
Pfam PF15053: Njmu-R1-like protein family (family)
This protein family represents the eukaryotic protein Njmu-R1, which is thought to have a role in spermatogenesis. In humans, it is found in chromosome 17 open reading frame 75 (C17orf75). It forms a complex with WDR11, which acts together with TBC1D23 to facilitate the golgin-mediates capture of vesicles generated using AP-1.
Pfam PF06455: NADH dehydrogenase subunit 5 C-terminus (domain)
This entry represents the C-terminal region of several NADH dehydrogenase subunit 5 proteins and is found in conjunction with [pfam:PF00361] and [pfam:PF00662].
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 PF15973: Domain of unknown function (DUF4766) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 106 and 128 amino acids in length. There is a conserved KVI 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.