SII-SWORD/CoKE huggingface dataset:
Pfam PF15891: Nucleoside 2-deoxyribosyltransferase like (family)
This entry includes a group of nucleoside 2-deoxyribosyltransferase like proteins, including (A6L9R1) (PDBe:4mcj).
Wikipedia: In enzymology, a nucleoside deoxyribosyltransferase is an enzyme that catalyzes the chemical reaction2-deoxy-D-ribosyl-base1 + base2  2-deoxy-D-ribosyl-base2 + base1
Pfam PF14696: Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal (domain)
This domain is one of two barrel-shaped regions that together form the active enzyme, 4-hydroxyphenylpyruvic acid dioxygenase, [ec:1.13.11.27]. As can be deduced from the disposition of the various Glyoxalase families, _2, _3 and _4 in Pfam, [pfam:PF00903], [pfam:PF12681], [pfam:PF13468], [pfam:PF13669], these two regions are similar to be indicative of a gene-duplication event. At the individual sequence level slight differences in conformation have given rise to slightly different functions. In the case of UniProt:P80064, 4-hydroxyphenylpyruvic acid dioxygenase catalyses the formation of homogentisate from 4-hydroxyphenylpyruvate, and the pyruvate part of the HPPD substrate (4-hydroxyphenylpyruvate), derived from L-tyrosine, and the O2 molecule occupy the three free coordination sites of the catalytic iron atom in the C-terminal domain. In plants and photosynthetic bacteria, the tyrosine degradation pathway is crucial because homogentisate, a tyrosine degradation product, is a precursor for the biosynthesis of photosynthetic pigments, such as quinones or tocopherols.
Pfam PF17198: Spirocyclase AveC-like (family)
AveC catalyzes the stereospecific spiroketalization of a dihydroxy-ketone polyketide intermediate in the biosynthetic pathway of Avermectin, a potent antiparasitic agent. Additionally, it has a unique dehydration activity that serves to determine the regiospecific saturation pattern for spiroketal diversity. MeiC, the counterpart in the biosynthesis of AVE-like meilingmycin, also has spirocyclase activity, but lacks the dehydratase activity.
Pfam PF08757: CotH kinase protein (family)
Members of this family include the spore coat protein H (cotH). This protein is an atypical protein kinase that phosphorylates CotB and CotG.
Pfam PF20515: Tet-like 2OG-Fe(II) oxygenase superfamily (domain)
This entry represents an uncharacterised family of fungal proteins. The AlphaFold prediction for an example protein shows that it is most closely related to Tet-like dioxygenases. This strongly suggests that this family of proteins are DNA modification enzymes.
Pfam PF16697: Inner membrane component of T3SS, cytoplasmic domain (domain)
Yop-YscD-cpl is the cytoplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus.
Wikipedia: In molecular biology, the forkhead-associated domain is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contains small helical insertions between the loops connecting the strands.
Pfam PF21270: Glycoside phosphorylase C-terminal domain (domain)
Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. This domain is the C-terminal domain found in the L. phytofermentans SOGP (sophoro-oligosaccharide beta-1,2-gluco-phosphorylase).
Pfam PF01582: TIR domain (family)
The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 ([swissprot:Q99836]) and TOLLIP (Toll interacting protein, [swissprot:Q9H0E2]). In turn, these associate with various kinases to set off signalling cascades.
Wikipedia: The toll-interleukin-1 receptor (TIR) homology domain is an intracellular signaling domain found in MyD88, SARM1, interleukin-1 receptors, toll receptors and many plant R proteins. It contains three highly conserved regions, and mediates protein-protein interactions between the toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins where they are involved in resistance to disease and in bacteria where they are associated with virulence. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 (UniProt Q99836) and TOLLIP (toll-interacting protein, UniProt Q9H0E2). In turn, these associate with various kinases to set off signaling cascades. Some TIR domains have also been found to have intrinsic NAD+ cleavage activity, such as in SARM1. In the case of SARM1, the TIR NADase activity leads to the production of Nam, ADPR and cADPR and the activation of downstream pathways involved in Wallerian degeneration and neuron death.
