SII-SWORD/CoKE huggingface dataset:
Pfam PF02194: PXA domain (family)
This domain is associated with PX domains [pfam:PF00787].
Pfam PF20665: Centromere/kinetochore protein zw10, middle domain (repeat)
Zw10 protein, in the context of the conserved Rod-Zwilch-Zw10 (RZZ) complex, is required for correct metaphase check-pointing during mitosis and it is also important in vesicle transport between Golgi and ER as part of a second complex together with the conserved conserved RINT1/Tip20p and NAG/Sec39p proteins. Zw10 is the metazoan homologue of yeast Dsl1, and are included in the complexes associated with tethering containing helical rods (CATCHR) family, sharing structural features. This entry represents the middle domain of zw10, which, from AlphaFold prediction, consists of four beta-strands and four alpha-helices.
Pfam PF18184: SMODS and SLOG-associating 2TM effector domain 3 (domain)
The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is always N-terminally fused to the SLATT_1 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels.
Pfam PF09036: Bcr-Abl oncoprotein oligomerisation domain (domain)
The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein.
Wikipedia: The breakpoint cluster region protein (BCR) also known as renal carcinoma antigen NY-REN-26 is a protein that in humans is encoded by the BCR gene. BCR is one of the two genes in the BCR-ABL fusion protein, which is associated with the Philadelphia chromosome. Two transcript variants encoding different isoforms have been found for this gene.
Pfam PF24523: Domain of unknown function (DUF7595) (repeat)
This entry represents a domain of unknown function found in uncharacterised plant sequences. This domain may have a beta-propeller structure.
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 PF06603: UpxZ family of transcription anti-terminator antagonists (family)
The UpxZ family of proteins acts to inhibit transcription of heterologous capsular polysaccharide loci in Bacteroides species by interfering with the action of the UpxY family of transcription anti-terminators. As antagonists of polysaccharide locus-specific UpxY transcription anti-terminators, the UpxZ proteins exert a hierarchical level of regulation, insuring that only one of the multiple phase-variable capsular polysaccharide loci per cell characteristic of this genus is transcribed at a time.
Pfam PF18655: SHIRT domain (domain)
The SHIRT domain is found in a range of presumed bacterial adhesin proteins.
Pfam PF03906: Phage T7 tail fibre protein, N-terminal (domain)
The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17. The tail spike protein of bacteriophage K1F is important for the initial absorption of the phage into its host bacterium by hydrolysing the alpha-sialosyl linkages in the polysialic acid capsule. This entry represents the N-terminal domain of gp17 and similar phage proteins.
Pfam PF14419: AF2226-like SPOUT RNA Methylase fused to THUMP (family)
SPOUT superfamily RNA methylase fused to RNA binding THUMP domain.
Pfam PF10174: RIM-binding protein of the cytomatrix active zone (coiled_coil)
This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains.
Pfam PF24559: DNA repair protein RAD5A UBA domain (domain)
This is the UBA domain found at the N-terminal of DNA repair protein RAD5A from Arabidopsis thaliana. RAD5A functions in error-free postreplication DNA repair or DNA-damage tolerance (DTT) pathway. It is required for homologous recombination (HR) induced by DNA double-strand break (DSB) in somatic cells.
Pfam PF03668: RapZ-like N-terminal domain (domain)
This entry represents the N-terminal P-loop kinase domain of RNase adapter protein RapZ and related proteins. RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. It is a RNA-binding protein that recruits the major endoribonuclease RNase E to sRNAs GlmZ.
Pfam PF07864: Protein of unknown function (DUF1651) (family)
This is a family containing 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 PF18431: Bacterial CdiA-CT RNAse A domain (domain)
Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. Structure analysis of CdiA-CT shows that it adopts the same fold (with two beta-sheets forming an overall kidney shape) as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Furthermore, structural comparison analysis identified human angiogenin, Rana pipiens protein P-30 (onconase) and mouse pancreatic ribonuclease (RNase 1) as the closest structural homologs of CdiA-CT.
Pfam PF18002: T6 antigen Ig like domain (domain)
This is the N-terminal immunoglobulin-like domain. Family members carrying this domain include Trypsin-resistant surface T6 protein found in Streptococcus pyogenes.
