SII-SWORD/CoKE huggingface dataset:
Pfam PF23831: Coiled-coil region of unknown function (DUF7201) (coiled_coil)
This entry represents a family of phage proteins found to be associated with membranes, based on transmembrane region predictions.  They are typically around 110 amino acids in length with a C-terminal membrane helix. Many also contain predicted coiled-coil region spanning the rest of the protein. The specific function is unknown. However, it could play a role in membrane fusion.
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 PF08800: BT4734-like, N-terminal domain (domain)
This presumed domain is found mainly in bacteroidetes. In some instances it is at the N-terminal of ([pfam:PF05272]) such as in the product of BT4734 ([swissprot:Q89YJ7]) which is incorrectly named as Virulence protein E. The function of this domain is unknown.
Pfam PF18753: Nucleotide modification associated domain 2 (domain)
A beta-strand rich domain containing a conserved cysteine and charged residues predicted to play a role in modified DNA base biosynthesis.
Pfam PF04384: Iron-sulphur cluster assembly (family)
This family of proteins is likely to be involved in the assembly of iron-sulphur clusters. It may function as an adaptor protein. In Escherichia coli [swissprot:P0C0L9] forms part of the isc operon, which encodes genes involved in iron-sulphur cluster assembly. Its structure is entirely alpha helical, and it contains a modified wing-helix structure, usually found in DNA-binding proteins. It binds to Fe2+ and Fe3+ ions and to the cysteine desulfurase IscS, the same surface of the protein is involved in both binding to iron and to IscS.
Pfam PF15314: Proline-rich acidic protein 1, pregnancy-specific uterine (family)
PRAP, or proline-rich acidic protein 1, is a family of eukaryotic proteins. PRAP is abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. It is significantly down-regulated in hepatocellular carcinoma and right colon adenocarcinoma compared with the respective adjacent normal tissues. In the mouse it is expressed in the epithelial cells of the mouse and rat gastrointestinal tracts, and pregnant mouse uterus. This article describes the isolation, distribution, and functional characterization of the human homologue. PRAP was abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. PRAP plays an important role in maintaining normal growth suppression.
Pfam PF21597: Transcriptional regulator SbtR-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Transcriptional regulator (TetR/AcrR family) from Thermus thermophilus (SbtR) and similar sequences predominantly found in actinobacteria. This domain is found associated with [pfam:PF00440].
Pfam PF17909: Htr2 transmembrane domain (domain)
Archaebacterial photoreceptors mediate phototaxis by regulating cell motility through two-component signaling cascades like those found in chemotaxis signaling chains of enteric bacteria. The photoreceptor sensory rhodopsin II from N. pharaonis (NpSRII) in complex with its cognate transducer NpHtrII serves as a system for transmembrane signal transfer. This entry is for the transmembrane domain of the transducer HtrII. Studies suggest that conformation changes of the NpSRII/NpHtrII complex may be crucial for the mechanism of signal propagation spanning the membrane domain and feeding into the HAMP domain. Furthermore, HtrII in H. salinarum not only transmits the signal from the photoreceptor SRII but also operates as a chemoreceptor.
Pfam PF11294: Protein of unknown function (DUF3095) (family)
Some members in this bacterial family of proteins are annotated as adenylyl cyclase however this cannot be confirmed. Currently no function is known.
Wikipedia: Adenylate cyclase is an enzyme with systematic name ATP diphosphate-lyase . It catalyzes the following reaction:ATP = 3′,5′-cyclic AMP + diphosphate
Pfam PF17225: Domain of unknown function (DUF5300) (family)
This small family of proteins is functionally uncharacterized. It is found mainly in Firmicutes. Proteins in this family are around 130  amino acids in length. Based on NMR structure 2MCT, it forms an  alpha/beta structure with a 6 stranded antiparallel b-sheet planked  by a single alpha helix. The only protein with similar structures is  a putative lipoprotein (PDB code 4R7R).
Pfam PF14204: Ribosomal L18 C-terminal region (domain)
This domain is the C-terminal end of ribosomal L18/L5 proteins.
Pfam PF19609: Family of unknown function (DUF6114) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora  echinospora and appears to be predominantly found in actinobacteria  and firmicutes.
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 PF03165: MH1 domain (domain)
The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however.  Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx.
Pfam PF07937: Protein of unknown function (DUF1686) (family)
The members of this family are all hypothetical proteins of unknown function expressed by the eukaryotic parasite Encephalitozoon cuniculi GB-M1. The region in question is approximately 250 amino acids long.
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 PF02519: Auxin responsive protein (family)
This family consists of the protein products of the ARG7 auxin responsive genes family none of which have any identified functional role.
Pfam PF13574: Metallo-peptidase family M12B Reprolysin-like (domain)
This zinc-binding metallo-peptidase has the characteristic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B.
