SII-SWORD/CoKE huggingface dataset:
Pfam PF14194: Cysteine-rich VLP (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. It contains 6 conserved cysteines and a conserved VLP sequence motif.
Pfam PF20932: Dicer, dsRNA-binding domain (domain)
This domain is found in Endoribonuclease Dicer from chordates. This dsRNA endoribonuclease is involved in the cleavage of long RNA precursors into short dsRNAs and plays a role in gene silencing. Dicer shows two N-terminal helicase domains ([pfam:PF04851] and [pfam:PF00271]), a dimerisation domain ([pfam:PF03368]), a Platform domain, a PAZ domain ([pfam:PF02170]), an RNase IIIa/b domain ([pfam:PF00636]) and a dsRNA-binding domain in its C-terminal region (this entry). This domain protrudes from the RNase IIIb domain in the middle of the protein. It may be involved in recruiting RNA substrates.
Pfam PF19471: Family of unknown function (DUF6008) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000112) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the neocarzinostatin biosynthetic gene cluster from  Streptomyces carzinostaticus subsp. neocarzinostaticus and  appears to be restricted to Actinobacteria.
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 PF07866: Protein of unknown function (DUF1653) (family)
This is a family of hypothetical bacterial proteins of unknown 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 PF03356: Viral late protein H2 (family)
All Members of this family show similarity to the vaccinia virus late protein H2. This protein is often referred to by its gene name of H2R. Members from this family all belong to the viral taxon Poxviridae.
Pfam PF09673: Type-F conjugative transfer system pilin assembly protein (family)
This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins is heterogeneous.
Pfam PF20652: Exocyst complex component Sec8 C-terminal (repeat)
Sec8 is a component of the exocyst complex, composed of Sec3, Sec5, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane. The exocyst promotes the assembly of SNARE complex for membrane fusion and it is also involved in many cellular processes such as cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis. Subunits of the exocyst have a rod structure which is a shared feature for the Complex Associated with Tethering Containing Helical Rods (CATCHRs) proteins such as those of the Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP), consisting of a N-terminal long coiled-coil followed by a region of antiparallel short helical bundle units. This entry represents a domain found at the C-terminal of Sec8 subunit, consisting of alpha-helical bundles.
Pfam PF13204: Protein of unknown function (DUF4038) (family)
A family of putative cellulases.
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 PF05862: Helicobacter pylori IceA2 protein (family)
This family consists of several Helicobacter pylori specific IceA2 proteins. The function of this family is unknown.
Pfam PF02398: Coronavirus protein 7 (family)
This is a family of proteins from coronavirus which may function in  viral assembly.
Pfam PF10938: YfdX protein (family)
YfdX is a protein found in Proteobacteria of unknown function. The protein coding for this gene is regulated by EvgA in E. coli.
Pfam PF09670: Csm6 HEPN domain (domain)
Members of this entry are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia). Among its members is Csm6 from Thermus thermophilus, a ssRNA-specific endoribonuclease that provides an auxiliary RNA-targeting interference mechanism in type III-A CRISPR-Cas systems, working together with the RNA- and DNA-targeting endonuclease activities of the Csm effector complex. Csm6 consists of a CARF domain at the N-terminal, a six-helix (6H) central domain and the HEPN domain at the C-terminal, which is represented in this entry. This domain forms a dimer that constitutes a composite ribonuclease active site.
Pfam PF02801: Beta-ketoacyl synthase, C-terminal domain (domain)
The structure of beta-ketoacyl synthase is similar to that of the  thiolase family ([pfam:PF00108]) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.
Wikipedia: In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It typically uses malonyl-CoA as a carbon source to elongate ACP-bound acyl species, resulting in the formation of ACP-bound β-ketoacyl species such as acetoacetyl-ACP.
Pfam PF16011: Carbohydrate-binding family 9 (family)
CBM9_2 is a family of putative endoxylanase-like proteins that belong to the Carbohydrate-binding family 9.