Pfam PF22688: Hda, lid domain (domain)
This entry represents the C-terminal lid domain of the Regulatory inactivation of DnaA Hda protein from Shewanella amazonensis, the essential component of RIDA (regulatory inactivation of DnaA). This domain is a short four-helix bundle that contains the sensor II motif.
Pfam PF22123: Exuperantia RNAse H-like domain (domain)
This entry represents the RNAse H-like domain found at the N-terminal of exuperantia (Exu) from Drosophila and similar sequences from insects. Exu is a RNA-binding pseudonuclease associated with bicoid mRNA and required for its localization. The catalytic site is degenerate and inactive, then, this domain mediates dimerization and RNA binding.
Pfam PF00607: gag protein p24 N-terminal domain (domain)
p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.
Pfam PF04474: Protein of unknown function (DUF554) (family)
Family of uncharacterised prokaryotic proteins.  Multiple predicted transmembrane regions suggest that the region is membrane associated.
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 PF10255: RNA polymerase I-associated factor PAF67 (repeat)
RNA polymerase I is a multisubunit enzyme and its transcription competence is dependent on the presence of PAF67. This family of proteins is conserved from worms to humans.
Pfam PF19965: vWA-MoxR associated protein middle region (VMAP-M) 2 (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 PF11132: Transcriptional regulator protein (SplA) (family)
The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore.
Pfam PF15620: Centromere assembly component CENP-C middle DNMT3B-binding region (family)
CENP-C is a component of the centromere assembly complex in eukaryotes. CENP-C recruits the DNA methyltransferases DNMT3B, in order to establish the necessary epigenetic DNA-methylation essential for maintenance of chromatin structure and genomic stability.  This middle region of CENP-C is the binding-domain for DNMT3B. Binding of CENP-C and DNMT3B to DNA occurs at both centromeric and peri-centromeric satellite repeats.  CENP-C and DNMT3B regulate the histone code in these regions.
Pfam PF21148: NOL1/NOP2/Sun domain family member 5, ferredoxin-like domain (domain)
This is a ferredoxin-like domain of NOL1/NOP2/Sun domain family member 5, found at the N-terminal of the methyltransferase domain. NSUN5 is a SAM-dependent methyltransferase that specifically methylates the C(5) position of cytosine 3782 in 28S rRNA.
Pfam PF24079: E3 ubiquitin-protein ligase UBR4-like domain (domain)
This domain is found in human E3 ubiquitin-protein ligase UBR4 and similar proteins mainly found in eukaryotes. UBR4 is a component of the N-end rule pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilising
Pfam PF19056: WD40 repeated domain (repeat)
This entry contains an array of WD40 repeats found in RhoGEF proteins such as [swissprot:O15013].
Wikipedia: The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Pfam PF13783: Domain of unknown function (DUF4177) (family)
This entry represents a group of prokaryotic proteins, including the uncharacterised protein YjzH from Bacillus subtilis. YjzH is a member of the sigma W regulon, which is induced in response to cell envelope stress caused by antibiotics, alkaline shock and salt shock . This family was previously known as DUF4177.
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 PF19127: Choline-binding repeat (repeat)
Pair of presumed choline-binding repeats often found adjacent to [pfam:PF01473].
Pfam PF09173: Initiation factor eIF2 gamma, C terminal (domain)
Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA.
Pfam PF11021: Protein of unknown function (DUF2613) (family)
This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known.
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 PF09799: Predicted membrane protein (family)
This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known.
Pfam PF07271: Cytadhesin P30/P32 (family)
This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localised on the tip organelle. It is thought that it is important in cytadherence and virulence. The N-terminus contains two predicted transmembrane helices followed by a long region of a short 6 residue proline rich repeat.
Pfam PF10004: Uncharacterized protein conserved in bacteria (DUF2247) (family)
This domain, found in various hypothetical bacterial 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 PF16334: Domain of unknown function (DUF4964) (family)
This family consists of uncharacterized proteins around 840 residues in length and is mainly found in various Bacteroides species.  Several proteins in this family are annotated as Glutaminases, but the function of this protein is unknown.