Pfam PF18259: Carbohydrate binding module 65 domain 1 (domain)
This domain is found in the non-catalytic carbohydrate binding module 65B (CMB65B) present in Eubacterium cellulosolvens. CBMs are present in plant cell wall degrading enzymes and are responsible for targeting, which enhances catalysis. CBM65s display higher affinity for oligosaccharides, such as cellohexaose, and particularly polysaccharides than cellotetraose, which fully occupies the core component of the substrate binding cleft. The concave surface presented by beta-sheet 2 comprises the beta-glucan binding site in CBM65s. C6 of all the backbone glucose moieties makes extensive hydrophobic interactions with the surface tryptophans of CBM65s. Three out of the four surface Trp are highly conserved. The conserved metal ion site typical of CBMs is absent in this CBM65 family.
Pfam PF07759: Protein of unknown function (DUF1615) (family)
This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family (e.g. [swissprot:Q8Z8Z7], [swissprot:Q8ZRF4]) are thought to be lipoproteins. Another member of this family ([swissprot:Q93SV8]) is thought to be involved in photosynthesis. Based on structure predictions (from AlphaFold and structural comparisons using DALI server), this family may have a lysozyme-like fold.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14681: Uracil phosphoribosyltransferase (domain)
This family includes the enzyme uracil phosphoribosyltransferase ([ec:2.4.2.9]). This enzyme catalyzes the first step of UMP biosynthesis.
Wikipedia: Uracil phosphoribosyltransferase is an enzyme which creates UMP from uracil and phosphoribosylpyrophosphate. This protein may use the morpheein model of allosteric regulation.
Pfam PF03221: Tc5 transposase DNA-binding domain (domain)
The CENPB-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 70-75 amino acids, present in eukaryotic centromere proteins and transposases. The domain is named after the mammalian major centromere autoantigen B or centromere protein B (CENP-B), which is a fundamental centromere component of chromosomes. The N terminus of CENP-B contains two DNA-binding HTH domains, which bind to adjacent major grooves of DNA. The N terminus of CENP-B is formed by a psq-type HTH domain and C-terminal to this domain lies the CENPB-type HTH domain. These two HTH domains together bind specifically to a 17-base-pair sequence, the CENP-B box, which occurs in alpha-satellite DNA in human centromeres .

The structure of the CENPB-type HTH domain is composed of three Î±-helices. The second and third helices connected via a turn comprise the helix-turn-helix motif. Helix 3 is termed the recognition helix as it binds the DNA major groove, like in other HTHs. In CENP-B this domain recognises site 3 of the CENP-B box, while the preceding psq-type HTH binds site 1 of the CENP-B box, and a connecting linker loop binds in the minor groove of DNA and recognises site 2 .

Some proteins known to contain a CENPB-type HTH domain:


 * Mammalian centromere protein B (CENP-B), associated with the centromere and specifically binding DNA to the CENP-B box.
 * Mammalian jerky protein, involved in epileptic seizures in mice .
 * Mammalian Pogo transposases  and tigger transposable elements .
 * Fission yeast ARS-binding protein 1 (abp1)  and CENP-B homologue proteins (CBHP-1 and 2), which are centromere proteins .
 * Candida albicans protein PDC2 (Pyruvate DeCarboxylase 2) .
 * Fungal transposases.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF10003: Integral membrane protein (DUF2244) (family)
This domain, found in various bacterial hypothetical and putative membrane 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 PF21886: BRF2-like, C-terminal cyclin repeat (repeat)
This domain is found in human Transcription factor IIIB 50 kDa subunit (BRF2) and similar sequences mainly found in eukaryotes. BRF2 is a general activator of RNA polymerase III transcription. This protein consists of an N-terminal zinc ribbon ([pfam:PF08271]), a core domain consisting of two cyclin fold imperfect repeats and a C-terminal domain. This entry represents the second or C-terminal cyclin repeat.
Pfam PF20325: Family of unknown function (DUF6620) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 366 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 PF13853: Olfactory receptor (family)
The members of this family are transmembrane olfactory receptors.
Wikipedia: Olfactory receptors (ORs), also known as odorant receptors, are chemoreceptors expressed in the cell membranes of olfactory receptor neurons and are responsible for the detection of odorants which give rise to the sense of smell. Activated olfactory receptors trigger nerve impulses which transmit information about odor to the brain. In vertebrates, these receptors are members of the class A rhodopsin-like family of G protein-coupled receptors (GPCRs). The olfactory receptors form the largest multigene family in vertebrates consisting of around 400 genes in humans and 1400 genes in mice. In insects, olfactory receptors are members of an unrelated group of ligand-gated ion channels.
Pfam PF19237: Family of unknown function (DUF5889) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF16236: Domain of unknown function (DUF4895) (family)
A small family of uncharacterized proteins around 250 residues in length and found in various Thermotoga species. The function of this family is unknown.
