SII-SWORD/CoKE huggingface dataset:
Pfam PF00168: C2 domain (domain)
The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about 116 amino-acid residues and is located between the two copies of the C1 domain in Protein Kinase C and the protein kinase catalytic domain . Regions with significant homology  to the C2-domain have been found in many proteins. The C2 domain is thought to be involved in calcium-dependent phospholipid binding  and in membrane targetting processes such as subcellular localisation.

The 3D structure of the C2 domain of synaptotagmin has been reported , the domain forms an eight-stranded Î²-sandwich constructed around a conserved 4-stranded motif, designated a C2 key . Calcium binds in a cup-shaped depression formed by the N- and C-terminal loops of the C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel Î²-sandwich.
Wikipedia: A C2 domain is a protein structural domain involved in targeting proteins to cell membranes. The typical version (PKC-C2) has a beta-sandwich composed of 8 β-strands that co-ordinates two or three calcium ions, which bind in a cavity formed by the first and final loops of the domain, on the membrane binding face. Many other C2 domain families don't have calcium binding activity.
Pfam PF11068: YlqD protein (family)
The structure of a representative of this family has been solved (pdb:4dci) and found to form a tetrameric structure of prefoldin-like architecture with the beta-barrel core and helical coiled coil tentacles. This suggests that this family may act as molecular chaperones.
Pfam PF23588: ATP-dependent helicase hrp3-like HTH domain (domain)
This domain is found in ATP-dependent helicase hrp3 (Hrp3) from Schizosaccharomyces pombe and similar eukaryotic proteins. Hrp3 is involved in heterochromatin silencing. It is predicted to adopt an HTH structure and is often found C-terminal to [pfam:PF18196].
Pfam PF15409: Pleckstrin homology domain (domain)
This Pleckstrin homology domain is found in some fungal species.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF24375: Family of unknown function (DUF7531) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an alpha-beta structure.
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 PF20937: Factor H binding protein, N-terminal (domain)
Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease. The structure of the N-terminal domain consists of a more unusual taco-shaped beta-barrel fold characterised by higher intrinsic flexibility than the C-terminal one.
Pfam PF00199: Catalase (domain)
Catalases (1.11.1.6) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects . Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760) that are found in bacteria . Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants .
This entry represent the core-forming domain of mono-functional, haem-containing catalases. It does not cover the region that carries an immune-responsive amphipathic octa-peptide that is found in the C-terminal of some catalases (IPR010582).
Wikipedia: Catalase is a common enzyme found in nearly all living organisms exposed to oxygen which catalyzes the decomposition of hydrogen peroxide to water and oxygen. It is a very important enzyme in protecting the cell from oxidative damage by reactive oxygen species (ROS). Catalase has one of the highest turnover numbers of all enzymes; one catalase molecule can convert millions of hydrogen peroxide molecules to water and oxygen each second.
Pfam PF04663: Phenol hydroxylase conserved region (family)
Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase.  This region is found in both types of enzymes.
Pfam PF22573: Sperm-associated microtubule inner protein 5 (domain)
This entry represents a domain found in the homologues of Sperm-associated microtubule inner protein 5 (SPMIP5 also known as C10orf82). SPMIP5 is a mammalian sperm-specific microtubule inner protein that probably plays a role in the stabilisation of the axonemal microtubules. This domain binds to tubulin.
Pfam PF10651: BppU N-terminal domain (domain)
This is the N-terminal domain of baseplate upper proteins (BppU, also known as ORF48) which is found in phage from a number of different bacteria. The N-terminal domain exhibits a beta-sandwich immunoglobulin fold.
Pfam PF23624: ORF68-like, C-terminal domain (domain)
This domain is found at the C-terminal end of ORF68 from Staphylococcus phage K and similar viral proteins. This domain adopts an all-beta configuration.
Pfam PF13355: ARC6-like, IMS domain (domain)
This domain corresponds to the C-terminal intermembrane space (IMS) region from protein accumulation and replication of chloroplasts 6 (ARC6) and its paralogue PARC6. ARC6 and PARC6 are components of the plastid division machinery which are essential for the chloroplast replication process, which implies the assembly and constriction of the tubulin-like FtsZ ring on the stromal surface of the inner envelope membrane (IEM) and the dynamin-like ARC5 ring on the cytosolic surface of the outer envelope membrane (OEM). ARC6 is evolutionarily related to the cyanobacterial cell division protein Ftn2/ZipN, having similar structures. This domain from ARC6 and PARC6 interacts with PDV2 and PDV1 respectively. PDV proteins recruit dynamin-like ARC5 ring to the chloroplast surface and mediates its constriction. ARC6/PARC6 are key to connect and coordinate Fst and ARC5 rings during fission.
Pfam PF02319: E2F/DP family winged-helix DNA-binding domain (domain)
This family contains the transcription factor E2F and  its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a  homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows  that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins.