Pfam PF05221: S-adenosyl-L-homocysteine hydrolase (domain)
Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase, 3.3.1.1) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. This enzyme is ubiquitous, highly conserved, and may play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. AdoHcyase requires NAD+ as a cofactor and contains a central glycine-rich region which is thought to be involved in NAD-binding. Since AdoHyc is a potent inhibitor of S-adenosyl-L-methionine dependent methyltransferases, AdoHycase plays a critical role in the modulation of the activity of various methyltransferases. The enzyme forms homotetramers, with each monomer binding one molecule of NAD+ .
This family also includes S-adenosylhomocysteine hydrolase-like 1 (Ahcyl1), also known as IRBIT, and S-adenosylhomocysteine hydrolase-like protein 2 (Ahcyl2). Ahcyl1/IRBIT was shown to interact with inositol 1,4,5-trisphosphate receptors (IP3Rs), which function as intracellular Ca(2+) channels, and suppresses IP3 binding of IP3R . By competing with IP3, it modulates the threshold IP3 concentration required for the activation of the receptor . Further studies indicate that Ahcyl1/IRBIT is in fact a multifunctional protein that regulates several ion channels and ion transporters . Despite its homology to S-adenosylhomocysteine hydrolases, Ahcyl1 has neither enzyme activity nor any effects on the enzyme activity of S-adenosylhomocysteine hydrolase . Ahcyl2 lacks binding activity to IP3R . Ahcyl2 upregulates NBCe1-B, which plays an important role in intracellular pH regulation .
Wikipedia: Adenosylhomocysteinase (EC 3.13.2.1, S-adenosylhomocysteine synthase, S-adenosylhomocysteine hydrolase, adenosylhomocysteine hydrolase, S-adenosylhomocysteinase, SAHase, AdoHcyase) is an enzyme that catalyzes the nicotinamide adenine dinucleotide (NAD+) dependent, reversible hydrolysis of S-adenosylhomocysteine to homocysteine and adenosine.S-adenosyl-L-homocysteine + H2O ⇌ L-homocysteine + adenosine
Pfam PF15579: Immunity protein 52 (family)
This family of proteins includes the type VI secretion system (T6SS) immunity protein TsiT from Pseudomonas aeruginosa ([swissprot:Q9HXA5]) and similar proteins mainly found in proteobacteria. TsiT, which belongs to the Imm52 family, can suppress the virulence of TseT. This protein adopts a beta-sandwich fold with nine alpha-helices and an eight-stranded antiparallel central beta-sheet. It has a large electro-negative pocket with hydrophobic surroundings that play a role in the interaction with TseT. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-REase-5 family.
Pfam PF22790: YkoP domain (domain)
This entry represents proteins that are related to the YkoP protein from B. subtilis [swissprot:O34495]. This protein is as yet uncharacterised. AlphaFold prediction shows that is is composed of a single domain. The structure shows similarity to GNAT family acetyltransferases. This domain is sometimes associated with [pfam:PF01522], which is a polysaccharide deacetylase enzyme.
Pfam PF23033: Domain of unknown function (DUF7034) (domain)
This domain is found in a group of uncharacterised proteins from Dictyostelia. It is predicted to adopt Ig-like fold with the fibronectin type III-like topology.
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 PF21378: YceM-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Putative oxidoreductase YceM from Escherichia coli and similar bacterial sequences. It adopts an alpha-beta configuration. It is often associated with [pfam:PF01408].
Pfam PF07382: Histone H1-like nucleoprotein HC2 (disordered)
This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles.
Pfam PF14264: Glucosyl transferase GtrII (family)
This family includes glucosyl transferase II from the Shigella phage SfII, [swissprot:O21944], which mediates seroconversion of S. flexneri when the phage is integrated into the host chromosome.
Pfam PF04300: F-box associated region (family)
Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. [swissprot:Q9UK22] is involved in binding to N-glycosylated proteins.
Pfam PF15155: MORF4 family-associated protein1 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between and 127 amino acids in length.
Wikipedia: MORF4 family-associated protein 1 is a protein that in humans is encoded by the MRFAP1 gene.
Pfam PF06385: Baculovirus LEF-11 protein (family)
This family consists of several Baculovirus LEF-11 proteins. The exact function of this family is unknown although it has been shown that LEF-11 is required for viral DNA replication during the infection cycle.