Pfam PF10300: Iml2/Tetratricopeptide repeat protein 39 (repeat)
This is a family of proteins conserved from fungi to humans, including fungal Inclusion body clearance protein Iml2 protein, animal tetratricopeptide repeat protein 39A/B/C (TT39A/B/C) and some uncharacterised proteins.  Members of this family carry a tetratricopeptide repeat [pfam:PF07719] at their C terminus. This entry includes Iml2 and its paralogue-YKR018C from S. cerevisiae; Iml2 localises to the cytoplasm and nucleus, and its expression is increased in response to DNA replication stress. It is found to be involved in lipid droplet-mediated inclusion body clearing after protein folding stress. In humans, TTC39A (also known as DEME6) is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. It is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive. TTC39B has been linked to lipid metabolism.
Pfam PF05672: MAP7 (E-MAP-115) family (coiled_coil)
The organisation of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent.
Pfam PF10378: Putative RRM domain (domain)
This is a putative RRM, RNA-binding, domain found only in fungi. It occurs in proteins annotated as Nrd1 yeast proteins, which are known to carry RRM domains.  It is not homologous with any of the other RRM domains, eg RRM_1 [pfam:PF00076].
Pfam PF21259: HTH-type transcriptional regulator Rgg, C-terminal domain (repeat)
This domain is found at the C-terminal end of HTH-type transcriptional regulator Rgg from Streptococcus gordonii, and similar proteins predominantly found in Firmicutes. Rgg is a peptide pheromone receptor that directly binds pheromones transported to the cytosol. The large C-terminal repeat domain contains five HTH folds and a capping helix that form a right-handed superhelical structure, resembling a TPR domain superhelix. This domain is found associated with the N-terminal [pfam:PF01381].
Pfam PF22299: BRISC complex subunit FAM175B, helical domain (domain)
This domain is found in BRISC complex subunit FAM175B from Camponotus floridanus and similar proteins mainly found in arthropods and nematodes. This protein is an homologue of human Abraxas 2 or KIAA0157, a component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates. This domain, which shows an alpha-helical configuration, is normally found C-terminal to [pfam:PF21125].
Pfam PF22792: Domain of unknown function (DUF7012) (domain)
This domain of unknown function is found in a group of proteins mainly from alphaproteobacteria. It is normally found N-terminal to [pfam:PF10074]. It is predicted to adopt a configuration formed mainly by beta-strands.
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 PF16830: Nucleotide-Binding Domain 94 of RH (domain)
NBD94 is a domain on one of the reticulocyte binding protein homologue family or RH proteins expressed by the malaria parasite merozoite. RH proteins recognise erythrocytes and are important in virulence. This domain has been shown to exhibit selective binding to ATP and ADP. Binding of ATP or ADP induces nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94 that directly impact on the ability of the RH to bind to the red blood cells.
Pfam PF11535: Calcium binding (family)
CcbP is a Ca(2+) binding protein which, in Anabaena, is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process. Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis.
Pfam PF23384: Family of unknown function (DUF7098) (family)
This family represents a group of proteins from halobacteria. It has several conserved motifs WHGP, QLWC and RxYxP. It is predicted to adopt a predominantly beta structure with a short 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 PF03723: Hemocyanin, ig-like domain (domain)
This family includes arthropod hemocyanins and insect larval storage proteins.
Wikipedia: Hemocyanins (also spelled haemocyanins and abbreviated Hc) are proteins that transport oxygen throughout the bodies of some invertebrate animals. These metalloproteins contain two copper atoms that reversibly bind a single oxygen molecule (O2). They are second only to hemoglobin in frequency of use as an oxygen transport molecule. Unlike the hemoglobin in red blood cells found in vertebrates, hemocyanins are not confined in blood cells, but are instead suspended directly in the hemolymph. Oxygenation causes a color change between the colorless Cu(I) deoxygenated form and the blue Cu(II) oxygenated form.
Pfam PF21235: E3 ubiquitin-protein ligase ARIH1, UBA-like domain (domain)
This entry represents the UBA-like (UBL) domain from the Human Homologue of Ariadne (HHARI) and its homologues, which are Ariadne subfamily E3 ubiquitin ligase proteins. This domain binds to Ubiquitin and NEDD8.
Pfam PF21808: Bacterial dynamin-like protein, helical domain (domain)
This is the helical region from bacterial dynamin-like proteins which covers the middle and GED domains which mediate extensive protein-protein contacts. These proteins are large GTPases with the same multidomain architecture that is found in dynamin-like proteins.
Pfam PF20349: Family of unknown function (DUF6644) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 156 and 167 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 PF24573: Dynein axonemal assembly factor 5, HEAT-repeat domain (repeat)
This entry represents a domain found in the central region of Dynein axonemal assembly factor 5 (DAAF5) from animals, which consists of HEAT repeats. DAAF5 is a cytoplasmic protein involved in the delivery of the dynein machinery to the motile cilium. It is required for the assembly of the axonemal dynein inner and outer arms, two structures attached to the peripheral outer doublet A microtubule of the axoneme, that play a crucial role in cilium motility.
