SII-SWORD/CoKE huggingface dataset:
Pfam PF20033: Domain of unknown function (DUF6438) (domain)
This domain of unknown function is found in uncharacterised proteins from bacteria and archaea. This domain is about 75 amino acids in length and it contains the conserved motif CxxxGxCP. Towards the C-terminal there are two conserved residues, a Glycine and an Aspartate. Some of the proteins containing this domain also have an ankyrin repeat-containing region.
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 PF02038: ATP1G1/PLM/MAT8 family (family)
The FXYD protein family contains at least seven members in mammals . Two other family members that are not obvious orthologs of any identified mammalian FXYD protein exist in zebrafish. All these proteins share a signature sequence of six conserved amino acids comprising the FXYD motif in the NH2-terminus, and two glycines and one serine residue in the transmembrane domain. FXYD proteins are widely distributed in mammalian tissues with prominent expression in tissues that perform fluid and solute transport or that are electrically excitable.

Initial functional characterisation suggested that FXYD proteins act as channels or as modulators of ion channels however studies have revealed that most FXYD proteins have another specific function and act as tissue-specific regulatory subunits of the Na,K-ATPase . Each of these auxiliary subunits produces a distinct functional effect on the transport characteristics of the Na,K-ATPase that is adjusted to the specific functional demands of the tissue in which the FXYD protein is expressed. FXYD proteins appear to preferentially associate with Na,K-ATPase alpha1-beta isozymes, and affect their function in a way that render them operationally complementary or supplementary to coexisting isozymes.
Wikipedia: The FXYD protein family is a family of small membrane proteins that share a 35-amino acid signature sequence domain, beginning with the amino acid sequence PFXYD and containing 7 invariant and 6 highly conserved amino acids. The approved human gene nomenclature for the family is FXYD-domain containing ion transport regulator.
Pfam PF09996: Uncharacterized protein conserved in bacteria (DUF2237) (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 PF02146: Sir2 family (family)
This region is characteristic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organisation and DNA damage repair processes.i
Wikipedia: Sirtuins are a family of signaling proteins involved in metabolic regulation. They are ancient in animal evolution and appear to possess a highly conserved structure throughout all kingdoms of life. Chemically, sirtuins are a class of proteins that possess either mono-ADP-ribosyltransferase or deacylase activity, including deacetylase, desuccinylase, demalonylase, demyristoylase and depalmitoylase activity. The name Sir2 comes from the yeast gene 'silent mating-type information regulation 2', the gene responsible for cellular regulation in yeast.
Pfam PF16104: Formyl peptide receptor-like 1 inhibitory protein (family)
This family consists of several formyl peptide receptor-like 1 inhibitory proteins from Staphylococcus aureus. These are secreted proteins that block the formyl peptide receptor-like 1 found in neutrophils, monocytes, B cells, and NK cells; and inhibit the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiate phagocyte mobilization towards the infection site.
Pfam PF23758: HPS5 TPR domain (repeat)
This entry represents the TPR domain found at the C-terminal of HPS5 protein from vertebrates, a component of the biogenesis of lysosome-related organelles complex-2 (BLOC-2) and which has a role in the endo-lysosomal dynamics of skin fibroblasts. Its mutation or absence has been linked to Hermansky-Pudlak type 5 syndrome (HPS-5) in mammals, a disease characterized by defects in lysosome-related organelles such as melanosomes and platelet dense granules. The function of this domain is unknown.
Pfam PF00425: chorismate binding enzyme (domain)
This family includes the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase.
Pfam PF10458: Valyl tRNA synthetase tRNA binding arm (domain)
This domain is found at the C-terminus of Valyl tRNA synthetases.
Pfam PF16917: Biotin/lipoate A/B protein ligase family (domain)
This entry represents the catalytic domain of a group of lipoyl ligases/lipoyltransferases, such as Lipoate-protein ligase A/B (LipA/B) from E.coli and mammalian lipoyltransferases . These proteins catalyse the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes. Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system.
