SII-SWORD/CoKE huggingface dataset:
Pfam PF04395: Poxvirus B22R protein (family)
This is highly conserved C-rich, central region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses. There are three pairs of conserved cysteine residues.
Pfam PF15624: Kinetochore CENP-C fungal homologue, Mif2, N-terminal (family)
Mif2_N is a family of fungal proteins homologous to mammalian CENP-C. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore.
Pfam PF08519: Replication factor RFC1 C terminal domain (domain)
This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.
Pfam PF00416: Ribosomal protein S13/S18 (family)
This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Pfam PF14792: DNA polymerase beta palm (domain)
The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.
Pfam PF19754: Family of unknown function (DUF6241) (family)
This family of proteins is functionally uncharacterised and it is found in bacteria and viruses. Proteins in this family are typically between 161 and 200 amino acids in length. There are some conserved sequences: HQK and KWG at the N-terminal, and HNxxW near the C-terminal.
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 PF22538: Hexaprenyl diphosphate synthase, small subunit (family)
This entry represents a group of bacterial sequences, including the small subunit of the Hexaprenyl diphosphate synthase from Micrococcus luteus (HexPS or HexA), a trans-prenyltransferase that catalyses consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates on a farnesyl diphosphate to form an hexaprenyl diphosphate. HexPS is directly involved in the control of the product chain length. It is composed of mostly antiparallel alpha-helices joined by connecting loops.
Pfam PF08790: LYAR-type C2HC zinc finger (domain)
This C2HC zinc finger is found in LYAR proteins such as [swissprot:Q08288] which are involved in cell growth regulation.
Pfam PF08256: Aurein-like antibiotic peptide (family)
This family of antibacterial peptides are secreted from the granular dorsal glands of the Green and Golden Bell Frog Litoria aurea, Southern Bell Frog L. raniformis, Blue Mountains tree-frog Litoria citropa (genus Litoria) and frogs from genus Uperoleia. They are a part of the FSAP peptide family.  Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides.
Pfam PF02628: Cytochrome oxidase assembly protein (family)
This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus  subtilis. COX15 is required for cytochrome c oxidase assembly in yeast ([swissprot:P40086]).
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF14246: AefR-like transcriptional repressor, C-terminal domain (domain)
This family comprises the C-terminal domain of transcriptional regulators of the TetR family. It includes the AefR transcriptional regulator from P. syringae. It is found in association with [pfam:PF00440].
Pfam PF16958: Pre-mRNA-splicing factor PRP9 N-terminus (domain)
This is the N-terminal domain of pre-mRNA-splicing factor PRP9.
Pfam PF03507: CagA exotoxin phosphopeptide substrate mimic region (conserved_site)
Helicobacter pylori is the most common world-wide infection and plays an important role in pathogenesis of peptic ulcers. The CagA (cytotoxin-associated gene A) protein is a cell-surface antigen which may play a role in determining the relative virulence of the viral strains. This entry represents the phosphopeptide substrate mimic region of CagA.
Pfam PF09474: Type III secretion system YscX (type_III_YscX) (family)
Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery.
Pfam PF22378: Tas3-like, N-terminal domain (domain)
This entry represents the N-terminal domain of Tas3 from Schizosaccharomyces pombe and similar proteins predominantly found in yeast. Tas3 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation.
Pfam PF10943: Protein of unknown function (DUF2632) (family)
This is a family of membrane proteins with 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 PF06397: Desulfoferrodoxin, N-terminal domain (domain)
Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubredoxin metal binding domain. It is also found as the N-terminal domain of desulfoferrodoxin, see ([pfam:PF01880]).
Pfam PF08756: YfkB-like domain (domain)
This protein is adjacent to YfkA in B. subtilis.  In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Pfam PF06826: Predicted Permease Membrane Region (family)
This family represents five transmembrane helices that are normally found flanking (five either side) a pair of [pfam:PF02080] domains. This suggests that the paired regions form a ten helical structure, probably forming the pore, whereas the [pfam:PF02080]) binds a ligand for export or regulation of the pore. [swissprot:Q8L3K8] is described as a aspartate-alanine antiporter (). In  conjunction with [swissprot:Q8L3K9] it forms a 'proton motive metabolic cycle catalysed by an aspartate-alanine exchange'. The general conservation of domain architecture in this family suggests that they are functional orthologues.
Pfam PF24907: Integrin beta-like protein A-E, N-terminal (domain)
This entry represents the N-terminal Ig-like domain (according to structure predictions) of Integrin beta-like proteins A-E (SIBA-E) from Dictyostelium discoideum and similar sequences. These proteins may be implicated in cellular adhesion to substrate or phagocytic particles.
