SII-SWORD/CoKE huggingface dataset:
Pfam PF03841: L-seryl-tRNA selenium transferase (domain)
In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.

This family describes SelA and pyridoxal phosphate enzymes of unknown function. A close homologue of SelA is found in Helicobacter pylori, but all other required elements are missing and the protein is shorter at the N terminus than SelA from other species.
Pfam PF12010: Domain of unknown function (DUF3502) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 140 amino acids in length. This domain is found associated with [pfam:PF01547].
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 PF24049: YOMG N-terminal domain (domain)
This entry represents the N-teminal domain of SPbeta prophage-derived uncharacterized protein YomG from Bacillus subtilis (strain 168). This domain adopts a beta-barrel fold and is usually found in association with a neighbour prophage endopeptidase tail domain ([pfam:PF06605]).
Pfam PF21192: NMD3 OB-fold domain (domain)
A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the third domain in NMD3 which adopts an OB-fold. The OB of Nmd3 does not recognise 25S rRNA. Instead it interacts with two ribosomal proteins, eL42 and uL1.
Pfam PF00352: Transcription factor TFIID (or TATA-binding protein, TBP) (domain)
The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box . TBP associates with a host of factors, including the general transcription factors SL1, TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins . TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site.

The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins . By contrast, the N-terminal region varies in both length and sequence.
Wikipedia: The TATA-binding protein (TBP) is a general transcription factor that binds to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters.
Pfam PF20705: Family of unknown function (DUF6821) (family)
This presumed domain is functionally uncharacterised. This family is found mainly in plants, and is approximately 300 amino acids in length. It contains a predicted transmembrane 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 PF14030: Protein of unknown function (DUF4245) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 235 amino acids in length.
Pfam PF11471: Maltoporin periplasmic N-terminal extension (domain)
This domain would appear to be the periplasmic, N-terminal extension of the outer membrane maltoporins, [pfam:PF02264], LamB.
Pfam PF23153: Aip3p/Bud6 N-terminal domain (domain)
This domain is commonly located in the N-terminus of Aip3p/Bud6 protein found in fungal organisms. This region is essential for its proper localization on the plasma membrane and to bind to the microtubule (+) end binding protein Bim1. Its absence results in altered localization patterns, although the secretory pathway remains functional. The N-terminal region of Bud6 contains the major binding site for Aip5, which is required for the formation of actin cables. This domain may adopt a four-helix bundle fold.
Pfam PF01841: Transglutaminase-like superfamily (domain)
This domain is found in animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease.
Wikipedia: Transglutaminases are enzymes that in nature primarily catalyze the formation of an isopeptide bond between γ-carboxamide groups ( -(C=O)NH2 ) of glutamine residue side chains and the ε-amino groups ( -NH2 ) of lysine residue side chains with subsequent release of ammonia ( NH3 ). Lysine and glutamine residues must be bound to a peptide or a protein so that this cross-linking (between separate molecules) or intramolecular (within the same molecule) reaction can happen. Bonds formed by transglutaminase exhibit high resistance to proteolytic degradation (proteolysis). The reaction isGln-(C=O)NH2 + NH2-Lys → Gln-(C=O)NH-Lys + NH3
Pfam PF22270: Transcriptional regulator MlrA, helical domain (domain)
The HTH transcription regulator MlrA belongs to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by re configuring the spacer between the -35 and -10 promoter elements. MlrA it is also known as YehV, and has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella yphimurium. MlrA is part of a signaling cascade that regulates curli biosynthesis. These proteins have dissimilar C-terminal domains that may bind specific coactivator molecules. This entry represents an helical domain, similar to the B12-binding module cap domain ([pfam:PF02607]).
Pfam PF05881: 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) (family)
This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity. CNPases belong to the 2H phosphoesterase superfamily. They share a common active site, characterised by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT, vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.
Pfam PF00123: Peptide hormone (family)
This family contains glucagon, GIP, secretin and VIP.
Wikipedia: Glucagon/gastric inhibitory polypeptide/secretin/vasoactive intestinal peptide hormones are a family of evolutionarily related peptide hormones that regulate activity of G-protein-coupled receptors from the secretin receptor family.
Pfam PF06135: IreB regulatory phosphoprotein (family)
IreB is a cytosolic 10.5-kDa protein that is highly conserved among low-GC Gram-positive bacteria . Studies of E. faecalis mutants lacking ireB revealed that IreB acts downstream of IreK as a negative regulator of cephalosporin resistance in E. faecalis.  IreB can be modified by phosphorylation in vivo, and mutations that prevent modification at the known sites of phosphorylation (T4 and T7) influence the ability of IreB to modulate cephalosporin resistance. Furthermore, mutations that impair dimerization abolish the regulation of cephalosporin resistance.