Biotin and lipoic acid are the covalently bound cofactors of various multicomponent enzyme complexes that catalyse key metabolic reactions. In these enzymes complexes, biotin and lipoic acid are attached via amide linkage through their carboxyl group and the Îµ-amino group of a specific lysine residue of a protein module known respectively as the biotinyl and the lipoyl domain. Covalent attachment of biotin and lipoic acid to these enzyme complexes occurs post-translationally, and it is mediated by biotinylating and lipoylating protein enzymes, which specifically recognise the biotinyl and lipoyl domains, ensuring their correct post-translational modification. Lipoylating and biotinylating enzymes are evolutionarily related protein families containing a homologous catalytic module .

Amino acid sequence conservation between the catalytic modules of biotinyl protein ligases (BPLs) and lipoyl protein ligases (LPLs) is very low, and mainly affects residues that are important for the scaffold of the structure, such as those contributing to the hydrophobic core. Despite the poor overall sequence similarity, a single lysine residue is strictly conserved in all LPL and BPL sequences. This lysine residue is likely to bind specifically to the carbonyl oxygen of the carboxyl group of biotin or at the end of the hydrogen- carbon tail of the lipoyl moiety . The BPL/LPL catalytic domain contains a seven-stranded mixed Î²-sheet on one side and four Î±-helices on the other side .
Pfam PF23907: Family of unknown function (DUF7249) (family)
This family represents an uncharacterized protein domain found in phage proteins, mostly from Caudovirales. The domain is around 70-120 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 PF11100: Conjugal transfer protein TrbE (family)
TrbE is essential for conjugation and phage adsorption. It contains four common motifs and one conserved domain.
Pfam PF14757: Immunogenic region of nsp2 protein of arterivirus polyprotein (domain)
This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes.
Pfam PF18138: Bacterial HORMA domain family 1 (domain)
Family of bacterial HORMA domains found in conserved genome contexts with Pch2/TRIP13 P-loop NTPases. Acts as a 'third component' in broad class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Together with Pch2/TRIP13, could act as co-effectors or in regulation of other effectors of the systems. It is found in proteins from the CBASS (cyclic oligonucleotide-based antiphage signaling system), a system that provides immunity against bacteriophage. This domain is found in CD-NTase-associated protein 7 (Cap7) from E.coli, that acts as a sensor protein of CBSS and binds to a closure peptide allowing it to activate the CD-NTase CdnC for second messenger synthesis and, therefore, it activates a diverse range of effectors.
Pfam PF15674: Coiled-coil domain-containing protein 23 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 66 and 78 amino acids in length. There are two completely conserved residues (K and E) that may be functionally important.
Pfam PF01314: Aldehyde ferredoxin oxidoreductase, domains 2 & 3 (domain)
Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible  oxidation of aldehydes to their corresponding carboxylic acids  with their accompanying reduction of the redox protein ferredoxin.  This family is composed of two structural domains that bind the  tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR.
Wikipedia: In enzymology, an aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) is an enzyme that catalyzes the chemical reactionan aldehyde + H2O + 2 oxidized ferredoxin ⇌ an acid + 3 H+ + 2 reduced ferredoxin
Pfam PF19326: AMP deaminase (domain)
AMP-deaminase (AMPD) (3.5.4.6) is a large, well-conserved eukaryotic protein that catalyses the hydrolytic deamination of adenosine monophosphate (AMP) to inosine monophosphate (IMP), and so plays an important role in purine and energy metabolism . This entry also includes inactive deaminases from yeast, which lack the conserved His residues essential for binding the catalytic zinc ion and the conserved residues important for substrate binding and catalysis.
Wikipedia: AMP deaminase 1 is an enzyme that in humans is encoded by the AMPD1 gene.
Pfam PF24145: K1 capsule-specific polysaccharide lyase, N-terminal domain (domain)
This entry represents the N-terminal domain of K1 capsule-specific polysaccharide lyase and related proteins. K1-lyase functions as a receptor binding protein (RBP) and mediates the attachment to the host capsular exopolysaccharides. This enzyme possesses a lyase activity that specifically degrades the K1-type polysaccharides of Klebsiella pneumoniae capsule. The N-terminal domain is known as a particle-binding domain. It folds into an open beta-barrel structure the curvature of which is completed by by an alpha-helix. Structurally, this domain is very similar to collagen XVIII trimerization domain [pfam:PF20010].