Pfam PF07833: Copper amine oxidase N-terminal domain (domain)
Copper amine oxidases catalyse the oxidative deamination  of primary amines to the corresponding aldehydes, while reducing molecular oxygen to hydrogen peroxide. These  enzymes are dimers of identical subunits, each comprising four domains. The N-terminal domain, which is absent in  some amine oxidases, consists of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the 'stalk' of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other.
Wikipedia: Amine oxidase (copper-containing) (AOC) (EC 1.4.3.21 and EC 1.4.3.22; formerly EC 1.4.3.6) is a family of amine oxidase enzymes which includes both primary-amine oxidase and diamine oxidase; these enzymes catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. They act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor:RCH2NH2 + H2O + O2  RCHO + NH3 + H2O2
Pfam PF20690: Bacterial Death-like domain 3 (domain)
This bacterial adaptor domain of the Death-domain fold is involved in protein-protein interactions in biological conflict systems. bDLDs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP and iSTAND. Further copies of the same bDLD are fused to either effector or signal-transducing domains, or additional Effector-associated domains (EADs). bDLD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the bDLD-bDLD coupling approximates the advantages of collinear transcription. bDLD3 is closest in sequence and likely progenitor of the metazoan Death-superfamily. bDLD3 shows a greater diversity of contextual associations in conflict systems in comparison to bDLD1 and bDLD2.
Pfam PF06030: WxL Interacting Protein, peptidoglycan binding domain (domain)
This domain (previously known as DUF916) is found in WxL interacting proteins (WxLIP) which play a role in virulence and are widely distributed in firmicutes. The WxL proteins usually occur within a gene cluster that contains two WxL proteins and a WxL interacting protein composed of three domains: peptidoglycan binding domain (PGBD), host binding domain (HBD), and transmembrane helix (TMH). The domain represented by this entry is involved in binding to peptidoglycan and to WxL, and anchoring the protein cluster onto the bacterial surface. This PGBD domain is frequently found in combination with HBD domain ([pfam:PF11797]) and both were shown to function synergistically as a single unit that binds to the peptidoglycan and interacts with the eukaryotic host. The PGBD domain is predicted to adopt a beta-sandwich with an Ig-like topology.
Pfam PF07308: Protein of unknown function (DUF1456) (domain)
This family consists of several hypothetical bacterial proteins of around 150 residues in length. 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 PF17261: Family of unknown function (DUF5327) (family)
This bacterial family of proteins has no known function and is mostly found in Bacilli.
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 PF15612: WSTF, HB1, Itc1p, MBD9 motif 1 (conserved_site)
A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module  found in diverse eukaryotic chromatin proteins.Based on the  Ioc3 structure, this module is inferred to interact with nucleosomal  linker DNA and the SLIDE domain of ISWI proteins.  The resulting complex forms a protein ruler that measures out the  spacing between two adjacent nucleosomes. The conserved basic  residue in WHIM1 is involved in packing with the DDT motif. The  module shows a great domain architectural diversity and is often  combined with other modified histone peptide recognising and  DNA binding domains, some of which discriminate methylated DNA.
Pfam PF18589: Obesity receptor immunoglobulin like domain (domain)
This is the immunoglobulin-like domain (IGD) found in obesity receptors (ObR). ObR is a single membrane-spanning receptor belonging to the class I cytokine receptor family. All isoforms have an identical extracellular part consisting of six domains: an N-terminal domain (NTD), two CRH domains (CRH1 and CRH2), an immunoglobulin-like domain (IGD), and two additional membrane-proximal fibronectin type III (FN III) domains. ObR activation depends on the CRH2, IGD, and FN III domains, however the CRH2 domain is the major leptin-binding determinant in the receptor. The IGD and membrane-proximal domains have no detectable affinity for the ligand, but are nonetheless indispensable for receptor activation. Deletion of the IGD results in a receptor with wild-type affinity for leptin, but completely devoid of biological activity.
Wikipedia: The immunoglobulin superfamily (IgSF) is a large protein superfamily of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. Molecules are categorized as members of this superfamily based on shared structural features with immunoglobulins ; they all possess a domain known as an immunoglobulin domain or fold. Members of the IgSF include cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins. They are commonly associated with roles in the immune system. Otherwise, the sperm-specific protein IZUMO1, a member of the immunoglobulin superfamily, has also been identified as the only sperm membrane protein essential for sperm-egg fusion.
Pfam PF04656: Pox virus E6 protein (family)
Family of pox virus E6 proteins.
