SII-SWORD/CoKE huggingface dataset:
Pfam PF09190: DALR domain (domain)
This DALR domain is found in cysteinyl-tRNA-synthetases.
Wikipedia: An aminoacyl-tRNA synthetase, also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. It does so by catalyzing the transesterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
Pfam PF12459: D-Ala-teichoic acid biosynthesis protein (family)
This entry represents a family of DltX proteins of approximately 50 amino acids in length predominantly found in firmicutes. DltX are small, single-pass transmembrane proteins required for the D-alanylation of teichoic acids.
Pfam PF23230: C2H2-type zinc finger (domain)
This C2H2-type zinc finger is found in a group of eukaryotic E3 ubiquitin-protein ligases, including Hel2 from Schizosaccharomyces pombe and ZNF598 from humans, which play a key role in the ribosome quality control, a pathway that that takes place when a ribosome has stalled during translation, leading to degradation of nascent peptide chains.
Pfam PF04836: Interferon-related protein conserved region (family)
Family of proteins thought to be involved in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF.
Pfam PF21947: Snake toxin cobra-type (family)
This family represents snake toxins, including short and long neurotoxins, cytotoxins and short toxins mainly from Naja genus of snakes (cobras). Cytotoxins (CTs, also known as cardiotoxins) are small (~60 amino acids) proteins that mediate their toxic effect through interaction with the cell membrane. Neurotoxins interfere with cholinergic transmission at postsynaptic sites in the peripheral and central nervous systems. Cobrotoxin binds to muscle nicotinic acetylcholine receptor (nAChR) and inhibit acetylcholine from binding to the receptor, thereby impairing neuromuscular transmission. In vivo rat model of arthritis, it showed anti-inflammation and immunosuppression effects. These toxins have three beta-stranded loops resembling three fingers.
Pfam PF04511: Der1-like family (family)
The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilisation of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localised to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.).
Pfam PF22707: S1/CSD-like domain 2 of the TOTE conflict systems (domain)
This entry represents a presumed ribonucleoprotein complex-forming domain of the TOTE ((TPR, OB, TBP, Effector) conflict systems, potentially binding ssRNAs derived from hybrid duplexes bound by the systems. It is typically found in a two-domain tandem repeat arrangement, this is the second domain of the two.
Pfam PF12559: Serine endopeptidase inhibitors (family)
This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C-terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation.
Wikipedia: In biology and biochemistry, protease inhibitors, or antiproteases, are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins.
Pfam PF18799: Large polyvalent protein-associated domain 5 (domain)
This domain is predicted to be an enzymatic alpha beta domain. It often found N-terminal to a metallopeptidase domain in polyvalent proteins. The domain contains a conserved aspartate, lysine, and two arginine residues.
Pfam PF08616: Stabilization of polarity axis (family)
[swissprot:Q99222] has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilization of the polarity axes during septation. and in S. cerevisiae it functions as a polarisation-specific docking factor.
Pfam PF07448: Secreted phosphoprotein 24 (Spp-24) cystatin-like domain (domain)
This family represents a conserved region approximately 60 residues long within secreted phosphoprotein 24 (Spp-24), which seems to be restricted to vertebrates. This is a non-collagenous protein found in bone that is related in sequence to the cystatin family of thiol protease inhibitors. This suggests that Spp-24 could function to modulate the thiol protease activities known to be involved in bone turnover. It is also possible that the intact form of Spp-24 found in bone could be a precursor to a biologically active peptide that coordinates an aspect of bone turnover.
Pfam PF24430: Family of unknown function (DUF7553) (family)
This is a small family of uncharacterised archaeal proteins. They are predicted to fold into a helical hairpin.
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 PF08950: Protein of unknown function (DUF1861) (repeat)
This hypothetical protein, found in bacteria and in the eukaryote Leishmania, 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 PF21161: P2R3B, EF-hand (domain)
This is a EF-hand domain found in Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta (P2R3B). This protein may modulate substrate selectivity and catalytic activity.
Pfam PF18107: Fission yeast centromere protein N-terminal domain (domain)
This domain is found in the fission yeast centromere protein (Abp1) in species such as Shizosaccharomyces pombe. The domain, referred to as Domain 1, is DNA-binding and makes up half of the N-terminal region.
Pfam PF10896: Protein of unknown function (DUF2714) (family)
This family of proteins with unknown function appears to be restricted to Mycoplasmataceae.
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 PF14719: Phosphotyrosine interaction domain (PTB/PID) (domain)
Proteins encoding phosphotyrosine binding (PTB) domains function as adaptors or scaffolds to organise the signaling complexes involved in wide-ranging physiological processes including neural development, immunity, tissue homeostasis and cell growth. Due to structural differences, PTB domains are divided into three groups represented by phosphotyrosine-dependent IRS-like, phosphotyrosine-dependent Shc-like, and phosphotyrosine-independent Dab-like PTBs. The last two PTBs have been named as phosphotyrosine interaction domain (PID or PI domain). PID domain has an average length of about 160 amino acids .
