SII-SWORD/CoKE huggingface dataset:
Pfam PF09226: Restriction endonuclease HincII (domain)
Members of this family of prokaryotic restriction endonucleases recognise the double-stranded sequence 5'-GTYRAC-3' and cleave after Y-3. They catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Pfam PF04004: Leo1-like protein (family)
Members of this family are part of the Paf1/RNA polymerase II complex. The Paf1 complex probably functions during the elongation phase of transcription. The Leo1 subunit of the yeast Paf1-complex binds RNA and contributes to complex recruitment. The subunit acts by co-ordinating co-transcriptional chromain modifications and helping recruitment of mRNA 3prime-end processing factors.
Pfam PF09127: Leukotriene A4 hydrolase, C-terminal (repeat)
Members of this family adopt a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. They are required for the formation of a deep cleft harbouring the catalytic Zn2+ site in Leukotriene A4 hydrolase.
Pfam PF07475: HPr Serine kinase C-terminal domain (domain)
This family represents the C terminal kinase domain of Hpr Serine/threonine kinase PtsK.  This kinase is  the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria.  This kinase in unusual in that it  recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating  enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF20221: Family of unknown function (DUF6580) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 200 amino acids in length. Some members are hypothetical ECF transporters related to the Gx transporter superfamily (CL0315).
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 PF06297: PET Domain (domain)
This domain is suggested to be involved in protein-protein interactions. The family is found in conjunction with [pfam:PF00412].
Pfam PF06149: Protein of unknown function (DUF969) (family)
Family of uncharacterised bacterial 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 PF16430: Domain of unknown function (DUF5027) (family)
This family consists of several uncharacterised proteins around 180 in length and is mainly found in various Clostridiales species. The function of this family is unknown.
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 PF18901: Family of unknown function (DUF5657) (family)
This family of small integral membrane proteins is found in bacteria. Proteins in this family are approximately 80 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 PF21931: ABM-like domain (domain)
This domain is found in [swissprot:Q8KDY2] from Chlorobaculum tepidum and similar bacterial proteins. It adopts an alpha-beta configuration.
Pfam PF21346: PcRGLX-like protein C-terminal alpha/alpha toroid domain (repeat)
This family of proteins includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX). The family also includes YetA from B. subtilis is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length.  This entry represents the C-terminal alpha/alpha-toroid domain. Members of this family share a 3 domain architecture.
Pfam PF16743: Periplasmic lysozyme inhibitor of I-type lysozyme (domain)
This entry includes the PliI protein from Aeromonas hydrophila (PliI-Ah). PliI is a dimeric periplasmic protein that enables bacteria to resist permeabilisation of the outer membrane by the bactericidal action of lysozyme. PliI achieves its inhibitory action via an insertion of a loop containing the conserved SGxY motif into the active centre of I-type lysozymes .
Pfam PF15306: LIN37 (family)
LIN37 is a component of the DREAM (or LINC) complex which represses cell cycle-dependent genes in quiescent cells and plays a role in the cell cycle-dependent activation of G2/M genes.
Pfam PF19996: N-terminal helical region fused to the FtsH ternary system vWA domain (family)
Functionally Uncharacterized helical domain fused a the N-terminus of the ivWA domain, a core component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems.
Pfam PF16961: Putative OmpA-OmpF-like porin family (family)
This is a family of putative OmpA-OmpF-like porins from Bacteroidetes.
Pfam PF03798: TLC domain (domain)
TLC is a protein domain with at least 5 transmembrane Î±-helices. Lag1p and Lac1p are essential for acyl-CoA-dependent ceramide synthesis , TRAM is a subunit of the translocon and the CLN8 gene is mutated in Northern epilepsy syndrome. Proteins containing this domain may possess multiple functions such as lipid trafficking, metabolism, or sensing. Trh homologues possess additional homeobox domains .
Pfam PF11894: Nuclear pore complex scaffold, nucleoporins 186/192/205 (repeat)
This is a family of eukaryotic nucleoporins of several different sizes. All of them are long and form the scaffold of the nuclear pore complex. Nup192 in particular modulates the permeability of the central channel of the NPC central or nuclear pore complex.
Pfam PF23074: PH domain found in tandem in fungal proteins (domain)
This PH domain is found as the N-terminal one of a pair that is found in a family of uncharacterised fungal proteins.
Pfam PF01863: YgjP-like, metallopeptidase domain (family)
This is a conserved domain containing the catalytic zinc-metallopeptidase (HExxH) catalytic motif. Proteins containing this domain are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines. This domain is found in YgjP from E. coli, a predicted metal-dependent hydrolase that hydrolyses UTP to UMP and diphosphate in vitro; and in MJ0123 from Methanocaldococcus jannaschii (also referred to as projannalysin).
Pfam PF13430: Domain of unknown function (DUF4112) (family)
This family has several highly conserved GD sequence-motifs of unknown function. The family is found in bacteria, archaea and fungi.
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 PF14295: PAN domain (domain)
Plasma kallikrein (3.4.21.34) and coagulation factor XI (3.4.21.27) are two related plasma serine proteases activated by factor XIIA and which share the same domain topology: an N-terminal region that contains four tandem repeats of about 90 amino acids and a C-terminal catalytic domain. The 90 amino-acid repeated domain contains 6 conserved cysteines. It has been shown  that three disulfide bonds link the first and sixth, second and fifth, and third and fourth cysteines. The domain can be drawn in the shape of an apple and has been accordingly called the 'apple domain'.

