SII-SWORD/CoKE huggingface dataset:
Pfam PF23952: Endo-beta-N-acetylglucosaminidase EndoS LRR domain (repeat)
This entry represents the leucine-rich repeat domain found in Endo-beta-N-acetylglucosaminidase EndoS from Streptococcus spp. EndoS is a secreted protein that catalyzes the hydrolysis of the N-linked oligosaccharides on opsonizing immunoglobulin G, thus contributing to immune response evasion and increased survival of the bacteria in patients. The function of this domain is unknown.
Pfam PF20733: Dimerization domain in LRIM1 (coiled_coil)
This entry represents the C-terminal coiled-coil dimerisation region of the anopheles LRIM protein. This region heterodimerises with a region of the APL1C protein. LRIM1 and APL1C are members of a family of proteins secreted by mosquitoes that contain an N-terminal LRR domain followed by a cysteine-rich region and a variable C terminus.
Pfam PF23508: MBB1 (family)
This protein family includes the uncharacterised protein MBB1 from Saccharomyces cerevisiae and similar fungal sequences. MBB1 is a small protein that may be involved in metabolic processes.
Pfam PF00508: E2 (early) protein, N terminal (family)
E2 is an early regulatory protein found in the dsDNA papillomaviruses. E2 regulates viral transcription and DNA replication. It binds to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory region. It can either activate or repress transcription, depending on E2RE's position with regard to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E1-E2 dimer complex binds to the origin of DNA replication .
Pfam PF03742: PetN (family)
PetN is a small hydrophobic protein, crucial for cytochrome b6-f complex assembly and/or stability.
Pfam PF18386: Roquin II domain (domain)
The ROQ domain is composed of three subdomains, I, II and III. This entry describes the second domain, ROQ II. Structural analysis reveals similarity of domain II to the helix-turn-helix (HTH) fold. Mutagenesis and biochemical studies show that that the HTH fold in domain II contributes to binding dsRNA at the 5'arm.
Pfam PF13886: TM7S3/TM198-like domain (domain)
This domain is found at the C-terminal end of human Transmembrane 7 superfamily member 3 (TM7SF3), which is is involved in the inhibition of cytokine-induced death of pancreatic beta cells, towards the N terminus of human Transmembrane protein 198 (TM198), which plays a role in Wnt signalling and in similar proteins mainly found in animal, fungi and bacteria. This domain is predicted to adopt an all alpha-helical structure.
Pfam PF22256: BDI_1685-like, C-terminal domain (repeat)
This domain is found at the C-terminal end of BDI_1685 from Parabacteroides distasonis ([swissprot:A6LCM3]) and similar bacterial sequences. This domain is usually found associated with [pfam:PF17128].
Pfam PF10224: Short coiled-coil protein (coiled_coil)
This entry represents a highly conserved 100 residue coiled-coil region which is found in short coiled-coil protein (SCOC) in human and UNC-69 in Caenorhabditis elegans. In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities.  In C. elegans, this small, evolutionarily conserved coiled-coil domain-containing protein, UNC-69, acts as a binding partner of UNC-76. Together they participate in a common genetic pathway necessary for axon extension and cooperate to regulate the size and position of synaptic vesicles in axons. Moreover, both proteins colocalize as puncta in neuronal processes and mutations in UNC-69 preferentially disrupt membrane traffic within axons.
Pfam PF15203: TMEM95 family (family)
TMEM95 and its homologues can be found in eukaryotes. Proteins in this family are typically between 102 and 231 amino acids in length and they have a conserved LGG sequence motif. TMEM95 is a sperm membrane protein required for sperm-oocyte fusion and is essential for mammalian fertilisation.
Pfam PF20447: Family of unknown function (DUF6704) (family)
This family of presumed integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 76 and 89 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 PF17589: Family of unknown function (DUF5487) (family)
This is a family of unknown function found in Myoviridae.
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 PF15416: Domain of unknown function (DUF4623) (repeat)
This family of proteins is found in bacteria. Proteins in this family are approximately 470 amino acids in length. There are two conserved sequence motifs: HLL and RYL.
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 PF03690: Uncharacterised protein family (UPF0160) (family)
This entry includes MYG1 exonuclease from human and its orthologues. MYG1 is a 3'-5' exonuclease which cleaves in situ on specific transcripts in both nucleus and mitochondrion. It is involved in regulating spatially segregated organellar RNA processing, acting as a coordinator of nucleo-mitochondrial crosstalk. In nucleolus, processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, it processes 3'-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. Overexpression of MYG1 has been associated with the autoimmune disorder vitiligo, suggesting that MYG1 may play some role in human innate immunity. Studies in yeast suggested a potential antiviral function of MYG1.
