SII-SWORD/CoKE huggingface dataset:
Pfam PF04267: Sarcosine oxidase, delta subunit family (family)
Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+).  This enzyme catalyses the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2.
Pfam PF07361: Cytochrome b562 (family)
This family contains the bacterial cytochrome b562. This forms a four-helix bundle that non-covalently binds a single heme prosthetic group..
Pfam PF03200: Glycosyl hydrolase family 63 C-terminal domain (repeat)
This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyse the specific  cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase [ec:3.2.1.106] is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the C-terminal catalytic domain.
Wikipedia: In molecular biology, glycoside hydrolase family 63 is a family of glycoside hydrolases.
Pfam PF22164: Dark, winged-helix domain (domain)
This entry represents a WH-like present in a set of Dark (Drosophila Apaf-1-related killer) proteins in arthropods. Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis.
Pfam PF24392: ParB-CE (domain)
This entry represents a ParB-like domain predicted to act as an effector in multiple antiviral immunity systems and predicted to target nucleotides.
Pfam PF24856: L-arabinose isomerase central domain (domain)
This entry represents a domain found central in L-arabinose isomerases, AraA, [ec:5.3.1.4]. These enzymes catalyse the reaction: L-arabinose  L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. The domain represented by this entry is composed of a central parallel beta-sheet packed with alpha-helices on both sides and with topology similar to the topology of the N-terminal domain.
Wikipedia: In enzymology, a L-arabinose isomerase is an enzyme that catalyzes the chemical reactionL-arabinose  L-ribulose
Pfam PF05554: Viral hemorrhagic septicemia virus non-virion protein (family)
This family consists of several viral hemorrhagic septicemia virus non-virion (Nv) proteins. The NV protein is a nonstructural protein absent from mature virions although it is present in infected cells. The function of this protein is unknown.
Pfam PF09491: AlwI restriction endonuclease (family)
This family includes the AlwI (recognises GGATC), Bsp6I (recognises GC^NGC) , BstNBI (recognises GASTC), PleI(recognises GAGTC) and MlyI (recognises GAGTC) restriction endonucleases.
Pfam PF19436: ACS/CODH beta subunit C-terminal (domain)
Acetyl-CoA synthase/CO dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyses the reversible reduction of CO2 to CO (CODH activity, the beta subunit) and the synthesis or degradation of acetyl-CoA (catalysed by ACS, the alpha subunit). CODH contains the B-, C-, and D-clusters. This domain represents the middle and C-terminal regions of CODH which have an alpha/beta Rossmann-like fold and are the contribute ligands to the active site C-cluster. The C-cluster generates CO from CO2 and contains one Ni atom, four Fe atoms, and five labile sulfur atoms, arranged as an asymmetrical heteronuclear [Ni-4Fe-5S] cluster.
Pfam PF06087: Tyrosyl-DNA phosphodiesterase (family)
Covalent intermediates between topoisomerase I and DNA  can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between  topoisomerase I and DNA.
Pfam PF00092: von Willebrand factor type A domain (domain)
The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders . In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins . Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands . A number of human diseases arise from mutations in VWA domains.
Wikipedia: The von Willebrand factor type A (vWA) domain is a protein domain named after its occurrence in von Willebrand factor (vWF), a large multimeric glycoprotein found in blood plasma. Mutant forms of vWF are involved in the aetiology of bleeding disorders. This type A domain is the prototype for a protein superfamily.
Pfam PF21779: Family of unknown function (DUF6874) (domain)
This entry represents a family of uncharacterised proteins that contain a small alpha helical bundle domain.
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 PF08831: Class II MHC-associated invariant chain trimerisation domain (domain)
The class II associated invariant chain peptide is required for folding and localisation of MHC class II heterodimers.  This domain is involved in trimerisation of the ectoderm and interferes with DM/class II binding.  The trimeric protein forms a cylindrical shape which is thought to be important for interactions between the invariant chain and class II molecules.
Pfam PF07213: DAP10 membrane protein (family)
This family consists of several mammalian DAP10 membrane proteins. In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells.
Pfam PF01281: Ribosomal protein L9, N-terminal domain (domain)
This entry represents a domain located in the N-terminal section of proteins belonging to the ribosomal protein bL9 family from bacteria and eukaryotes.
This entry represents the large ribosomal subunit protein bL9. In Escherichia coli, bL9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities .

The crystal structure of Bacillus stearothermophilus bL9 shows the 149-residue protein comprises two globular domains connected by a rigid linker . Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an Î±-helix and a three-stranded mixed parallel, anti-parallel Î²-sheet packed against the central Î±-helix. The long central Î±-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends.
