SII-SWORD/CoKE huggingface dataset:
Pfam PF22675: KHDC4/BBP-like, KH-domain type I (domain)
This entry represents eukaryotic type I KH domain. The core KH domain is accompanied by additional alpha-helix and beta-sheet motifs at the C terminus. This entry includes proteins involved in pre-mRNA splicing such as KH domain-containing BBP from fungi, KH homology domain-containing protein 4 (KHDC4, also known as BLOM7) and splicing factor 1 (SF1) from animals, and homologues from plants, including RIK. KHDC4 interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. It binds preferentially RNA with A/C rich sequences and poly-C stretches. Branchpoint binding proteins (BBP) from fungi and its mammalian homologue SF1 are required for pre-spliceosome formation.
Pfam PF20186: Family of unknown function (DUF6549) (family)
This presumed domain is functionally uncharacterised. This domain family is mainly found in bacteria, and is typically between 120 and 180 amino acids in length. There are two highly conserved residues, an aspartate and a tryptophan, and a NP conserved motif.
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 PF18069: DR2241 stabilising domain (domain)
This is the middle domain found in DR2241, a multi-domain protein with an N-terminal cobalamin (vitamin B12) chelatase domain. DR2241 is found in D. radiodurans. The middle domain has four alpha-helices (alpha7-alpha10) in contact with the N-terminal domains and C-terminal domain and five anti-parallel beta-strands with strand order 12354 at the outer side of one monomer. The middle domain, as well as the C-terminal domain, are heavily involved in the tetramer stabilisation.
Pfam PF07545: Vestigial/Tondu family (family)
The mammalian TEF and the Drosophila scalloped genes belong to a conserved family of transcriptional factors that possesses a TEA/ATTS DNA-binding domain. Transcriptional activation by these proteins likely requires interactions with specific coactivators. In Drosophila, Scalloped (Sd) interacts with Vestigial (Vg) to form a complex, which binds DNA through the Sd TEA/ATTS domain. The Sd-Vg heterodimer is a key regulator of wing development, which directly controls several target genes and is able to induce wing outgrowth when ectopically expressed. This short conserved region is needed for interaction with Sd.
Pfam PF22938: Integrase p58, C-terminal domain (domain)
This domain is found at the C-terminal end of Integrase p58, the last chain cleaved from the Transposon Ty3-G Gag-Pol polyprotein from Saccharomyces cerevisiae. This domain, found C-terminal to [pfam:PF17919], is also called SH3 domain. Proteins in this group are found in eukaryota.
Pfam PF14654: Mucin, cleavage site, TM and cytoplasmic tail region (domain)
This family represents the non-tandem repeat domain including cleavage site, the transmembrane helix domain, and the cytoplasmic tail of epiglycanin and related mucins.
Pfam PF10493: Rough deal protein C-terminal region (repeat)
Rod, the Rough deal protein, displays a dynamic intracellular staining pattern, localising first to kinetochores in pro-metaphase, but moving to kinetochore microtubules at metaphase. Early in anaphase the protein is once again restricted to the kinetochores, where it persists until the end of telophase. This behaviour is in all respects similar to that described for ZW10, and indeed the two proteins function together, localisation of each depending upon the other. These two proteins are found at the kinetochore in complex with a third, Zwilch, in both flies and humans. The C-terminus is the most conserved part of the protein. During pro-metaphase, the ZW10-Rod complex, dynein/dynactin, and Mad2 all accumulate on unattached kinetochores; microtubule capture leads to Mad2 depletion as it is carried off by dynein/dynactin; ZW10-Rod complex accumulation continues, replenishing kinetochore dynein. The continuing recruitment of the ZW10-Rod complex during metaphase may serve to maintain adequate dynein/dynactin complex on kinetochores for assisting chromatid movement during anaphase. The ZW10-Rod complex acts as a bridge whose association with Zwint-1 links Mad1 and Mad2, components that are directly responsible for generating the diffusible 'wait anaphase' signal, to a structural, inner kinetochore complex containing Mis12 and KNL-1AF15q14, the last of which has been proved to be essential for kinetochore assembly in C. elegans. Removal of ZW10 or Rod inactivates the mitotic checkpoint.