Pfam PF20280: C-terminal domain 4 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF19028: Spondin-like TSP1 domain (domain)
This entry represents a sub-type of TSP1 domains that have an alternative disulphide binding pattern compared to the canonical TSP1 domain.
Pfam PF13987: YedD-like protein (family)
This family of proteins related to the YedD protein is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins are lipoproteins.
Pfam PF24950: Dep-1 sixth Fn3-like domain (domain)
This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the beta-integrin subunit pat-3. It is involved in the regulation of the  cell fate during the development of the vulva and the excretory system. It is also involved indirectly in the negative regulation of let-23 signaling and vulval induction. Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem. This entry represents the sixth of them.
Pfam PF05507: Microfibril-associated glycoprotein (MAGP) (family)
This family consists of several mammalian microfibril-associated glycoprotein (MAGP) 1 and 2 proteins. MAGP1 and 2 are components of elastic fibres. MAGP-1 has been proposed to bind a C-terminal region of tropoelastin, the soluble precursor of elastin. MAGP-2 was found to interact with fibrillin-1 and -2, as well as fibulin-1, another component of elastic fibres this suggests that MAGP-2 may be important in the assembly of microfibrils.
Pfam PF00606: Herpesvirus Glycoprotein B ectodomain (domain)
This domain corresponds to the ectodomain of glycoprotein B according to ECOD.
Wikipedia: Herpesvirus glycoprotein B is a viral glycoprotein that is involved in the viral cell entry of Herpes simplex virus (HSV). Herpesviruses have a lipid bilayer, called the envelope, which contains twelve surface glycoproteins. For infectivity to be attained, the double stranded DNA genome of HSV must enter the host cell through means of fusion of its envelope with the cellular membrane or via endocytosis. Other viral glycoproteins involved in the process of viral cell entry include gC, gB, gD, gH, and gL, but only gC, gB, gD, and gH are required for the fusion of the HSV's envelope with the cellular membrane. It can be noted that all herpesviruses have glycoproteins gB, gH, and gL.
Pfam PF01081: KDPG and KHG aldolase (domain)
This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate  aldolase (KDPG-aldolase)
Pfam PF04857: CAF1 family ribonuclease (family)
The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 [swissprot:P39008] encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain [pfam:PF01424]. This family of proteins is related to other exonucleases [pfam:PF00929] (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 ([swissprot:P39008]) has been resolved at 2.3 Angstrom resolution.
Pfam PF23767: Domain of unknown function (DUF7166) (domain)
This protein domain is found in a variety of staphylococcus phage. It is composed of two alpha helices and a beta hairpin and shows weak structural similarity to archaeal prefoldins. The function of this protein 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 PF00616: GTPase-activator protein for Ras-like GTPase (family)
All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position.
Wikipedia: GTPase-activator protein for Ras-like GTPase is a family of evolutionarily related proteins. Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras.
Pfam PF02899: Phage integrase, N-terminal SAM-like domain (domain)
Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment .

The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104).
Pfam PF22021: RbmA-like, FnIII domain (domain)
This entry represents both fibronectin type III (FnIII) domains found in RbmA protein from Vibrio cholerae ([swissprot:Q9KTH4]), a biofilm matrix protein essential for both maintenance of rugose colony morphology and development of wild-type biofilm architecture. RbmA contains two FnIII domains connected by a linker segment. The two folds run antiparallel to each other but do not form extensive interactions. Each FnIII domain shows a beta-sandwich comprised of three beta-sheets plus four beta-sheets.
Pfam PF11262: Transcription factor/nuclear export subunit protein 2 (family)
THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability. Tho2, along with four other subunits forms THO
Pfam PF18816: Importin repeat (repeat)
The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam  entry includes a single repeat unit and includes sequences not  captured by [pfam:PF18808].
Pfam PF09245: Mycoplasma arthritidis-derived mitogen (domain)
Mycoplasma arthritidis-derived mitogen (MA-Mit) adopts a completely alpha-helical structure consisting of ten alpha helices. It is a superantigen that can activate large fractions of T cells bearing particular TCR V-beta elements. Two MA-Mit molecules form an asymmetric dimer and cross-link two MHC antigens to form a dimerised MA-Mit-MHC complex.
Pfam PF24323: Domain of unknown function (DUF7494) (domain)
This domain is found in a group of uncharacterised proteins mainly from Epsilonproteobacteria. It is predicted to adopt a globular structure with a beta-sandwich topology.
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 PF12202: Oxidative-stress-responsive kinase 1 C-terminal domain (domain)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00069]. There is a single completely conserved residue F that may be functionally important. OSR1 is involved in the signalling cascade which activates Na/K/2Cl cotransporter during osmotic stress. This domain is the C terminal domain of OSR1 which recognises a motif (Arg-Phe-Xaa-Val) on the OSR1-activating protein WNK1.