The Shc-like PID specifically binds to the Asn-Pro-Xaa-Tyr(P) motif found in many tyrosine-phosphorylated proteins including growth factor receptors. On the other hand the Dab-like PID domain binds to non-phosphorylated tyrosine residue or even a phenylalanine at the same position . Most of the ligands for Shc-like PID domains are RTK or cytokine, whereas phosphotyrosine independent Dab-like PID domains seems to mediate other types of signaling pathways, like endocytosis/processing or exocytosis. This domain binds both peptides and headgroups of phosphatidylinositides, utilising two distinct binding motifs to mediate spatial organisation and localisation within cells .

The 3D structure of PID domain has been solved . It shares a folding pattern, commonly referred to as the PH-domain "superfold". The core "superfold" consists of seven antiparallel Î² strands forming two orthogonal Î² sheets. This Î² sandwich is capped at the C terminus by an Î± helix. It contains a peptide binding pocket (formed by the Î² strand 5 and C-terminal Î± helix) and a highly basic phospholipid binding "crown" (largely composed of residues from loop regions near the N terminus). Both Shc and Dab1 have two additional Î± helices, one of which is located at the N terminus and the other between Î²1 and Î²2 strands.
Pfam PF08590: Domain of unknown function (DUF1771) (domain)
This domain is highly charged and may represent a small helical extension of the Smr domain ([pfam:PF01713]), known as N-ext, whose function is not yet clear.
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 PF16631: Unstructured region 4 on terminal uridylyltransferase 7 (disordered)
TUTF7_u4 is the fourth natively unstructured region found on a set of higher eukaryote Terminal uridylyltransferase 7 proteins. The function is not known. The region is rich in arginine and lysine.
Pfam PF04179: Rit1 DUSP-like domain (domain)
This enzyme ([ec:2.4.2.-]) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the  initiation and elongation of translation, the 2'-O-ribosyl phosphate  modification discriminates the initiator tRNAs from the elongator  tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases.
Pfam PF18524: High potential iron-sulfur protein like (domain)
This is a C-terminal domain found in 4-hydroxyphenylacetate decarboxylase small subunit ([ec:4.1.1.83]), which catalyzes the last reaction in the fermentative production of p-cresol from tyrosine. The C-terminal domain [4F-4S] cluster bears structural similarity to high-potential iron-sulfur proteins (HiPIPs). HiPIPs have an N-terminal extension of 20-40 residues, so the structural similarity is limited to their Fe/S cluster-binding scaffold. Furthermore, despite of the weak amino acid sequence identity, the cluster binding motifs are remarkably similar to H/CX2CX12-13CX16-17C for the gamma-subunit and CX2CX13-19CX14-19C for HiPIPs.
Pfam PF19249: Family of unknown function (DUF5897) (family)
This is a family of uncharacterised proteins of unknown function found in viruses.
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 PF00300: Histidine phosphatase superfamily (branch 1) (domain)
The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle.  Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue.  The superfamily may be divided into two main branches.  The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase.  The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases.  The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members.
Pfam PF11959: Domain of unknown function (DUF3473) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is about 130 amino acids in length. This domain is found associated with [pfam:PF01522]. This domain has two completely conserved residues (P and H) that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF10564: Sialic-acid binding micronemal adhesive repeat (repeat)
This domain is a novel carbohydrate-binding domain found on micronemal proteins. Micronemal proteins (MICs) are released onto the parasite surface just before invasion of host cells and play important roles in host cell recognition, attachment and penetration. Toxoplasma gondii can infect and replicate within all nucleated cells. This domain interacts with sialylated oligosaccharides; the protein in Toxoplasma gondii is a monomer but several MAR domains are carried on the protein. Each MAR domain contains one central sialic acid-binding pocket.
Pfam PF09330: D-lactate dehydrogenase, membrane binding (domain)
Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association.
Wikipedia: Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the conversion of pyruvate to lactate and back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.
Pfam PF06711: Protein of unknown function (DUF1198) (family)
This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
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 PF19119: Family of unknown function (DUF5803) (family)
Family of unknown function predominantly found in Halobacteria.
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 PF23550: DNA repair protein rhp7 treble clef domain (domain)
This domain is found in the DNA repair protein rhp7 and related proteins. Rhp7 is involved in nucleotide excision repair. It is forming a complex with Rhp16 which was shown to be essential for global genome repair in S.pombe. The domain represented by this entry is predicted to adopt a treble clef fold. It contains a pair of two highly conserved CxxC sequence motifs.
Pfam PF04362: Bacterial Fe(2+) trafficking (family)
This is a family of bacterial Fe(2+) trafficking proteins.