Pfam PF16098: Fragile X messenger ribonucleoprotein 1, C-terminal region 2 (family)
FXMR_C2 is a small highly conserved region at the very C-terminus of Fragile X messenger ribonucleoprotein 1, FMR1. The family is found in association with [pfam:PF05641], [pfam:PF00013], PF16096.
Pfam PF11203: Putative type VII ESX secretion system translocon, EccE (family)
EccE is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterised in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope.
Pfam PF19026: HYPK UBA domain (domain)
This entry represents the UBA domain found at the C-terminus of the HYPK protein and its homologues. This domain in HYPK mediates a protein interaction with the Naa15 C-terminus.
Pfam PF17139: Domain of unknown function (DUF5112) (family)
This domain is frequently found upstream of family HATPase_c [pfam:PF00025]1.
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 PF16571: FBP C-terminal treble-clef zinc-finger (domain)
FBP_C is a family from the C terminal end of fibronectin-binding proteins. It forms an extended four-cysteine zinc-finger with a unique structural fold. Fibronectin-binding proteins bind to elongation factor G - EF-G, which is mediated by the zinc-finger binding to the C-terminus of EF-G. FBPs release ribosomes by competing with them for EF-G.
Pfam PF00118: TCP-1/cpn60 chaperonin family (family)
This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family.
Wikipedia: HSP60, also known as chaperonins (Cpn), is a family of heat shock proteins originally sorted by their 60kDa molecular mass. They prevent misfolding of proteins during stressful situations such as high heat, by assisting protein folding. HSP60 belong to a large class of molecules that assist protein folding, called molecular chaperones.
Pfam PF06812: ImpA, N-terminal, type VI secretion system (family)
This family represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans. The ImpA gene in Vibrio cholera and many other bacteria is expressed from the virulence factor operon which produces the pathogenic injection, type VI secretion system; although the exact function of this gene-product is not known it appears to be an essential component of the pathogenic effect.
Pfam PF01014: Uricase (domain)
Uricase (1.7.3.3) (urate oxidase)  is the peroxisomal enzyme responsible for the degradation of urate into allantoin:

Urate + O2 + H2O = 5-hydroxyisourate + H2O2

Some species, like primates and birds, have lost the gene for uricase and are therefore unable to degrade urate . Uricase is a protein of 300 to 400 amino acids, its sequence is well conserved. It is mainly localised in the liver, where it forms a large electron-dense paracrystalline core in many peroxisomes . The enzyme exists as a tetramer of identical subunits, each containing a possible type 2 copper-binding site . In legumes, 2 forms of uricase are found: in the roots, the tetrameric form; and, in the uninfected cells of root nodules, a monomeric form, which plays an important role in nitrogen-fixation .
Wikipedia: The enzyme urate oxidase (UO), uricase or factor-independent urate hydroxylase, absent in humans, catalyzes the oxidation of uric acid to 5-hydroxyisourate:Uric acid + O2 + H2O → 5-hydroxyisourate + H2O2
5-hydroxyisourate + H2O → 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline → allantoin + CO2
Pfam PF18076: Formylglycinamide ribonucleotide amidotransferase N-terminal (domain)
This is the N-terminal domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase ([ec:6.3.5.3]), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide and glutamine to formylglycinamidine ribonucleotide, ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway.
Pfam PF08278: DNA primase DnaG DnaB-binding (domain)
Eubacterial DnaG primases interact with several factors to from the replisome.  One of these factors in DnaB, a helicase.  This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB.
Pfam PF19844: Family of unknown function (DUF6319) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 251 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 PF22211: Type six secretion immunity 3 domain (domain)
This entry represents the Tsi3 domain. Tsi3 immunity protein prevents early activation of toxin Tse3. Three loops of Tsi3 deeply insert into the groove of Tse3, fully blocking its active site. This interaction serves as the structural basis for Tse3 inactivation.
Pfam PF02402: Lysis protein (family)
These small bacterial proteins are required for colicin release and partial cell lysis. This family contains lysis proteins for several different forms of colicin. [swissprot:Q02112] has been included in this family, the similarity is not highly significant, however it is also a short protein, that is involved in secretion of other proteins (Bateman A pers. obs.). This family includes a signal peptide motif and a lipid attachment site.
Pfam PF09244: Sucrose phosphorylase, C-terminal (domain)
This domain is C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain which adopts a beta-sandwich fold with Greek-key topology.
Pfam PF01876: RNase P subunit p30 (domain)
This protein is part of the RNase P complex that is involved in tRNA maturation.
Pfam PF24165: Tape measure protein C-terminal (family)
This entry represents the C-terminal conserved region of the Tape measure protein PB2 and related proteins found mainly in T5-like phages. PB2 functions as a tape measure protein that serves as a base for tail tube protein polymerization and acts as a template for tail length determination. This protein fills the tail tube with its long coiled-coil domain and is expelled during the conformation changes that follow T5 binding to host FhuA receptor. The tape measure protein C-terminal region is composed of two alpha-helices that are organized in an extended L-shape. The C-terminal region of the TMP was found within the tail tip suggesting that the tail tip complex returns to its original state after DNA ejection.