Pfam PF22404: ToxT, N-terminal cupin-like domain (domain)
This entry represents a cupin-like domain present in ToxT from Vibrio Cholerae. ToxT serves as the culminating factor in the  regulatory pathway, ensuring the coordinated production of two virulence factors: the toxin-coregulated pilus (TCP) and cholera toxin (CT), which are crucial for the pathogenicity of V. cholerae in causing cholera. ToxT possesses dimerization and regulatory elements in its cupin-like N-terminal domain, while its C-terminus harbors two HTH AraC-like DNA binding domains.
Pfam PF03881: Fructosamine kinase (family)
This family includes eukaryotic fructosamine-3-kinase enzymes. The family also includes bacterial members that have not been characterised but probably have a similar or identical function.
Wikipedia: In molecular biology the fructosamine kinase family is a family of enzymes. This family includes eukaryotic fructosamine-3-kinase enzymes which may initiate a process leading to the deglycation of fructoselysine and of glycated proteins and in the phosphorylation of 1-deoxy-1-morpholinofructose, fructoselysine, fructoseglycine, fructose and glycated lysozyme. The family also includes ketosamine-3-kinases (KT3K). Ketosamines derive from a non-enzymatic reaction between a sugar and a protein. Ketosamine-3-kinases (KT3K) catalyse the phosphorylation of the ketosamine moiety of glycated proteins. The instability of a phosphorylated ketosamine leads to its degradation, and KT3K is thus thought to be involved in protein repair.
Pfam PF15313: Hexamethylene bis-acetamide-inducible protein (family)
HEXIM is a transcriptional regulator that functions as a general RNA polymerase II transcription inhibitor. In cooperation with 7SK snRNA it sequesters P-TEFb in a large inactive 7SK snRNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. HEXIM may also regulate NF-kappa-B, ESR1, NR3C1 and CIITA-dependent transcriptional activity.
Pfam PF15375: Domain of unknown function (DUF4602) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 173 and 294 amino acids in length. This family includes Human C1orf131.
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 PF24807: CDC20/Fizzy WD40 domain (repeat)
This entry represents the beta-propeller found in WD40 protein Cdc20/Fizzy, a protein that associates and phosphorylates anaphase promoting complex/cyclosome (APC/C) at the end of mitosis. It is required for full ubiquitin ligase activity of the APC/C and confers substrate specificity upon the complex.
Pfam PF03008: Archaea bacterial proteins of unknown function (family)
This entry represents a domain of unknown function found in bacterial and archaeal sequences. In some instances it is fused to a prokaryotic putative DEXX-box ATPase domain, found at its C-terminal (IPR011579) .
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 PF06050: 2-hydroxyglutaryl-CoA dehydratase, D-component (family)
Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate.
Pfam PF10685: Stress-induced bacterial acidophilic repeat motif (family)
This repeat is found in proteins which are expressed under conditions of stress in bacteria. The repeat contains a highly conserved, characteristic sequence motif,KGG, that is also recognised by plants and lower eukaryotes and repeated in their LEA (late embryogenesis abundant) family of proteins, thereby rendering those proteins bacteriostatic. An example of such an LEA family is LEA_5, [pfam:PF00477]. Further downstream from this motif is a Walker A, nucleotide binding, motif GXXXXGK(S,T), that in YciG of E coli, eg [swissprot:Q8X7B4], is QSGGNKSGKS [URL]. YciG is expressed as part of a three-gene operon, yciGFE, and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress.
Pfam PF24319: Coiled-coil region of unknown function (DUF7491) (coiled_coil)
This is a coiled-coil region found at the C-terminal of a group of uncharacterised sequences from 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 PF17635: Betacoronavirus uncharacterised protein 14 (SARS-CoV-2 like) (family)
This family contains proteins found in SARS and SARS-like coronaviruses. It includes uncharacterised protein 14 from SARS coronavirus 2 (SARS-CoV-2), human SARS coronavirus (SARS-CoV) and bat coronavirus Rp3/2004 (SARS-like coronavirus Rp3). In SARS-CoV, orf14 is completely contained within the ORF encoding the nucleocapsid protein (N). In SARS-CoV-2 uncharacterised protein 14 is predicted to contain one transmembrane helix.