Pfam PF01916: Deoxyhypusine synthase (domain)
Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DS) [ec:1.1.1.249]. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation.
Pfam PF16277: Domain of unknown function (DUF4926) (family)
This family consists of uncharacterized proteins around 70 residues in length and is mainly found in various Caulobacter, Microcystis and Cyanothece species. The function of this  family is unknown.
Pfam PF04604: Type-A lantibiotic (family)
Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyl-lanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II.
Pfam PF16553: BCORL-PCGF1-binding domain (domain)
PUFD is the minimal domain at the C-terminus of BCORL (BCL6 corepressor) that is needed for binding and giving specificity to some of the PCGF proteins, polycomb-group RING finger homologues. PUFD binds to the RAWUL (RING finger- and WD40-associated ubiquitin-like) domain of the particular PCGF PCGF1, [pfam:PF16207].  Polycomb group proteins form repressive complexes (PRC) that mediate epigenetic modifications of histones. In humans there are many different PCGF homologues whose functions all vary, but the direct binding partner of PCGF1 is BCOR. BCOR has emerged as an important player in development and health.
Pfam PF01183: Glycosyl hydrolases family 25 (domain)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Glycoside hydrolase family 25 GH25 comprises enzymes with only one known activity; lysozyme (3.2.1.17).

It has been shown  that a number of cell-wall lytic enzymes are evolutionary related and can be classified into a single family. Two residues, an aspartate and a glutamate, have been shown  to be important for the catalytic activity of theCharalopsisenzyme. These residues as well as some others in their vicinity are conserved in all proteins from this family.
Wikipedia: In molecular biology, glycoside hydrolase family 25 is a family of glycoside hydrolases.
Pfam PF00829: Ribosomal prokaryotic L21 protein (family)
This entry represents large ribosomal subunit protein bL21(previously known as L21) that is found in bacteria and eukaryotic organelles such as chloroplast and mitochondria. This entry also includes the S. pombe Aco2 protein, a fusion of mitochondrial ribosomal protein bL21m (Mrpl49) and aconitase  that has essential function in mitochondrial translation in fission yeast. bL21 consists of a small Î²-barrel-like domain that is connected to an extended loop .
In Escherichia coli, bL21 is known to bind to the 23S rRNA in the presence of bL20. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups:


 * Bacterial bL21 (old name L21).
 * Marchantia polymorpha chloroplast bL21 (old name L21).
 * Plant chloroplast bL21 (old name L21, nuclear-encoded).


Bacterial bL21 is a protein of about 100 amino-acid residues, the mature form of the spinach chloroplast L21 has 200 residues.
Pfam PF16535: Type III cell invasion protein SipB (domain)
T3SSipB is a family of pathogenic Gram-negative bacterial proteins that invade human intestinal cells via the type III secretion system translocators. T3SSipB represents the coiled -coil region of the proteins and is shown to be homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia.
Pfam PF12659: Telomere capping C-terminal wHTH (domain)
This domain consists of tandem winged helix-turn-helix motifs. Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution.
Pfam PF05521: Phage head-tail joining protein (domain)
This entry describes the head-tail adaptor protein of bacteriophage SPP1 and related proteins in other bacteriophage and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) , including ORFg7 (RCAP_rcc01689) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) .

In bacteriophage SPP1, the gp16 protein functions as a stopper, locking the viral DNA into the capsid. When the tail attachment binds to the entry receptor, gp16 opens by a diaphragm-like motion, allowing the genome to exit the capsid through the tail tube to the host cell. During virion assembly, gp16 functions as a docking platform to which the preassembled tail binds .
The SPP1 head-to-tail connector is composed of cyclical dodecamers of the portal protein gp6 and of the 2 head completion proteins gp15 and gp16 .