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 PF17708: Gasdermin PUB domain (domain)
The precise function of this protein is unknown. A deletion/insertion mutation is associated with an autosomal dominant non-syndromic hearing impairment form. In addition, this protein has also been found to contribute to acquired etoposide resistance in melanoma cells. This family also includes the gasdermin protein
Pfam PF17315: Found in mitochondrial proteome (family)
FMP23 gene encodes a putative mitochondrial protein involved in iron-copper homoeostasis. It was observed to be induced in response to ATX1 deletion and high copper conditions.
Pfam PF00821: Phosphoenolpyruvate carboxykinase C-terminal P-loop domain (domain)
Catalyses the formation of phosphoenolpyruvate by decarboxylation of  oxaloacetate.
Wikipedia: Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
Pfam PF11062: Protein of unknown function (DUF2863) (family)
This bacterial family of proteins have 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 PF16747: Surface-adhesin protein E (domain)
Adhesin E plays a role in pathogenesis. It binds to host proteins including plasminogen, vitronectin and laminin. The domain consists of a 6-stranded antiparallel beta sheet with an alpha helix at the C terminus tethered to the concave side of the sheet by a disulfide bridge.
Pfam PF14171: Toxin SpoIISA, type II toxin-antitoxin system (family)
SpoIISA is a toxin which causes lysis of vegetatively growing cells.  It forms part of a type II toxin-antitoxin system, where the SpoIISB protein, [pfam:PF14185], acts as an antitoxin. It is a transmembrane protein, with a cytoplasmic domain accounting for approximately two-thirds of the protein. The structure of the cytoplasmic domain resembles that of the GAF domains, Pfam: PF01590. SpoIISB binds to the cytoplasmic domain of SpoIISA with high affinity.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF02191: Olfactomedin-like domain (repeat)
The olfactomedin-like or OLF domain is a module of ~260 residues present in metazoan secreted glycoproteins with a characteristic tissue-specific expression. The domain is named after bullfrog olfactomedin, an extracellular matrix protein of olfactory neuroepithelium, whereof it forms the C-terminal part. Other proteins of the olfactomedin family contain the OLF domain in the C-terminal part, while the N terminus is more variable. Proteins of the latrophilin subfamily have an OLF domain in the N-terminal extracellular part, C-terminal to a SUEL-type lectin domain, and their C-terminal part contains domains of the G-protein coupled receptors family 2. Some OLF domain proteins are involved in the formation of the extracellular matrix, e.g. bullfrog olfactomedin, sea urchin amassin and C. elegans unc-122. In addition, OLF domain proteins can function in developmental processes, e.g. noelin and tiarin .

Secondary structure predictions show that the OLF domain contains several Î²-strands . A disulfide bond between two conserved cysteines within the OLF domain of human myocilin is implicated in mutations associated with severe forms of primary open angle glaucoma .
Pfam PF14779: Ciliary BBSome complex subunit 1 (repeat)
The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialised for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS1 predominantly localizes to the basal body and or transitional zone of ciliated cells. It has been found in a heptameric complex with BBS2, BBS5, BBS7, BBS8, and BBS9, termed the BBSome. Mutations in BBS1 can lead to retinal inadequacy.
Pfam PF23083: Rho GTPase-activating protein 35-like, FF domain (domain)
This domain is found in Rho GTPase-activating protein 35 from Rattus norvegicus (RHG35) and similar animal sequences. RHG35 is involved in cell differentiation, cell adhesion and migration, retinal tissue morphogenesis, neural tube fusion, midline fusion of the cerebral hemispheres and mammary gland branching morphogenesis. This domain is predicted to adopt an all alpha-helical structure.
Pfam PF01658: Myo-inositol-1-phosphate synthase (family)
This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyses the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated  to inositol. Inositol phosphates play an important role in  signal transduction.
Wikipedia: In enzymology, an inositol-3-phosphate synthase is an enzyme that catalyzes the chemical reactionD-glucose 6-phosphate  1D-myo-inositol 3-phosphate
Pfam PF14939: DDB1-and CUL4-substrate receptor 15, WD repeat (repeat)
DCAFs, Ddb1- and Cul4-associated factors, are substrate receptors for the Cul4-Ddb1 Ubiquitin Ligase. There are 18 different factors, the majority of which are WD40-repeat-proteins.
Pfam PF15682: Musculoskeletal, temporally activated-embryonic nuclear protein 1 (family)
Mustang is a family of short, approx 80 residue, proteins found in chordates. It localises to the nucleus and specifically, spatially in mesenchymal cells of the developing limbs and tail as well as in the fracture callus, especially in periosteal osteoprogenitor cells, proliferating chondrocytes, and young active osteoblasts. It is highly expressed during embryogenesis and inactivated in most adult tissues with the exception of skeletal muscle and tendon where is is acutely and differentially expressed during bone regeneration.