Pfam PF09444: MRC1-like domain (family)
This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.
Pfam PF01704: UTP--glucose-1-phosphate uridylyltransferase (family)
This family consists of UTP--glucose-1-phosphate uridylyltransferases, [ec:2.7.7.9]. Also known as UDP-glucose pyrophosphorylase (UDPGP) and  Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uridylyltransferase catalyses the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi. UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type. In Dictyostelium (slime mold) mutants in this enzyme abort the development cycle. Also within the family is UDP-N-acetylglucosamine [swissprot:Q16222] or AGX1 and two hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete [swissprot:O51893] and [swissprot:O51036].
Pfam PF20268: SBDS protein, C-terminal domain (domain)
Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. The SBDS protein is composed of three domains. The N-terminal ([pfam:PF01172]) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, [pfam:PF09377]) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold.
Wikipedia: Ribosome maturation protein SBDS is a protein that in humans is encoded by the SBDS gene. An alternative transcript has been described, but its biological nature has not been determined. This gene has a closely linked pseudogene that is distally located. This gene encodes a member of a highly conserved protein family that exists in all archaea and eukaryotes.
Pfam PF13163: Protein of unknown function (DUF3999) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 440 and 470 amino acids in length. There is a single completely conserved residue D 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 PF20420: Domain of unknown function (DUF6702) (domain)
This entry represents an uncharacterised family of proteins. Some members of the family are annotated as Peptidase E, but the does not appear to be any evidence to support that assertion.
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 PF18769: APOBEC1 (family)
APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing and ssDNA mutagenesis as part of the defense against retroviruses and genomic retrotransposons.
Pfam PF11233: Protein of unknown function (DUF3035) (family)
This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
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 PF18264: CXC domain (domain)
This domain is found to the N-terminus of the SET domain in the EZH2 protein. It is a zinc binding domain.
Pfam PF03944: delta endotoxin (domain)
This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding.
Wikipedia: Delta endotoxins (δ-endotoxins) are a family of pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action and are the primary toxin produced by the genetically modified (GM) Bt maize/corn and other GM crops. During spore formation the bacteria produce crystals of such proteins that are also known as parasporal bodies, next to the endospores; as a result some members are known as a parasporin. The Cyt (cytolytic) toxin group is another group of delta-endotoxins formed in the cytoplasm. VIP toxins are formed at other stages of the life cycle.
Pfam PF06295: Z-ring associated protein G-like (family)
This family includes Z-ring associated protein G from Escherichia coli (ZapG) and similar proteins predominantly found in gammaproteobacteria. ZapG is involved in cell division, cell envelope biogenesis and cell shape maintenance. It is a key regulator of cell envelope growth, playing a crucial role in coordinating cell width, elongation and division to maintain cell envelope integrity. It plays an important role in the lipopolysaccharide (LPS) assembly/transport. This protein adopts an alpha helical configuration.
Pfam PF17963: Bacterial Ig domain (domain)
This entry represents a wide variety of bacterial Ig domains.
Pfam PF09014: Beta-2-glycoprotein-1 fifth domain (domain)
The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies.
Wikipedia: β2-glycoprotein 1, also known as beta-2 glycoprotein 1 and Apolipoprotein H (Apo-H), is a 38 kDa multifunctional plasma protein that in humans is encoded by the APOH gene. One of its functions is to bind cardiolipin. When bound, the structure of cardiolipin and β2-GP1 both undergo large changes in structure. Within the structure of Apo-H is a stretch of positively charged amino acids, Lys-Asn-Lys-Glu-Lys-Lys, are involved in phospholipid binding.
Pfam PF14492: Elongation Factor G, domain III (domain)
This domain is found in Elongation Factor G. It shares a similar structure with domain V ([pfam:PF00679]). Structural studies in drosophila indicate this is domain 3.
Pfam PF14352: Domain of unknown function (DUF4402) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 182 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 PF22973: Alpha-glucan water dikinase, phosphohistidine-like domain (domain)
This domain is found in the homologues of Alpha-glucan water dikinase (GWD1). This enzyme is involved in the incorporation of phosphate into starch-like alpha-glucan, with preferred C-6 position of glucose units. It acts as an overall regulator of starch mobilization and it is required for starch degradation. The domain represented by this entry is predicted to adopt a globular structure consisting of a beta-barrel decorated with alpha-helices. This domain has a significant sequence and structural similarity to phosphohistidine domain found in phosphate dikinases and PEP:sugar phosphotransferases.