Pfam PF01216: Calsequestrin (family)
Calsequestrin is the principal calcium-binding protein present in the sarcoplasmic reticulum of cardiac and skeletal muscle . It is a highly acidic protein that is able to bind over 40 calcium ions and acts as an internal calcium store in muscle. Sequence analysis has suggested that calcium is not bound in distinct pockets via EF-hand motifs, but rather via presentation of a charged protein surface.

Two forms of calsequestrin have been identified. The cardiac form is present in cardiac and slow skeletal muscle and the fast skeletal form is found in fast skeletal muscle. The release of calsequestrin-bound calcium (through a a calcium release channel) triggers muscle contraction. The active protein is not highly structured, more than 50% of it adopting a random coil conformation . When calcium binds there is a structural change whereby the Î±-helical content of the protein increases from 3 to 11% . Both forms of calsequestrin are phosphorylated by casein kinase II, but the cardiac form is phosphorylated more rapidly and to a higher degree .
Wikipedia: Calsequestrin is a calcium-binding protein that acts as a calcium buffer within the sarcoplasmic reticulum. The protein helps hold calcium in the cisterna of the sarcoplasmic reticulum after a muscle contraction, even though the concentration of calcium in the sarcoplasmic reticulum is much higher than in the cytosol. It also helps the sarcoplasmic reticulum store an extraordinarily high amount of calcium ions. Each molecule of calsequestrin can bind 18 to 50 Ca2+ ions. Sequence analysis has suggested that calcium is not bound in distinct pockets via EF-hand motifs, but rather via presentation of a charged protein surface. Two forms of calsequestrin have been identified. The cardiac form Calsequestrin-2 (CASQ2) is present in cardiac and slow skeletal muscle and the fast skeletal form Calsequestrin-1(CASQ1) is found in fast skeletal muscle. The release of calsequestrin-bound calcium (through a calcium release channel) triggers muscle contraction. The active protein is not highly structured, more than 50% of it adopting a random coil conformation. When calcium binds there is a structural change whereby the alpha-helical content of the protein increases from 3 to 11%. Both forms of calsequestrin are phosphorylated by casein kinase 2, but the cardiac form is phosphorylated more rapidly and to a higher degree. Calsequestrin is also secreted in the gut where it deprives bacteria of calcium ions..
Pfam PF12800: 4Fe-4S binding domain (domain)
This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF00393: 6-phosphogluconate dehydrogenase, C-terminal domain (domain)
This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase.              The domain contains two structural repeats of 5 helices each.
Wikipedia: 6-Phosphogluconate dehydrogenase (6PGD) is an enzyme in the pentose phosphate pathway. It forms ribulose 5-phosphate from 6-phosphogluconate:6-phospho-D-gluconate + NAD(P)+  D-Ribulose 5-phosphate + CO2 + NAD(P)H + H+
Pfam PF06126: Herpesvirus Latent membrane protein 2 (family)
Family of Kaposi's sarcoma-associated herpesvirus (HHV8) latent membrane protein.
Pfam PF08849: BrxA (family)
BrxA is part of the phage resistance system BREX (Bacteriophage Exclusion). It shares structural homology with the RNA-binding antitermination protein NusB.
Pfam PF22680: Glycoside hydrolase 123 N-terminal domain (domain)
This entry represents the N-terminal domain of a group of glycoside hydrolases 123, from bacteria.
Pfam PF13091: PLD-like domain (domain)
Phospholipase D hydrolyses glycerol-phospholipids at the terminal phosphodiesteric bond. This entry represents a phospholipase D-like domain, found in phospholipase D and related proteins. In cardiolipin synthases it is found duplicated.
Pfam PF24593: Domain of unknown function (DUF7617) (domain)
This domain is found in multiple copies in a number of bacterial proteins mainly from Actinomycetales. It is closely related to domains represented by [pfam:PF01345] and [pfam:PF24346]. Similarly to them, this domain contains a conserved N-terminal lysine and a C-terminal asparagine with central aspartate/glutamate residues suggesting that some members may contain an isopeptide bond. This domain is sometimes found in combination with [pfam:PF01345] or [pfam:PF24346].