Pfam PF15953: Putative propanediol utilisation (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length.
Pfam PF12538: DNA transporter (family)
This domain family is found in bacteria, and is typically between 107 and 121 amino acids in length. The family is found in association with [pfam:PF01580]. The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division.
Pfam PF16818: Protein SLM4 (domain)
The fungal protein SLM4 (EGO3, GSE1) is a component of the GSE complex and the EGO (TOR) complex . The GSE complex is required for trafficking GAP1 out of the endosome. The EGO complex is involved in the regulation of autophagy and cell growth. SLM4 is required for the integrity and function of the EGO complex.
Pfam PF02512: Virulence determinant (family)
The UK protein is an African swine fever virus (ASFV) protein that  is highly conserved amongst strains, and is an important viral virulence determinant for domestic pigs.
Pfam PF12654: Domain of unknown function (DUF3786) (domain)
This presumed domain is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 201 and 257 amino acids in length. Some proteins also contains an iron-sulfur cluster.
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 PF24904: REVEILLE 6-like domain (domain)
This domain is found towards the C-terminal end of Protein REVEILLE 6 from Arabidopsis thaliana (RVE6), which is likely to be a transcription factor. This domain is usually found associated with [pfam:PF00249] and is predicted to adopt an all alpha structure.
Pfam PF07797: Protein of unknown function (DUF1639) (family)
This approximately 50 residue region is found in a  number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre.
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 PF04886: PT disordered repeat (disordered)
This short repeat is composed on the tetrapeptide XPTX. This repeat is found in a variety of proteins, however it is not clear if these repeats are homologous to each other. The alignment represents nine copies of this repeat.
Pfam PF09020: YopE, N terminal (domain)
The N terminal YopE domain targets YopE for secretion from the bacterium and translocation into eukaryotic cells.
Pfam PF14032: PknH-like extracellular domain (domain)
This domain is functionally uncharacterised. It is found as the periplasmic domain of the bacterial protein kinase PknH. The domain is also found in isolation in numerous proteins, for example the lipoproteins lpqQ, lprH, lppH and lpqA from M. tuberculosis. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 268 amino acids in length. There are two completely conserved C residues that are likely to form a disulphide bond.  A second pair of cysteines are less well conserved probably form a second disulphide bond. It seems likely that this domain functions to bind some as yet unknown ligand.
Pfam PF18258: Interleukin-4 inducing immunoglobulin-binding domain (domain)
This domain is found in Interleukin-4 inducing protein alpha-1 (IPSE/alpha-1) present in Schistosoma mansoni, a parasite of humans. IPSE/alpha-1 triggers the release of IL-4 from basophils in the liver which is a major site of egg deposition during S. mansoni infection. This domain adopts a beta gamma-crystallin fold that is stabilized by three disulfide bonds within the domain (23/26, 59/93, and 111/121). The domain is involved in immunoglobulin binding.
Pfam PF02524: KID repeat (repeat)
This is family contains the KID repeat as found in Borrelia spirochete RepA / Rep+ proteins.  The function of these proteins is unknown. RepA and related Borrelia proteins have been suggested to play an important genus-wide role in the biology of the Borrelia.
Pfam PF12038: tRNA-queuosine alpha-mannosyltransferase N-terminal (domain)
This is the N-terminal domain of tRNA-queuosine alpha-mannosyltransferase (QTMAN, also known as GTDC1) from animals. QTMAN is a glycosyltransferase that specifically catalyses mannosylation of cytoplasmic tRNA(Asp) modified with queuosine at position 34 (queuosine(34)) to form mannosyl-queuosine(34). Mannosylation of queuosine(34) in tRNA(Asp) is required to slow-down elongation at cognate codons GAC and GAU, thereby regulating protein translation. This domain is about 170 amino acids in length and adopts a Rossmann-fold. This domain is found associated with [pfam:PF00534] found at the C-terminal. This domain has two conserved sequence motifs: HENQ and FNS and it also has a single completely conserved residue S that may be functionally important. This domain is also found in uncharacterised bacterial sequences.
Pfam PF02531: PsaD (family)
This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the  electrostatic binding of ferredoxin within the reaction centre. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment.
Pfam PF13771: PHD-like zinc-binding domain (domain)
The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains.  The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.
Wikipedia: The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain proteins HAT3.1 in Arabidopsis and maize ZmHox1a. 
The PHD zinc finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.
Pfam PF20321: Family of unknown function (DUF6616) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 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 PF04508: Viral A-type inclusion protein repeat (coiled_coil)
The repeat is found in the A-type inclusion protein of the Poxvirus family.