Pfam PF18830: Large polyvalent protein-associated domain 16 (domain)
This is an alpha and beta fold domain that is mainly found in polyvalent proteins of conjugative elements.
Pfam PF09460: Saf-pilin pilus formation protein (domain)
This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N-terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N-terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit.
Wikipedia: Pilin refers to a class of fibrous proteins that are found in pilus structures in bacteria. These structures can be used for the exchange of genetic material, or as a cell adhesion mechanism. Although not all bacteria have pili or fimbriae, bacterial pathogens often use their fimbriae to attach to host cells. In Gram-negative bacteria, where pili are more common, individual pilin molecules are linked by noncovalent protein-protein interactions, while Gram-positive bacteria often have polymerized LPXTG pilin.
Pfam PF23976: Family of unknown function (DUF7302) (family)
This entry represents a family of uncharacterised phage proteins that have a small N-terminal domain composed of three beta strands and an alpha helix.
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 PF11475: Virion protein N terminal domain (family)
This is the N terminal domain of a family of virion proteins which contains a zinc finger domain. Currently no function is known.
Pfam PF16210: Keratin type II cytoskeletal 1 tail (disordered)
All intermediate filament proteins feature a central Î±-helical rod domain and variable nonhelical domains located at the N-terminal (head) and C-terminal (tail). The central rod domain is the main driver of self-assembly into filaments, whereas the N- and C-terminal domains are involved in post-translational modifications and interactions with other proteins . Keratin 1 (KRT1) belongs to a large family of intermediate filament protein genes and is normally expressed in keratinocytes in the spinous layer of the epidermis . This entry represents the C-terminal domain (tail) of type II keratin KRT1.
Pfam PF25146: Vertebrate GH3, N-terminal domain (domain)
This domain is found at the N-terminal end of human GH domain -containing protein and similar sequences from vertebrates. This domain is normally found associated with [pfam:PF23571] and [pfam:PF23572].
Pfam PF18417: L-lysine epsilon oxidase C-terminal domain (domain)
This is the C-terminal domain of L-Lysine epsilon-oxidase (LodA, EC 1.4.3.20), an enzyme which catalyses the oxidative deamination of free L-lysine into L-2-aminoadipate 6-semialdehyde, ammonia and hydrogen peroxide.
Pfam PF24127: Domain of unknown function (DUF7395) (domain)
This entry represents a small family of uncharacterised phage proteins, that includes the L1 protein from Lactococcus phage c2 [swissprot:Q38296]. Structure prediction indicates this small protein adopts a compact domain composed of a three stranded sheet with a single alpha helix.
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 PF05804: Kinesin-associated protein (KAP) (repeat)
This family consists of several eukaryotic kinesin-associated (KAP) proteins. Kinesins are intracellular multimeric transport motor proteins that move cellular cargo on microtubule tracks. It has been shown that the sea urchin KRP85/95 holoenzyme associates with a KAP115 non-motor protein, forming a heterotrimeric complex in vitro, called the Kinesin-II. It includes kinesin-associated protein 3 (KAP3, also known as SMAP). In human and mouse, KAP3 is involved in tethering the chromosomes to the spindle pole and in chromosome movement. It binds to the tail domain of the KIF3A/KIF3B heterodimer to form a heterotrimeric KIF3 complex and may regulate the membrane binding of this complex.
Pfam PF16434: Domain of unknown function (DUF5031) (family)
This family consists of several uncharacterized proteins around 380 in length and is mainly found in Bacteroides fragilis and sp. 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 PF01865: Protein of unknown function DUF47 (family)
This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Sinorhizobium meliloti [swissprot:O30498]. However, the function of this protein is also unknown (Pit stands for Phosphate transport). It is probably distantly related to [pfam:PF01895] (personal obs:Yeats C).
Pfam PF22173: Acylamino-acid-releasing enzyme-like, N-terminal domain (repeat)
This domain is found at the N-terminal end of Acylamino-acid -releasing enzyme from Aeropyrum pernix (APH) and similar archaeal sequences. APH catalyses the removal of an N-acylated amino acid from peptides. This domain folds as a regular seven-bladed beta-propeller.