Pfam PF11891: Protein RETICULATA-related (family)
This entry represents RETICULATA and related proteins from plants.  Arabidopsis RETICULATA protein is involved in differential  development of bundle sheath and mesophyll cell chloroplasts.
Pfam PF09338: Glycine/sarcosine/betaine reductase component B subunits (family)
This is a family of glycine reductase, sarcosine reductase and betaine reductases.  These enzymes catalyse the following reactions.  sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin Acetyl phosphate + NH(3) + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin.
Pfam PF23623: IRG7 N-terminal galactose binding domain (domain)
This domain is found N-terminal in the nematode IRG7 protein and related proteins. IRG7 is known as mediator of longevity in germlineless animals. It plays a role in the innate immunity, probably via the atf-7 pathway, and confer resistance to pathogenic bacteria. The domain represented by this entry is predicted to fold into a beta-sandwich with topology similar to galactose-binding domains.
Pfam PF19446: Family of unknown function (DUF5984) (family)
This entry represents a member of a biosynthetic gene cluster (BGC).  This BGC (BGC0000838) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the flexirubin biosynthetic gene cluster from Flavobacterium johnsoniae. This protein has no known function. It is found in Actinobacteria, Proteobacteria and Bacteroidetes. Proteins in this family are typically between 234 and 271 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 PF00432: Prenyltransferase alpha-alpha toroid domain (repeat)
The entry includes enzymes involved in the biosynthesis of various terpenes and the prenylation of proteins. Terpene cyclases/mutases catalyze the cyclization of squalene or oxidosqualene into various triterpenes, such as lanosterol, beta-amyrin, and hopene, which are crucial for sterol biosynthesis and other metabolic pathways. Protein prenyltransferase subunit beta enzymes facilitate the transfer of farnesyl or geranylgeranyl groups to specific cysteine residues in target proteins, which is essential for their proper localization and function. These processes are vital for cellular functions, including membrane integrity, signal transduction, and stress responses.
Wikipedia: Prenyltransferases (PTs) are a class of enzymes that transfer allylic prenyl groups to acceptor molecules. Prenyl transferases commonly refer to isoprenyl diphosphate syntheses (IPPSs). Prenyltransferases are a functional category and include several enzyme groups that are evolutionarily independent.
Pfam PF16845: Aspartic acid proteinase inhibitor (domain)
SQAPI, aspartic acid inhibitor first isolated from squash, inhibits a wide range of aspartic proteinases. This particular family of PAAPIs (proteinaceous aspartic acid inhibitors) seems to have evolved quite recently from an ancestral cystatin. Structurally it consists of a four-stranded anti-parallel beta-sheet gripping an alpha-helix in much the same manner that a hand grips a tennis racket. The unstructured N-terminus and the loop connecting beta-strands 1 and 2 are important for pepsin inhibition, but the loop connecting strands 3 and 4 is not.
Wikipedia: The cystatins are a family of cysteine protease inhibitors which share a sequence homology and a common tertiary structure of an alpha helix lying on top of an anti-parallel beta sheet. The family is subdivided as described below.
Pfam PF03378: CAS/CSE protein, C-terminus (repeat)
Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation.  Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localisation (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.
Wikipedia: In molecular biology, the CAS/CSE protein family is a family of proteins which includes mammalian cellular apoptosis susceptibility (CAS) proteins and yeast chromosome-segregation protein, CSE1. CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle, and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins, it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.
Pfam PF10534: Connector enhancer of kinase suppressor of ras (domain)
The CRIC - Connector enhancer of kinase suppressor of ras - domain functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis.
Pfam PF05275: Copper resistance protein B precursor (CopB) (family)
This family consists of several bacterial copper resistance proteins. Copper is essential and serves as cofactor for more than 30 enzymes yet a surplus of copper is toxic and leads to radical formation and oxidation of biomolecules. Therefore, copper homeostasis is a key requisite for every  organism. CopB serves to extrude copper when it approaches toxic levels.
Pfam PF03966: Trm112p-like protein (domain)
The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length.  The C terminus contains the strongest conservation.  Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices.
Pfam PF18802: CxC1 like cysteine cluster associated with KDZ transposases (domain)
A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.
Pfam PF03484: tRNA synthetase B5 domain (domain)
This domain is found in phenylalanine-tRNA synthetase beta subunits.
