SII-SWORD/CoKE huggingface dataset:
Pfam PF22955: RECK-like, EGF-like 1 domain (domain)
This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar proteins mainly found in vertebrates. RECK is a membrane-anchored glycoprotein that plays a role in Wnt7-specific responses in the central nervous system angiogenesis and in the blood-brain barrier regulation. This protein consists of five repeats of an uncommon domain with six cysteines (the CC domain, [pfam:PF22961], [pfam:PF23332], [pfam:PF23332]), a Frizzled-likee cysteine-rich domain (Fz-like CRD, [pfam:PF23298]), two epidermal growth factor-like domains (EGF-like 1, [pfam:PF25027], and EGF-like 2, represented by this entry),  and three Kazal-like motifs (Kazal-like 1 to 3, [pfam:PF07648]).
Pfam PF07618: Protein of unknown function (DUF1580) (family)
A family of short hypothetical proteins found in Rhodopirellula baltica.
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 PF14248: Domain of unknown function (DUF4345) (family)
This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 125 and 141 amino acids in length. There is a single completely conserved residue E that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05848: CtsR N-terminal HTH domain (domain)
This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. This entry is the N-terminal HTH domain.
Pfam PF12772: Growth hormone receptor binding (family)
Growth hormone receptor binding protein is produced either by proteolysis of the GHR (growth hormone receptor) at the cell surface thereby releasing its extracellular domain, the GHBP (growth hormone-binding protein), or, in rodents, by alternative processing of the GHR transcript. The sheddase proteolytic enzyme responsible for the cleavage is TACE (tumour necrosis factor-alpha-converting enzyme). Growth hormone (GH) binding to GH receptor (GHR) is the initial step that leads to the physiological functions of the hormone. The biological effects of GHBP are determined by the serum levels of growth hormone (GH), which can vary. Low levels of GH can result in a dwarf phenotype and have been positively correlated with an increased life expectancy. High levels of GH can lead to gigantism or a clinical syndrome termed acromegaly and have been implicated in diabetic eye and kidney damage.
Pfam PF15636: GHH signature containing HNH/Endo VII superfamily nuclease toxin (family)
A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteristic sG[HQ]H signature motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, type 7 or TcdB/TcaC-type secretion system. The metazoan teneurin proteins possess an inactive  of this domain at their C-terminus.
Pfam PF16884: N-terminal domain of oxidoreductase (family)
N-terminal region of oxidoreductase and prostaglandin reductase and alcohol dehydrogenase.
Pfam PF16567: Pathogenicity island component CagD (domain)
CagD is a tightly conserved family of proteins found in the pathogenic strains of Helicobacter species. It is one of some 30 proteins, produced from the genomic insert termed the pathogenicity island, required for the type IV secretion system - T4SS - that delivers CagA oncoprotein toxin into the host cell. CagD is a covalent dimer in which each monomer folds as a single domain composed of five beta-strands and three alpha-helices.  CagD partially associates with the inner membrane, where it may be exposed to the periplasmic space; this may indicate that CagD is released into the supernatant during host cell infection in order then to bind to the host cell surface, or to be incorporated into the pilus structure.
Pfam PF02569: Pantoate-beta-alanine ligase (family)
Pantoate-beta-alanine ligase, also know as pantothenate synthase, ([ec:6.3.2.1]) catalyses the formation of pantothenate from pantoate and alanine.
Pfam PF03068: Protein-arginine deiminase (PAD) (family)
Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes [ec:3.5.3.15] catalyse the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-arginine + H2O  Protein L-citrulline + NH3. Several types are recognised (and included in the family) on the basis of molecular mass, substrate specificity, and tissue localisation. The expression of type I PAD is known to be under the control of oestrogen.
Pfam PF13593: SBF-like CPA transporter family (DUF4137) (domain)
These family members are 7TM putative membrane transporter proteins. The family is similar to the SBF family of bile-acid symporters, [pfam:PF01758].
Pfam PF04985: Phage tail tube protein FII (family)
The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively.
Pfam PF15984: Bacterial collagen, middle region (domain)
Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins.
Pfam PF13643: Domain of unknown function (DUF4145) (domain)
This domain is found in a variety of restriction endonuclease enzymes. The exact function of this domain is uncertain.
Pfam PF19988: Family of unknown function (DUF6424) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000379) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the glycinocin A biosynthetic gene cluster from  streptomyces viridochromogenes.
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 PF24861: Sucrose synthase N-terminal (domain)
This entry represents the N-terminal domain of sucrose synthases,  which corresponds to the cellular targeting domain (CTD, also referred to as SSN1) and together with the EPBD domain (SSN2), they have regulatory functions in plant species, however, the function of these domains in bacteria is not yet clear. Sucrose synthases are sucrose-cleaving enzymes that provide UDP-glucose and fructose for various metabolic pathways.