Pfam PF22843: CATSPERE second N-terminal domain (domain)
This entry includes CATSPERE, the auxiliary subunit epsilon of the CatSper complex, a complex involved in sperm cell hyperactivation. This process is needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which has a similar domain organisation as the other auxiliary subunits, beta, gamma and delta. The epsilon subunit has two N-terminal domains (NTD1/2). This entry represents the second N-terminal domain.
Pfam PF16095: C-terminal of Roc, COR, domain (family)
The C-terminal of Roc domain, COR, along with Roc functions as the putative regulator of kinase activity. It functions as a proper GTP-binding protein with a low GTPase activity somehow stimulating the kinase activity.
Pfam PF20899: Pasteurella multocida toxin, C2 domain (domain)
Pasteurella multocida toxin (PMT) inhibits osteoblastic differentiation in mammals and birds. Its N-terminal region binds to target cells, while its C-terminal region, with a Trojan horse-like shape, carries the intracellularly active moiety. The latter consists of three distinct domains: C1 ([pfam:PF11647]), C2 and C3. This entry represents the larger of these domains, the central region C2, which has 18 helices and nine beta-strands and is organised into two subdomains with typical alpha-beta structures characteristic of nucleotide-binding proteins. This domain is also found in the Ras/Rap1-specific endopeptidase (RRSP), an effector domain from the multifunctional-autoprocessing repeats-in- toxin (MARTX) toxin from Vibrio vulnificus responsible for the disruption of host innate immune defenses during infection.
Pfam PF04085: Rod shape-determining protein MreC, barrel core (domain)
MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. This entry represents the periplasmic core of these proteins which is composed of two six-stranded beta-barrels. MreC self-associates into polar filaments. The periplasmic part of MreC contains also a coiled-coil region which is involved in the formation of dimer essential for its function.
Pfam PF23929: Family of unknown function (DUF7267) (family)
This entry represents a family of uncharacterised phage proteins. Structure prediction suggests this protein adopts a rather open conformation of three alpha helices and a possible beta strand suggesting it must interact with other proteins to 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 PF00151: Lipase (domain)
Triglyceride lipases (3.1.1.3) are lipolytic enzymes that hydrolyse ester linkages of triglycerides . Lipases are widely distributed in animals, plants and prokaryotes. At least three tissue-specific isozymes exist in higher vertebrates, pancreatic, hepatic and gastric/lingual. These lipases are closely related to each other and to lipoprotein lipase (3.1.1.34), which hydrolyses triglycerides of chylomicrons and very low density lipoproteins (VLDL) . The most conserved region in all these proteins is centred around a serine residue which has been shown  to participate, with an histidine and an aspartic acid residue, in a charge relay system. Such a region is also present in lipases of prokaryotic origin and in lecithin-cholesterol acyltransferase (2.3.1.43) (LCAT) , which catalyzes fatty acid transfer between phosphatidylcholine and cholesterol.
Wikipedia: Triglyceride lipases are a family of lipolytic enzymes that hydrolyse ester linkages of triglycerides. Lipases are widely distributed in animals, plants and prokaryotes.
Pfam PF00831: Ribosomal L29 protein (family)
This family includes ribosomal proteins, which constitute the uL29 family . These were previously known as L29 from eubacteria and archaea and L35 from eukaryotes.
Ribosomal protein uL29 is one of the proteins from the large ribosomal subunit. uL29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities, groups:


 * Red algal uL29.
 * Bacterial uL29.
 * Mammalian uL29 (known as L35)
 * Caenorhabditis elegans uL29 (known as L35) (ZK652.4).
 * Yeast uL29 (known as L35).


uL29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome . uL29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, uL29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel . uL29 forms numerous interactions with L23 and with the 23S rRNA.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF04405: Domain of Unknown function (DUF542) (family)
This domain is always found in conjunction with the HHE domain ([pfam:PF03794]) at the  N-terminus.
Pfam PF18791: Transport inhibitor response 1 protein domain (repeat)
The F-box protein Transport inhibitor response 1 (TIR1) is a receptor for auxin, triggering an auxin-enhanced and ubiquitin-mediated  degradation of substrates. The targets are recruited via  interaction with the leucine-rich repeat region of the protein. This  Pfam entry represents a specific unit of the LRR region, including  an insertion of one short alpha-helix in the loop between the  beta-strand and the following helix. It shares some sequence homology with a unit with similar structure of Coronatine-insensitive protein  1.
Pfam PF10595: Protein FAM161A/B (family)
This family of proteins includes FAM161A and FAM161B. FAM161A is involved in ciliogenesis and associated with retinal cilipathies.