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 PF10069: Sensory domain in DIguanylate Cyclases and Two-component system (domain)
DICT is a sensory domain found associated with GGDEF, EAL, HD-GYP, STAS, and two component systems (histidine-kinase type). It assumes an alpha+beta fold with a 4-stranded beta-sheet and might have a role in light response (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter)
Pfam PF12877: UPF0606 protein KIAA1549 (family)
This family contains KIAA1549 from human ([swissprot:Q9HCM3]) which has been implicated in pilocytic astrocytomas. It has been found to be fused to BRAF gene in many cases of pilocytic astrocytomas. The fusion is due mainly to a tandem duplication of 2 Mb at 7q34. The BRAF protein is a well characterised oncoprotein. It is a serine/threonine protein kinase which is implicated in MAP/ERK signalling, a critical pathway for the regulation of cell division, differentiation and secretion. More recently, KIAA1549 has been described to play a role in photoreceptor function.
Pfam PF18638: Cysteine-Rich Protective Antigen 6 bladed domain (repeat)
Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a 42.8 kDa protein of 362 residues with a predicted N-terminal secretion signal. It is part of a multi-protein complex including the PfRH5-interacting protein PfRipr and the reticulocyte binding-like homologous protein PfRH5, which binds to the erythrocyte receptor basigin. PfRH5, PfCyRPA, and PfRipr colocalize during parasite invasion at the junction between merozoites and erythrocytes. The complex seems to be required both for triggering Ca2+ release and establishment of tight junctions. PfCyRPA adopts a 6-bladed beta-propeller structure with similarity to the classic sialidase fold, but it has no sialidase activity and fulfills a purely non-enzymatic function. Each blade of the propeller is constructed by a four-stranded anti-parallel beta-sheet.
Pfam PF04812: Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus (family)
This family consists of a region found within the alpha isoform and at  the C terminus of the beta isoform of the homeobox-containing transcription factor of HNF-1.  Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative  splicing.  The C-terminal region of HNF-1 is responsible for the  activation of transcription. Mutations and polymorphisms in HNF-1  cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Pfam PF10578: Seminal vesicle protein repeat (repeat)
The rat seminal vesicle contains six major androgen-dependent secretory proteins referred to as SVS I-VI. The SVS I-III proteins appear to be components of the rat copulatory plug, with the SVS II protein being the major component .

This entry represents a repeat that is found in seminal vesical proteins.
Pfam PF06485: RNA-binding protein Tab2/Atab2 N terminal (domain)
This is the N-terminal domain of proteins from photosynthetic organisms including plants and cyanobacteria, such as Tab2 proteins. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit. Later, the Tab2 homologue (ATAB2) from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII.
Pfam PF15009: STING ligand-binding domain (domain)
Transmembrane protein 173, also known as stimulator of interferon genes protein (STING), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA. It consists of an N-terminal transmembrane (TM) and a C-terminal ligand-binding (LBD) domains. This entry represents the LBD which binds to c-di-GMP. Cyclic dinucleotides induce a conformational change to the STING LBD, leading to high-order oligomerization of STING that is essential for triggering the downstream signalling pathways.
Pfam PF08773: Cathepsin C exclusion domain (domain)
Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases.  This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini.  It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands. Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor.
Wikipedia: Cathepsin C (CTSC) also known as dipeptidyl peptidase I (DPP-I) is a lysosomal exo-cysteine protease belonging to the peptidase C1 protein family, a subgroup of the cysteine cathepsins. In humans, it is encoded by the CTSC gene.
Pfam PF06342: Alpha/beta hydrolase of unknown function (DUF1057) (family)
This family consists of several Caenorhabditis elegans specific proteins of unknown function. Members of this family have an alpha/beta hydrolase fold.
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.