Pfam PF08494: DEAD/H associated (family)
This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain ([pfam:PF00270]) and the [pfam:PF00271] domain.
Pfam PF05235: CHAD domain (domain)
The CHAD domain is an alpha-helical domain functionally associated with the [pfam:PF01928] domains. It has conserved histidines that may chelate metals.
Pfam PF05318: Tombusvirus movement protein (family)
This family consists of several Tombusvirus movement proteins. These proteins allow the virus to move from cell-to-cell and allow host-specific systemic spread.
Pfam PF00849: RNA pseudouridylate synthase (family)
Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD [swissprot:P33643], a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.
Pfam PF21887: RhiE branching domain (domain)
This entry represents the RhiE branching domain, which is part of a non-canonical polyketide synthase (PKS) module found in the endofungal bacterium Burkholderia rhizoxinica. Unlike typical PKS modules, RhiE catalyzes a Michael-type acetyl addition to generate a branch in the carbon chain, expanding the biosynthetic scope of polyketide biosynthesis. The module consists of a ketosynthase domain, an acyl carrier protein domain, and a cryptic branching ('B') domain in between, featuring a double hot dog (DHD) fold that is structurally homologous to the product template domain of a fungal PKS. The RhiE B domain alone is not sufficient to catalyze the Michael addition, and mutagenesis experiments revealed a crucial role of the ketosynthase domain in branching the carbon chain.
Pfam PF00833: Ribosomal S17 (family)
A number of eukaryotic and archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, eS17 (RPS17) . They include, vertebrate, Drosophila and Neurospora crassa (crp-3) eS17's as well as yeast eS17a (RP51A) and eS17b (RP51B)  and archaebacterial eS17 .
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 PF07450: Formate hydrogenlyase maturation protein HycH (family)
This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form.
Pfam PF03042: Birnavirus VP5 protein (family)
Birnaviruses are ds RNA viruses. Non structural protein VP5 is found in RNA segment A. The function of this small viral protein is unknown. The proteins are about 150 amino acids long and contain several conserved histidines and cysteines that might form a zinc binding site (Bateman A pers. obs.).
Wikipedia: Birnaviridae is a family of double-stranded RNA viruses. Salmonid fish, birds and insects serve as natural hosts. There are currently 11 species in this family, divided among seven genera. Diseases associated with this family include infectious pancreatic necrosis in salmonid fish, which causes significant losses to the aquaculture industry, with chronic infection in adult salmonid fish and acute viral disease in young salmonid fish.
Pfam PF15866: Domain of unknown function (DUF4729) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in insects. Proteins in this family are typically between 238 and 666 amino acids in length. This domain has been identified as structurally similar to TRAF-like domains ([pfam:PF03145]).
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 PF08648: U4/U6.U5 small nuclear ribonucleoproteins (family)
This is a family of eukaryotic proteins including U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein may play a role in mRNA splicing.
Pfam PF20641: TAF1C, beta-propeller (repeat)
This is the beta-propeller domain of TAF1C from mammals, the orthologue of yeast Rrn6. TAF1C is a component of the transcription factor SL1/TIF-IB complex which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription.
Pfam PF11761: Cobalamin biosynthesis central region (domain)
Members of this family are involved in cobalamin synthesis. The gene encoded by [swissprot:P72862] has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF13375: RnfC Barrel sandwich hybrid domain (domain)
This domain is part of the barrel sandwich hybrid superfamily. It is found at the N-terminus of the RnfC Electron transport complex protein. It appears to be most related to the N-terminal NQRA domain ([pfam:PF05896]).
Pfam PF06780: Erp protein C-terminus (family)
This family represents the C-terminus of bacterial Erp proteins that seem to be specific to Borrelia burgdorferi (a causative agent of Lyme disease). Borrelia Erp proteins are particularly heterogeneous, which might enable them to interact with a wide variety of host components.
Pfam PF03035: Calicivirus putative RNA polymerase/capsid protein (family)
This entry represents Minor capsid protein VP2 from Caliciviruses. VP2 is a minor structural protein that forms a portal-like structure at a unique three-fold axis of symmetry, following binding to the host receptor . This structure contains twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. VP2 is known to be essential for productive replication that results in the synthesis and maturation of infectious virions and thus critical for the production of infectious virus .
Caliciviruses are a small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity.
Pfam PF18724: Amino acid:DNA transferase (domain)
This entry represents the alpha-helical domain of the glycinyl, putrescine and serinyltransferases (grouped as amino acid:DNA transferases, formerly known as alpha-putrescinyl/glutamylthymidine pyrophosphorylases (aGPT-Pplases)) which catalyse thymidine hypermodifications in the viral genome, transferring glycine, putrescine or serine to 5-phosphomethyl-2'-deoxyuridine (5-PmdU) to produce Nalpha-GlyT, Nalpha-PutT and O-SerT, respectively. These modifications probably prevent degradation of the viral genome by the host restriction-modification antiviral defense system.