Pfam PF09453: HIRA B motif (conserved_site)
The HirA B (Histone regulatory homologue A binding) motif is the essential binding interface between HIRA [pfam:PF07569] and ASF1a, of approx. 40 residues. It forms an antiparallel beta-hairpin that binds perpendicular to the strands of the beta-sandwich of ASF1a N-terminal core domain, via beta-sheet, salt bridge and van der Waals interactions. The two histone chaperone proteins, HIRA and ASF1a, form a heterodimer with histones H3 and H4. HIRA is the human orthologue of Hir proteins known to silence histone gene expression and create transcriptionally silent heterochromatin in yeast, flies, plants and humans. The yeast CAF1B proteins which bind H3 also carry this motif at their very C-terminus.
Pfam PF13482: RNase_H superfamily (domain)
This entry represents the ribonuclease H-like domain found in a group of uncharacterised proteins, including YprB from Bacillus subtilis.
Pfam PF05089: Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain (domain)
Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains.  This central domain has a tim barrel fold.
Wikipedia: In molecular biology, glycoside hydrolase family 89 is a family of glycoside hydrolases.
Pfam PF02304: Scaffold protein B (family)
This is a family of proteins from single-stranded DNA bacteriophages.  Scaffold proteins B and D are required for procapsid formation.  Sixty copies of the internal scaffold protein B are found in the procapsid.
Wikipedia: In molecular biology, bacteriophage scaffolding proteins are proteins involved in bacteriophage assembly.
Pfam PF06536: Avian adenovirus fibre, N-terminal (repeat)
This family is the N-terminal region of avian adenovirus fibre proteins; the domain is frequently found repeated several times along the fibre. These fibres have been linked to variations in virulence. Avian adenoviruses possess penton capsomers that consist of a pentameric base associated with two fibres.
Pfam PF13026: Protein of unknown function (DUF3887) (domain)
This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length.
Pfam PF19359: Family of unknown function (DUF5936) (family)
This presumed domain is functionally uncharacterised although it is found in the Type 2 secretion protein F. This domain family is found in Actinobacteria, and is approximately 140 amino acids in length. The family is found in association with [pfam:PF00482].
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 PF03383: Caenorhabditis serpentine receptor-like protein, class xa (family)
This family contains various Caenorhabditis proteins, some of which are annotated as being serpentine receptors, mainly of the xa class.
Pfam PF11440: DNA alpha-glucosyltransferase (family)
The T4 bacteriophage of E.coli protects its DNA via two glycosyltransferases which glucosylate 5-hydroxymethyl cytosines (5-HMC) using UDP-glucose. These two proteins are the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). The proteins in this family are AGT. AGT adopts the GT-B fold and binds both the sugar donor and acceptor to the C-terminal domain. There is evidence for a role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base.
Pfam PF06567: Neural chondroitin sulphate proteoglycan cytoplasmic domain (family)
This family represents the C-terminal cytoplasmic domain of vertebrate neural chondroitin sulphate proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis. This domain contains a number of potential sites of phosphorylation by protein kinase C.
Pfam PF24067: BT_1020-like, N-terminal beta propeller (repeat)
This entry represents the N-terminal region of BT_1020 from Bacteroides thetaiotaomicron, which covers part of its 5-bladed beta propeller domain. It is usually found associated with [pfam:PF22585].
Pfam PF09044: Kp4 (domain)
Members of this fungal family of toxins specifically inhibit voltage-gated calcium channels in mammalian cells. They adopt an alpha/beta-sandwich structure, comprising a five-stranded antiparallel beta-sheet with two antiparallel alpha-helices lying at approximately 45 degrees to these strands.
Wikipedia: In molecular biology, the killer toxin Kp4 family is a family of killer toxins, which includes the Kp4 killer toxin from the smut fungus Ustilago maydis.
Pfam PF04151: Bacterial pre-peptidase C-terminal domain (domain)
This domain is normally found at the C-terminus of secreted bacterial peptidases. They are  not present in the active peptidase. It is  possible that they fulfill a similar role to the PKD ([pfam:PF00801]) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C).
Pfam PF14897: EpsG family (family)
This family of proteins are related to the EpsG protein from B. subtilis [swissprot:P71056]. These proteins are likely glycosyl transferases belonging to the membrane protein GT-C clan.