Pfam PF21164: Dumpy, DPY module (repeat)
This entry represents the DPY repeat module described in dumpy from Drosophila melanogaster, a gigantic extracellular matrix protein that contains epidermal growth factor (EGF) modules interspersed with DPY modules. The DPY module forms a compact fold consisting of a small N-terminal 3-10 helix packed against a double-stranded anti-parallel disulphide-stabilised beta-sheet motif capable of linking end-to-end with EGF modules to form a fibre.
Pfam PF07526: Associated with HOX (domain)
The function of this domain is unknown. It is often found in plant proteins associated with [pfam:PF00046].
Pfam PF00919: Uncharacterized protein family UPF0004 (family)
This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with [pfam:PF04055] and [pfam:PF01938] although its function is uncertain.
Pfam PF03171: 2OG-Fe(II) oxygenase superfamily (domain)
This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.  This family includes the C-terminal of prolyl 4-hydroxylase  alpha subunit. The holoenzyme has the activity [ec:1.14.11.2]  catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2  procollagen trans- 4-hydroxy-L-proline + succinate + CO2.  The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.
Pfam PF21563: Methyl-accepting chemotaxis sensory transducer, class 40H, sensor (domain)
This domain is found in Methyl-accepting chemotaxis sensory transducer, class 40H from Geobacter sulfurreducens (Mcp40H-20, [swissprot:Q74EM7]) and similar proteins predominantly from proteobacteria. This entry represents the periplasmic c-type heme-containing sensor domain, which is located between two transmembrane helices near the N terminus of the protein. This domain adopts a PAS-type domain fold with two helical segments followed by a four-stranded beta-sheet.
Pfam PF20084: Conjugative transfer region protein TrbK (family)
Members of this family regularly are encoded between the TrbJ and TrbL proteins essential for P-type conjugal transfer, and therefore are designated TrbK. Positional analogy to family IPR027584 (the entry exclusion lipoprotein TrbK of IncP plasmid RP4), which is a lipoprotein and not homologous, suggests this protein may also be involved in entry exclusion. Members of this family are small, with a non-lipoprotein signal peptide and a conserved disulfide bond.
Pfam PF14644: Domain of unknown function (DUF4456) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. There is a single completely conserved residue E 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 PF18667: Baseplate upper protein immunoglobulin like domain (domain)
This is a beta-sandwich immunoglobulin fold domain, which resembles the plexin-A2 C-terminal domain in structure. In baseplate upper protein (BppU, also known as ORF48) trimer, this domain plays part in surrounding the Dit hexameric core.
Pfam PF20049: Domain of unknown function (DUF6451) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, predominantly in Platyhelminthes, and is approximately 40 amino acids in length. It contains the conserved sequences QLxNIWNSK and KxRIFN. Many sequences containing this domain also contain a reverse transcriptase domain ([pfam:PF00078]).
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 PF08588: Domain of unknown function at the cortex 1 (Duc1) (domain)
This entry represents the Duc1 (Domain of Unknown Function at the Cortex 1) protein, which is involved in maintaining proper plasma membrane lipid composition and cytokinetic ring anchoring in Schizosaccharomyces pombe.  Duc1 localizes to the plasma membrane, except at the cell division site, and its localization is controlled by interactions with the ER-PM contact site proteins Scs2 and Scs22 through a FFAT-like motif. Duc1 promotes proper localization of the PI-5 kinase Its3, thereby maintaining appropriate levels of PI(4,5)P2 at the plasma membrane. This function is important for proper anchoring of the cytokinetic ring during cell division. Duc1 contains a conserved domain previously known as the DUF1769 domain of unknown function.
Pfam PF16235: Domain of unknown function (DUF4894) (family)
A small family of uncharacterized proteins around 180 residues in length and found in various Thermotoga species. The function of this family is unknown.
Pfam PF13714: Phosphoenolpyruvate phosphomutase (domain)
This domain includes the enzyme Phosphoenolpyruvate phosphomutase ([ec:5.4.2.9]). This protein [swissprot:O86937] has been characterised as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr). This enzyme has a TIM barrel fold.
Wikipedia: In enzymology, a phosphoenolpyruvate mutase is an enzyme that catalyzes the chemical reactionphosphoenolpyruvate  3-phosphonopyruvate