The apple domains of plasma prekallikrein are known to mediate its binding to high molecular weight kininogen , the apple domains of factor XI bind to factor XIIa, platelets, kininogen, factor IX and heparin .

The apple domains display some sequence similarity with the N domain of plasminogen/hepatocyte growth factor (HGF) and to some nematode and protozoan proteins . They all belong to the same domain superfamily that have been called the PAN module . The N domain of hepatocyte growth factor binds to the c-Met receptor and to the heparin molecule. The structure of the PAN module of HGF has been solved. It contains a characteristic hairpin-loop structure stabilised by two disulfide bridges, Cys-1 and 6 are not conserved in HGF PAN modules .

Apart from the cysteines, there are a number of other conserved positions in the apple domain. This entry represents the PAN domain of the plasma kalllikrein/coagulation factor XI subgroup proteins.
Pfam PF08903: Domain of unknown function DUF1846, N-terminal (domain)
This domain is found in a family of proteins that are functionally uncharacterised, known as UPF0371. Some members of the family are annotated as ATP-dependent peptidases. This is a P-loop-like domain (pdbe:3BH1).
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 PF08699: Argonaute linker 1 domain (domain)
ArgoL1 is a region found in argonaute proteins. It normally co-occurs with [pfam:PF02179] and [pfam:PF02171]. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold.
Pfam PF20073: Domain of unknown function (DUF6469) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in plants, and is approximately 120 amino acids in length. It is found in hypothetical UvrD-like Helicases and related sequences, all containing a P-loop motif that is characteristic of the AAA superfamily. This domain is located towards the N-terminal, adjacent the AAA domain ([pfam:PF13086]). There are two conserved motifs, GD and RIW. There is also a highly conserved D residue.
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 PF06481: COX Aromatic Rich Motif (conserved_site)
COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It  transfers electrons from a quinol to the binuclear centre  of the catalytic subunit 1. The function of this region is not known.
Pfam PF12044: Putative peptidase family (family)
This family of proteins is functionally uncharacterised. However, it does contain an HEXXH motif characteristic of metallopeptidases. This protein is found mainly in  fungi. Proteins in this family are typically between 625 to 773 amino acids in length.
Pfam PF16706: Izumo-like Immunoglobulin domain (domain)
Izumo-Ig is the immunoglobulin domain on Izumo proteins from higher eukaryotes. Izumo is a typical type I membrane glycoprotein with one immunoglobulin-like domain and a putative N-glycoside link motif - glycosylation site. The full-length protein, eg [swissprot:Q8IYV9], is a molecule with a single immunoglobulin (Ig) domain. It is thought that Izumo proteins bind to putative Izumo receptors on the oocyte.  Izumo is not detectable on the surface of fresh sperm but becomes exposed only after an exocytotic process, the acrosome reaction, has occurred. Studies have shown that knock-out mice (Izumo-/- males) were sterile despite normal mating behaviour and ejaculation, indicating the importance of the protein in fertilisation. There is a conserved GCL sequence motif. Izumo expression has been found to be testis-specific.
Wikipedia: The immunoglobulin superfamily (IgSF) is a large protein superfamily of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. Molecules are categorized as members of this superfamily based on shared structural features with immunoglobulins ; they all possess a domain known as an immunoglobulin domain or fold. Members of the IgSF include cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins. They are commonly associated with roles in the immune system. Otherwise, the sperm-specific protein IZUMO1, a member of the immunoglobulin superfamily, has also been identified as the only sperm membrane protein essential for sperm-egg fusion.
Pfam PF17020: Domain of unknown function (DUF5097) (family)