Pfam PF22113: Outer membrane cytochrome MtrC/MtrF-like, domains II/IV (domain)
This entry includes decaheme cytochrome c component MtrC from the MtrCAB complex and its homologues MtrF (which is part of the MtrFDE complex) and OmcA. In Shewanella oneidensis, these proteins are located at the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilization of extracellular mineral forms of iron and manganese as respiratory electron acceptors. MtrC/MtrF/OmcA consist of four domains: domain I and III containing seven antiparallel beta-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core, flanked by domains I ([pfam:PF22111]) and III. This entry represents domains II and IV.
Pfam PF18334: Exoribonuclease Xrn1 D2/D3 domain (domain)
This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 [pfam:PF18332] in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment [pfam:PF03159].
Pfam PF15354: Kidney-associated antigen 1 (family)
KAAG1, kidney-associated antigen 1, or RU2AS (RU2 antisense gene protein) has been found in mammals. It is expressed in testis and kidney, and, at lower levels, in urinary bladder and liver. It is expressed by a high proportion of tumours of various histologic origin, including melanomas, sarcomas and colorectal carcinomas.
Pfam PF23703: DExH-box ATP-dependent RNA helicase DExH18, N-terminal (domain)
This domain is found at the N-terminal end of DExH-box ATP-dependent RNA helicase DExH18, mitochondrial from Arabidopsis thaliana and similar sequences from plants. DExH18 is a major helicase player in mitochondrial RNA metabolism. It plays a role in the RNA surveillance system in mitochondria; regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. This domain is predicted to adopt an all alpha-helical configuration.
Pfam PF04422: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (family)
Coenzyme F420 hydrogenase ([ec:1.12.99.1]) reduces the low-potential two-electron acceptor coenzyme F420.  This family contains the N termini of F420 hydrogenase and dehydrogenase beta subunits,.  The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain ([ec:1.2.1.2], [swissprot:P06130]) is also a member of this family. This region is often found in association with the 4Fe-4S binding domain, fer4 ([pfam:PF00037]).
Pfam PF07964: Rec10 / Red1 (family)
Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation.  This protein  localises to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe. This family is currently only found in fungi.
Pfam PF08019: Phosphoethanolamine transferase EptA/EptB (domain)
This entry represents a domain found in a group of bacterial phosphoethanolamine transferases, including eptA from Helicobacter pylori and eptB from Escherichia coli [ec:2.7.8.42]. This domain is found immediately N-terminal to the sulphatase domain in many sulphatases.
Pfam PF06936: Selenoprotein S (SelS) (family)
This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. Selenoprotein S (SelS) is an intrinsically disordered protein. It formsa selenosulfide bond between cys 174 and Sec 188, that has a redox potential -234 mV. In vitro, SelS is an efficient reductase that depends on the presence of selenocysteine. Due to the high reactivity, SelS also has peroxidase activity that can catalyze the reduction of hydrogen peroxide. It is also resistant to inactivation by hydrogen peroxide which might provide evolutionary advantage compared to cysteine containing peroxidases.
Pfam PF04670: Gtr1/RagA G protein conserved region (domain)
GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family.  The RagA/B proteins are the human homologues of Gtr1.     Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.
Pfam PF09845: Origin-associated protein OapC (family)
This entry includes archaeal Zinc-ribbon containing proteins which are mostly uncharacterised. Some members of this entry have been described as OapC/ArvC, encoded by oapC gene which is part of the three-gene cluster oapABC, involved in generation of extracellular vesicles (arv, archaeal vesiculating GTAse). Knockout of OapC/ArvC leads to over vesiculation, possibly due to dysregulation of OapA/ArvA, a small GTPase, therefore, it has been suggested that OapC/ArvC may represent a GAP.
Pfam PF24024: Domain of unknown function (DUF7336) (domain)
This entry represents a family of uncharacterised domains found in a variety of phage and bacterial genomes. Structure prediction suggests the domain is composed of a small beta sheet of three strands and an alpha helix. There is some evidence from prediction that these domains might form a dimeric arrangement.
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 PF22128: Alp7A C-terminal domain (domain)
Bacterial Actin-Like Proteins (ALPs) participate in many biologically, clinically and commercially important processes, including segregation of low-copy plasmids. Alp7A is a bacterial actin that functions in plasmid segregation. It is composed of two domains both structurally similar to domains of actin-like ATPases. This entry represents the C-terminal domain.