Pfam PF08984: Domain of unknown function (DUF1858) (domain)
This domain has no known function. It is found in various hypothetical bacterial 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.
Pfam PF12660: Putative zinc-finger of transcription factor IIIC complex (domain)
This zinc-finger domain is at the very C-terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions.
Pfam PF06255: Neisseria toxin MafB (family)
MafB constitutes a family of secreted toxins in pathogenic Neisseria species, probably involved in interbacterial competition. Genes immediately downstream of mafB encode a specific immunity protein (MafI). MafB proteins exhibit a signal peptide sequence, a N-terminal conserved domain and a C-terminal variable region. Toxic domains identified at the C terminus include [pfam:PF15542], [pfam:PF14437], [pfam:PF15524], and [pfam:PF14436].
Pfam PF04285: Protein of unknown function (DUF444) (family)
Bacterial protein of unknown function. One family member ([swissprot:Q97LI1]) is predicted to contain a von Willebrand factor (vWF) type A domain (Smart:VWA). Another family member YeaH is predicted  to be part of a conserved signalling pathway with the kinase YeaG  and the SpoVR protein YcgB. The pathway may be involved in nitrogen  metabolism (see Supplementary note 5 in.)
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 PF03306: Alpha-acetolactate decarboxylase (domain)
Alpha-acetolactate decarboxylase converts acetolactate into acetoin. In Streptococcus thermophilus, it regulates leucine and valine biosynthesis by diverting the flux of alpha-acetolactate towards acetoin when the branched-chain amino acids are present in high concentration .
Pfam PF23515: YibY (family)
This protein family includes Protein YibY from Escherichia coli, a 36-residues micropeptide encoded by a small open reading frame (smORF) that is found antisense to waaL. Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF06235: NADH dehydrogenase subunit 4L (NAD4L) (family)
This family consists of NADH dehydrogenase subunit 4L (NAD4L) proteins from the mitochondria of several parasitic flatworms.
Pfam PF11383: Protein of unknown function (DUF3187) (domain)
This family of proteins with unknown function appear to be restricted to Proteobacteria. These proteins are likely to be outer membrane 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.
Pfam PF12316: Segment polarity protein dishevelled (Dsh) C terminal (family)
This domain family is found in eukaryotes, and is typically between 177 and 207 amino acids in length. The family is found in association with [pfam:PF00778], [pfam:PF02377], [pfam:PF00610], [pfam:PF00595]. The segment polarity gene dishevelled (dsh) is required for pattern formation of the embryonic segments. It is involved in the determination of body organisation through the Wingless pathway (analogous to the Wnt-1 pathway).
Pfam PF12022: COG complex component, COG2, C-terminal (repeat)
The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function. It is necessary for retrograde trafficking in the Golgi apparatus and for protein glycosylation. COG complex, together with exocyst, Golgi-associated retrograde protein (GARP) and Dsl1 complexes, is a member of the CATHR (complexes associated with tethering containing helical rods) family sharing an evolutionary origin and structural features. This domain represents the C-terminal of COG complex subunit 2 and consists of a conserved alpha-helical bundle. In Arabidopsis, COG2 forms a complex with FPP3/VETH1 and FPP2/VETH2 and ensures the correct secondary cell wall (SCW) deposition pattern by recruiting exocyst components to cortical microtubules in xylem cells during secondary cell wall deposition.
Pfam PF21885: TMEM181, GOLD domain (domain)
This is the N-terminal domain of TMEM181, which is a Golgi-dynamics (GOLD) domain. The function of this protein is not yet known. It is homologous to GPR180, TMEM145, and WLS which, together with TMEM87A/B, GPR107 and GPR108, they have been grouped as GOLD domain seven-transmembrane helix (GOST) proteins as they share the same domain architecture.
Pfam PF21915: Sputnik virophage major capsid protein 1st domain (domain)
This entry represents the first jelly roll domain in the sputnik virophage major capsid protein. Sputnik is a dsDNA virus, referred to as a virophage, that is co-assembled with Mimivirus in the host amoeba. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double jelly-roll major capsid proteins creating pseudohexameric capsomer symmetry.
Pfam PF01399: PCI domain (domain)
This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Pfam PF19905: Domain of unknown function (DUF6378) (domain)
This domain of unknown function is found in proteins from bacteria and phages which are functionally uncharacterised. This domain is about 100 amino acids in length. It contains two conserved sequence motifs, KxxR and DxxxDxxGY.
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 PF13764: E3 ubiquitin-protein ligase UBR4 (family)
This is a family of E3 ubiquitin ligase enzymes.
Pfam PF05756: S-antigen protein (domain)
This domain is found at the N terminus of S-antigen proteins from Plasmodium falciparum. S-antigens are heat stable proteins that are found in the blood of individuals infected with malaria.