Pfam PF10400: Virulence activator alpha C-term (family)
This structure is homo-dimeric, and the domain here is the C-terminal half of the structure, often associated with PadR upstream, ([pfam:PF03551]), which is a transcriptional regulator.
Pfam PF18951: Family of unknown function (DUF5695) (family)
This is a family of unknown function mainly found in fungi and bacteria.
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 PF03459: TOBE domain (domain)
The TOBE domain (Transport-associated OB) always occurs  as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (eg [swissprot:P46930]) and sulfate ([swissprot:P16676]). Found in ABC transporters immediately  after the ATPase domain.
Pfam PF13704: Glycosyl transferase family 2 (family)
Members of this family of prokaryotic proteins include putative glucosyltransferases,
Pfam PF03710: Glutamate-ammonia ligase adenylyltransferase (domain)
Conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase  (ADP-forming)}. The family is related to the  [pfam:PF01909] domain.
Pfam PF11129: Rev protein of equine infectious anaemia virus (family)
The sequence of this family is highly conserved and carries a nuclear export signal from residues 31-55, and RNA binding/nuclear localisation signals of RRDR at residue 76 and KRRRK at residue 159. Rev is an essential regulatory protein required for nucleocytoplasmic transport of incompletely spliced viral mRNAs that encode structural proteins. Rev has been shown to down-regulate the expression of viral late genes and alter sensitivity to Gag-specific cytotoxic-T-lymphocytes (CTL). Equine infectious anaemia virus (EIAV) exhibits a high rate of genetic variation in vivo, and results in a clinically variable disease in infected horses.
Pfam PF19421: Furry protein C-terminal (domain)
This is the C-terminal domain of Furry (Fry) protein. Fry plays a crucial role in the structural integrity of mitotic centrosomes and in the maintenance of spindle bipolarity. This domain binds to polo-like kinase 1 (Plk1) through the polo-box domain (PBD) of Plk1 in a manner dependent on the cyclin-dependent kinase 1-mediated Fry phosphorylation, promoting Plk1 activity during early mitosis. Fry also binds to Aurora A and may function as a scaffold promoting the interaction between AURKA and PLK1, thereby enhancing AURKA-mediated PLK1 phosphorylation.
Pfam PF10956: Protein of unknown function (DUF2756) (family)
Some members in this family of proteins are annotated yhhA however currently no function is known. The family appears to be restricted to Enterobacteriaceae.
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 PF16045: LisH (domain)
The 33-residue LIS1 homology (LisH) motif is found in eukaryotic intracellular proteins involved in microtubule dynamics, cell migration, nucleokinesis and chromosome segregation. The LisH motif is likely to possess a conserved protein-binding function and it has been proposed that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly. The LisH motif is found associated to other domains, such as WD-40, SPRY, Kelch, AAA ATPase, RasGEF, or HEAT .

The secondary structure of the LisH domain is predicted to be two Î±-helices .
Wikipedia: In molecular biology, the LisH domain is a protein domain found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerisation motif, and that other structural elements are likely to play an important role in dimerisation.
Pfam PF17053: Genetic interactor of prohibitin 5 (family)
Genetic interactor of prohibitin 5 (GEP5), also known as required for respiratory growth protein5 (RRG5), has been shown to interact with prohibitin ring complexes in the mitochondrial inner membrane that regulate cell proliferation as well as the dynamics and function of mitochondria. It is required for mitochondrial genome maintenance and is essential for respiratory growth.
Pfam PF13536: Putative multidrug resistance efflux transporter (family)
This is a membrane protein family whose members are purported to be related to the DMT or Drug/Metabolite Transporter (DMT) Superfamily. Members are all uncharacterised.
Pfam PF11673: Protein of unknown function (DUF3269) (family)
This family of proteins has no known 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 PF18892: Family of unknown function (DUF5651) (domain)
This entry represents a probable zinc binding domain found at the C-terminus of some Firmicute bacteria.  The function of these proteins 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.