Pfam PF22095: BT_3535-like (family)
This family represents the functionally uncharacterised protein BT_3535 from Bacteroides thetaiotaomicron ([swissprot:Q8A1X3]) and similar sequences found in bacteroidetes. This protein is organised into two domains.
Pfam PF02832: Flavivirus glycoprotein, immunoglobulin-like domain (domain)
Flaviruses are small, enveloped RNA viruses that use arthropods such as mosquitoes for transmission to their vertebrate hosts, and include Yellow fever virus, West Nile virus, Tick-borne encephalitis virus, Japanese encephalitis virus, and Dengue virus 2 . Flaviviruses consist of three structural proteins: the core nucleocapsid protein C (IPR001122), and the envelope glycoproteins M (IPR000069) and E. Glycoprotein E is a class II viral fusion protein that mediates both receptor binding and fusion. Class II viral fusion proteins are found in flaviviruses and alphaviruses, and are structurally distinct from class I fusion proteins from influenza-type viruses and retroviruses. Glycoprotein E is comprised of three domains: domain I (dimerisation domain) is an 8-stranded Î² barrel, domain II (central domain) is an elongated domain composed of twelve Î² strands and two Î± helices, and domain III (immunoglobulin-like domain) is an IgC-like module with ten Î² strands. This entry represents the Ig-like domain III, which contains a putative receptor-binding loop .
Pfam PF01956: Integral membrane protein EMC3/TMCO1-like (family)
This entry represents a group of eukaryotic and archaeal proteins. Eukaryotic members include EMC3, a subunit of the ER membrane protein complex (EMC) required for protein folding, and TMCO1, a ER calcium load-activated calcium channel. Archaeal members may function as insertases of the archaeal plasma membrane.
Pfam PF08945: Bcl-x interacting, BH3 domain (domain)
This domain is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11. This domain is also known as the BH3 domain between residues 146 and 161.
Wikipedia: In molecular biology, the Bcl-x interacting domain is a protein domain found in BAM, Bim and Bcl2-like protein 11. It is a long alpha helix, which is required for interaction with Bcl-x.
Pfam PF21803: Nab2-type CCCH zinc finger 4 (domain)
Poly(A)-binding proteins (PABPs) protect against nuclease activity and are co-transcriptionally recruited to the nascent poly(A) tail. Nab2 belongs to one of the three major families of PABPs. It contains seven CCCH-type zinc fingers (zf1-7) that are found in three structurally independent tandems, Nab2p zf1-2, Nab2p zf3-4 and Nab2p zf5-7. This entry was build using Nab2p zf4 that doesn't participate in RNA binding.
Pfam PF10761: Protein of unknown function (DUF2590) (family)
This family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF06420: Mitochondrial genome maintenance MGM101 (family)
The mgm101 gene was identified as essential for maintenance of the mitochondrial genome in Saccharomyces cerevisiae. Based on its DNA-binding activity, and experimental work with a temperature-sensitive mgm101 mutant, it has been proposed that the mgm101 gene product performs an essential function in the repair of oxidatively damaged mitochondrial DNA.
Pfam PF13597: Anaerobic ribonucleoside-triphosphate reductase (family)
This entry represents anaerobic, class III ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centred radical , a C-terminal zinc binding site , and a set of conserved active site cysteines and asparagines . This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (IPR012837). Together the two form an alpha-2/beta-2 heterodimer.
Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical . Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded Î±-Î² barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase) . The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.
Pfam PF00877: NlpC/P60 family (family)
The function of this domain is unknown. It is found in several lipoproteins.
Pfam PF14857: TMEM151 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 338 and 558 amino acids in length.
Pfam PF19442: Cysteine-rich motor neuron 1 protein C-terminal (domain)
Cysteine-rich motor neuron 1 protein (CRIM1) interacts with growth factors implicated in motor neuron differentiation and survival, playing a role in central nervous system development. It is upregulated in endothelial cells during tube formation. CRIM1 also modulates BMP activity, which affects its processing and delivery to the cell surface. This is CRIM1 C-terminal domain containing the transmembrane region.
Pfam PF10929: Protein of unknown function (DUF2811) (family)
This is a bacterial family of uncharacterised proteins.
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.