This is a family of microsporidia-specific proteins of unknown function. There is the possibility of very distant homology to the WAC 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 PF23388: Domain of unknown function (DUF7099) (repeat)
This is a beta-propeller domain found in a group on uncharacterised proteins from fungi. The function of this domain is unknown.
Wikipedia: In structural biology, a beta-propeller (β-propeller) is a type of all-β protein architecture characterized by 4 to 8 highly symmetrical blade-shaped beta sheets arranged toroidally around a central axis. Together the beta-sheets form a funnel-like active site.
Pfam PF04621: PEA3 subfamily ETS-domain transcription factor N terminal domain (family)
The N terminus of the PEA3 transcription factors is implicated in transactivation and in inhibition of DNA binding. Transactivation is potentiated by activation of the Ras/MAP kinase and protein kinase A signalling cascades.  The N terminal region contains conserved MAP kinase phosphorylation sites.
Pfam PF19850: Family of unknown function (DUF6325) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 142 and 156 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 PF01025: GrpE (family)
Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. In prokaryotes the dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . GrpE participates actively in response to heat shock by preventing aggregation of stress-denatured proteins: unfolded proteins initially bind to DnaJ, the J-domain ATPase-activating protein (Hsp40 family), whereupon DnaK hydrolyzes its bound ATP, resulting in a stable complex. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle .

In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent. Over-expression of Hsp70 molecular chaperones is important in suppressing toxicity of aberrantly folded proteins that occur in Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis, as well as several polyQ-diseases such as Huntington's disease and ataxias.

The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPasemonomer . GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.
Wikipedia: GrpE is a bacterial nucleotide exchange factor that is important for regulation of protein folding machinery, as well as the heat shock response. It is a heat-inducible protein and during stress it prevents unfolded proteins from accumulating in the cytoplasm. Accumulation of unfolded proteins in the cytoplasm can lead to cell death.
Pfam PF20411: Domain of unknown function (DUF6697) (domain)
This entry represents a fungal domain 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 PF23513: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7ARG9] from the parasite Babesia bovis.
Pfam PF22977: Winged helix domain, variant (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to adopt a globular structure with similarity to MarR family of transcription factors ([pfam:PF12802]). This domain is found usually in combination with AAA ATPase domains ([pfam:PF00004]).
Pfam PF02881: SRP54-type protein, helical bundle domain (domain)
This entry represents the N-terminal helical bundle domain of the 54kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.

Other proteins with this domain include signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures (in conjunction with SRP) the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; and bacterial FtsY protein, which is believed to play a similar role to that played by the eukaryotic docking protein.
Pfam PF17487: Ribosomal protein S12 (family)
This is a family of unknown function. Family members are ribosomal proteins found in the mitochondria (RPS12). Homologus RPS12 proteins in bacterial ribosoms participate in stabilizing the second base pair of the codon-anticodon duplex in the A site and is likely to be critical for the fidelity of decoding process. A similar role can be anticipated for this protein in mitochondrial ribosomes. This has been shown where the product of edited RPS12 mRNA translation represented a component of the mitoribosome's small subunit.
Pfam PF15880: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (family)
NADH dehydrogenase [ubiquinone] flavoprotein 3 (NDUFV3) is a accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone .
Wikipedia: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial is an enzyme that in humans is encoded by the NDUFV3 gene.