Pfam PF24493: INTS4 8 helical bundle domain (domain)
This domain is found in the homologs of Integrator complex subunit 4 (INTS4).  INTS4 along with INTS9 and INTS11 constitute the Integrator cleavage module, which contains endonuclease activity and resembles the cleavage module of the cleavage and polyadenylation specific factor required for 3' processing of mRNA transcripts. The domain represented by this entry makes extensive contacts with INTS7 and stabilize the beta-CASP domain of INTS9 in the cleavage module. It folds into an eight alpha-helical bundle.
Pfam PF07468: Agglutinin domain (domain)
Agglutinins are sugar-specific lectins that can agglutinate erythrocytes and other cell types. Lectins occur widely in plants, as well as some microorganisms and animal . Agglutinin from Amaranthus caudatus (amaranthin) is a lectin from the ancient South American crop, amaranth grain. Although its biological function is unknown, it can agglutinate A, B and O red blood cells, and has a carbohydrate-binding site that is specific for the methyl-glycoside of the T-antigen found linked to serine or threonine residues of cell surface glycoproteins . The protein is comprised of a homodimer, with each homodimer consisting of two Î²-trefoil domains . Lectin B chains from ricin and related toxins also contain Î²-trefoil domain, however they are not related to agglutinin, showing little sequence similarity .
Pfam PF15795: Ectodermal ciliogenesis protein (family)
Spec3 is a family of eukaryotic membrane proteins. In the sea urchin, Spec3 is expressed predominantly during ectodermal ciliogenesis.
Pfam PF10826: Protein of unknown function (DUF2551) (family)
This Archaeal 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 PF15073: Spermatogenesis-associated protein 48 (family)
Spermatogenesis-associated protein 48 is also known as post-meiotic spermatogenesis protein 1. Proteins in this family are typically between 109 and 302 amino acids in length. In humans, it is found in the chromosomal position, C7orf72.
Pfam PF04207: Tetrahydromethanopterin S-methyltransferase, subunit D (family)
The N5-methyltetrahydromethanopterin: coenzyme M ([ec:2.1.1.86]) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump.
Pfam PF22493: NOP9-like PUF repeat domain (repeat)
This entry represents the PUF repeat domain found in the NOP9 protein.ED   L9JDG0.1/603-752; L9JDG0.1/603-716;
Pfam PF05384: Sensor protein DegS (coiled_coil)
This is small family of Bacillus DegS proteins.  The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterise the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon. The family also contains one sequence [swissprot:Q8R9D3] from Thermoanaerobacter tengcongensis which are described as sensory transduction histidine kinases.
Pfam PF17829: Glycosyl hydrolase family 115 C-terminal domain (domain)
This domain is found at the C-terminus of glycosyl hydrolase family 115 proteins. This domain has a beta-sandwich fold.
Pfam PF09604: F subunit of K+-transporting ATPase (Potass_KdpF) (family)
This entry describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (IPR004623). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.
Pfam PF00153: Mitochondrial carrier protein (repeat)
A variety of substrate carrier proteins that are involved in energy transfer are found in the inner mitochondrial membrane or integral to the membrane of other eukaryotic organelles such as the peroxisome . Such proteins include: ADP, ATP carrier protein (ADP/ATP translocase); 2-oxoglutarate/malate carrier protein; phosphate carrier protein; tricarboxylate transport protein (or citrate transport protein); Graves disease carrier protein; yeast mitochondrial proteins MRS3 and MRS4; yeast mitochondrial FAD carrier protein; and many others. Structurally, these proteins can consist of up to three tandem repeats of a domain of approximately 100 residues, each domain containing two transmembrane regions.
Wikipedia: Adenine nucleotide translocator (ANT), also known as the ADP/ATP translocase (ANT), ADP/ATP carrier protein (AAC) or mitochondrial ADP/ATP carrier, exchanges free ATP with free ADP across the inner mitochondrial membrane. ANT is the most abundant protein in the inner mitochondrial membrane and belongs to the mitochondrial carrier family.
Pfam PF11083: C-terminal helical hairpin domain from relaxase (domain)
This entry represents a C-terminal helical domain hairpin found in some relaxase enzymes. Proteins found related to this domain have been previously misannotated as a lantibiotic immunity protein SrtI.
Pfam PF01521: Iron-sulphur cluster biosynthesis (domain)
This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins.
Wikipedia: In biochemistry, the iron–sulfur cluster biosynthesis describes the components and processes involved in the biosynthesis of iron–sulfur proteins. The topic is of interest because these proteins are pervasive. The iron sulfur proteins contain iron–sulfur clusters, some with elaborate structures, that feature iron and sulfide centers. One broad biosynthetic task is producing sulfide (S2-), which requires various families of enzymes. Another broad task is affixing the sulfide to iron, which is achieved on scaffolds, which are nonfunctional. Finally these Fe-S cluster is transferred to a target protein, which then become functional.