Pfam PF18861: TM proximal of protein tyrosine phosphatase, receptor type J (family)
Protein tyrosine phosphatases (PTPs) are known to be signaling molecules that regulate a variety of cellular processes, including cell growth, differentiation, mitotic cycle, and oncogenic transformation. PTP receptor type J possesses an extracellular region containing five fibronectin type III repeats, the transmembrane region included in this Pfam entry, and a intracytoplasmic catalytic domain.  This entry probably contains part of a Fn3 domain at the N-terminus.
Pfam PF23949: TSTD2 protein N-terminal domain (domain)
This entry represents the N-terminal domain found in the TSTD2 (thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 2) proteins.  Thiosulfate sulfurtransferase/rhodanese-like domain-containing proteins are involved in the transfer of sulfur from thiosulfate to cyanide, forming thiocyanate. These proteins play a role in cyanide detoxification and sulfur metabolism. The rhodanese-like domain is crucial for their catalytic activity, facilitating the transfer of sulfur atoms.
Pfam PF16523: betaPIX coiled coil (coiled_coil)
betaPIX_CC is the very C-terminal coiled-coil region of betaPIX or p21-activated kinase interacting exchange factor proteins. The coiled-coil runs from residues 589-646 in UniProtKB:G31IU6, and the PDZ-binding site is the final eight residues immediately downstream.  The coiled-coil trimerises and thus exposes three potential PZD-binding surfaces, although only one of these is maximally used.  One of the C-terminal ends of the coiled-coil forms an extensive beta-sheet interaction with the Shank PDZ, while the other two ends are not involved in ligand binding and form random coils. Thus the coiled-coil domain allows multimerisation of betaPIX that is vital for its physiological functions. betaPIX and the Shank/ProSAP protein form a complex that acts as a protein scaffold for integrating signalling pathways and regulating postsynaptic structure.**   Forced reload
Pfam PF24107: Domain of unknown function (DUF7382) (domain)
This is a Ig-like domain found in a group of uncharacterised sequences, mainly from archaea.
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 PF19572: Type IX secretion system protein PorV (domain)
This entry represents the PorV protein.  The Bacteroidete T9SS contains at least 15 proteins. PorQ, PorU, PorV and PorZ form a cell surface-exposed attachment complex that proteolytically removes the substrate CTD following transport and covalently links some substrate proteins to a lipopolysaccharide anchor. A pool of PorV proteins in the outer membrane is thought to shuttle substrate proteins from the translocon to the attachment complex. The PorV protein has a membrane beta barrel topology.
Wikipedia: Bacterial secretion systems are protein complexes present on the cell membranes of bacteria for secretion of substances. Specifically, they are the cellular devices used by pathogenic bacteria to secrete their virulence factors to invade the host cells. They can be classified into different types based on their specific structure, composition and activity. Generally, proteins can be secreted through two different processes. One process is a one-step mechanism in which proteins from the cytoplasm of bacteria are transported and delivered directly through the cell membrane into the host cell. Another involves a two-step activity in which the proteins are first transported out of the inner cell membrane, then deposited in the periplasm, and finally through the outer cell membrane into the host cell.
Pfam PF22398: Family of unknown function (DUF6978) (family)
This is a family of uncharacterised proteins. They are predicted to adopt a globular alpha/beta structure consisting of a meander beta-sheet and two helices packed on one side on the sheet. These proteins contain three highly conserved histidines that in the predicted structure cluster close in space and could potentially form a metal binding site.
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 PF08671: Anti-repressor SinI (domain)
SinR is a pleiotropic regulator of several late growth processes. It is a tetrameric DNA binding protein whose activity is down-regulated thorough the formation of a SinI:SinR protein complex.  When complexed with SinI, the SinR tetramer is disrupted such that is no longer able to bind DNA.
Pfam PF23668: CDCP1 CUB domain (domain)
This domain is found in the human CUB domain-containing protein 1 (CDCP1) and related proteins. CDCP1 may be involved in cell adhesion and cell matrix association. It also may play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. CDCP1 contains a tandem of CUB domains. This entry represents the second of the tandem.
Pfam PF00379: Insect cuticle protein (domain)
Many insect cuticular proteins include a 35-36 amino acid motif known as the R&R consensus. The extensive conservation of this region led to the suggestion that it functions to bind chitin. Provocatively, it has no sequence similarity to the well-known cysteine-containing chitin-binding domain found in chitinases and some peritrophic membrane proteins. Chitin binding has been shown experimentally for this region. Thus arthropods have two distinct classes of chitin binding proteins, those with the chitin-binding domain found in lectins, chitinases and peritrophic membranes (cysCBD) and those with the cuticular protein chitin-binding domain (non-cysCBD).