Wikipedia: In molecular biology, Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.
Pfam PF06210: Protein of unknown function (DUF1003) (family)
This family consists of several 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 PF04506: Rft protein (family)
This entry represents the Man(5)GlcNAc(2)-PP-dolichol translocation protein RFT1, and related proteins, requited for the translocation of lipid-linked oligosaccharides across the ER membrane . Rft1 may have a critical accessory role in translocating Man(5)GlcNAc(2)-PP-Dol in vivo .

Asymmetric lipid distribution is a fundamental characteristic of biological lipid bilayers, one such axample is the translocation of the Man5GlcNAc2-PP-Dol intermediate from the cytosolic side of the ER membrane to the lumen before the completion of the biosynthesis of Glc3Man9GlcNAc2-PP-Dol . RFT1 encodes an evolutionarily conserved protein required for this translocation.
Pfam PF03550: Outer membrane lipoprotein LolB (domain)
This protein, LolB, is known so far only in the gamma subdivision of the Proteobacteria. It is a processed, lipid-modified outer membrane protein. In Escherichia coli, lipoproteins are anchored to the periplasmic side of either the inner or outer membrane through N-terminal lipids, depending on the lipoprotein-sorting signal present at position 2 . Five Lol proteins are involved in the sorting and outer membrane localization of lipoproteins. LolCDE, an ATP binding cassette (ABC) transporter, in the inner membrane releases outer membrane-directed lipoproteins from the inner membrane in an ATP-dependent manner, leading to the formation of a water-soluble complex between the lipoprotein and LolA. The LolA-lipoprotein complex crosses the periplasm and then interacts with outer membrane receptor LolB, which is essential for the anchoring of lipoproteins to the outer membrane.
Pfam PF24797: WDR35/TULP4 N-terminal (repeat)
This entry represents a beta-propeller domain found at N-terminal of WDR35 (in which corresponds to the first one) and TULP4 proteins. TULP4 may be a substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex. WDR35 (also known as IFT121) is a component of the IFT-A complex, which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. Proteins in this entry are part of the non-core subcomplex, together with IFT43 and IFT139. This entry represents the second beta-propeller of WDR35. Knock-out WDR35 cells showed defective retrograde trafficking within cilia.
Pfam PF15523: Novel toxin 16 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an all-alpha helical fold and conserved (DNE)xxH motif and arginine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or Photorhabdus virulence cassette (PVC)-type secretion system.
Pfam PF09289: Follistatin/Osteonectin-like EGF domain (domain)
Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like fold.
Pfam PF04334: Protein of unknown function (DUF478) (family)
This family contains uncharacterised protein encoded on Trypanosoma kinetoplast minicircles.
Pfam PF19781: Family of unknown function (DUF6266) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length. There are two conserved sequence motifs: AMSY and DNS.
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 PF08676: MutL C terminal dimerisation domain (domain)
MutL and MutS are key components of the DNA repair machinery that corrects replication errors.  MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.
Pfam PF17871: AAA lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.
Pfam PF08855: Domain of unknown function (DUF1825) (domain)
This uncharacterised family of proteins are principally found in cyanobacteria.
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 PF19523: Family of unknown function (DUF6053) (family)
This entry describes 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 PF24828: Domain of unknown function (DUF7713) (domain)
This entry represents a protein domain that forms an intimate self-self dimer. The domain is found at the C-terminus of proteins that often have a [pfam:PF24735] 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 PF24536: NXPE family member 4-like, C-terminal domain (domain)
This domain is found at the C-terminal end of human NXPE family member 4 (NXPE4) and similar eukaryotic proteins, mainly from animals. This domain is predicted to adopt an alpha-beta structure with similarity to hydrolase domains.
Pfam PF21069: CRISPR-associated endonuclease Cas9 alpha-helical lobe (domain)
This entry represents the alpha-helical lobe of the Francisella novicida Cas9 protein.
Pfam PF04418: Domain of unknown function (DUF543) (domain)
This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long.  However the Arabidopsis homologue is over 300 residues long.  The presumed domain contains a conserved amino terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half 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 PF19191: HEF_HK domain (domain)
This is a dimerization and histidine phosphotransfer (DHp) domain found in Histidine Kinases (HK). This domain is belongs to the His_Kinase_A (CL0025) clan. HK domain architectures typically contain DHp domains adjacent to GHKL domains, such as HATPase_c ([pfam:PF02518]) and HATPase_c_3 ([pfam:PF13589]) which comprise the ATP-binding regions.