Pfam PF18592: Tho1/MOS11 C-terminal domain (domain)
THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. Some studies show that Tho1, like Sub2, can assemble onto the nascent mRNA during transcription and that Tho1 and Sub2 can provide alternative pathways for mRNP biogenesis in the absence of a functional THO complex. This is the C-terminal domain found in Tho1 and MOS11 proteins. The C-terminal region of Tho1 from Saccharomyces cerevisiae, adopts a helical fold similar to that of the WHEP RNA-binding domains of metazoan aminoacyl-tRNA synthetases.
Pfam PF17433: Glycosyl hydrolase family 49 N-terminal Ig-like domain (domain)
Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers. This domain corresponds to the N-terminal Ig-like fold.
Wikipedia: In molecular biology, glycoside hydrolase family 49 is a family of glycoside hydrolases.
Pfam PF17045: Centrosomal protein of 63 kDa (coiled_coil)
CEP63 is a family of eukaryotic proteins involved in centriole activity.
Pfam PF22215: Mixed lineage kinase domain-like N-terminal domain (domain)
Mixed-lineage kinase domain-like (MLKL) is crucial for necroptosis, permeabilizing membranes via its N-terminal domain upon phosphorylation of its kinase-like domain by RIP3. The MLKL N-terminal domain forms a four-helical up-and-down bundle that is sufficient to induce liposome leakage and a fifth C-terminal helix that inhibits this activity.
Pfam PF24991: NUP210 forth Ig-like domain (domain)
This is the forth Ig-like domain of NUP210 and its homologues. NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen.
Pfam PF00269: Small, acid-soluble spore proteins, alpha/beta type (family)
Small, acid-soluble spore proteins (SASP or ASSP) are proteins bound to the spore DNA of bacteria of the genera Bacillus, Thermoactynomycetes, and Clostridium . They are double-stranded DNA-binding proteins that cause DNA to change to an A-like conformation. They protect the DNA backbone from chemical and enzymatic cleavage and are thus involved in dormant spore's high resistance to UV light. SASP are degraded in the first minutes of spore germination and provide amino acids for both new protein synthesis and metabolism.

There are two distinct families of SASP: the Î±/Î² type and the gamma-type. Alpha/beta SASP are small proteins of about sixty to seventy amino acid residues that are generally coded by a multigene family. The N terminus of alpha/beta SASP contains the site which is cleaved by a SASP-specific protease that acts during germination while the C terminus and is probably involved in DNA-binding.
Pfam PF24277: DmsR, N-terminal (domain)
This domain is found at the N-terminal of Dimethyl sulfoxide reductase transcriptional activator from Haloferax volcanii (DmsR) and similar proteins from halobacteria. DmsR is required for anaerobic respiration on dimethyl sulfoxide (DMSO). This domain is predicted to adopt an alpha-beta structure. It is often found associated with [pfam:PF04967].
Pfam PF12667: NigD-like N-terminal OB domain (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream. This domain has an OB fold.
Pfam PF19322: E3 ubiquitin-protein ligase RKP N-terminus (domain)
This domain represents the N-terminal region of the E3 ubiquitin-protein ligase RKP from plants. It was demonstrated that RKP is a functional ubiquitin E3 ligase and is able to interact with cell-cycle inhibitor ICK/KRP proteins.
Pfam PF00110: wnt family (family)
Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families.
Wikipedia: In cellular biology, the Wnt signaling pathways are a group of signal transduction pathways which begin with proteins that pass signals into a cell through cell surface receptors. The name Wnt, pronounced "wint", is a portmanteau created from the names Wingless and Int-1. Wnt signaling pathways use either nearby cell-cell communication (paracrine) or same-cell communication (autocrine). They are highly evolutionarily conserved in animals, which means they are similar across animal species from fruit flies to humans.
Pfam PF10888: Protein of unknown function (DUF2742) (family)
Members in this family of phage proteins are the product of the gene phiRv1, however no function is known.
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 PF08916: Phenylalanine zipper (domain)
The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS and SH2-B/Lnk.
Pfam PF11438: 36-mer N-terminal peptide of the N protein (N36) (family)
The arginine-rich motif of the N protein is involved in transcriptional antitermination of phage lambda. N36 forms a complex with boxB RNA by binding tightly to the major groove of the boxB hairpin via hydrophobic and electrostatic interactions forming a bent alpha helix.
Pfam PF21334: Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain (domain)
F-type ATPases consist of two structural domains, F1 containing the extramembraneous catalytic core, and F0 which contains the membrane proton channel. This entry includes ATP synthase subunit delta from fungi (called epsilon in bacteria or chloroplast ATPase), which interacts with subunit C from F0 which is important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 (C subunit). This entry represents the C-terminal alpha-helical domain which is likely to act as an inhibitor of ATPase activity.
Pfam PF01336: OB-fold nucleic acid binding domain (domain)
This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See [pfam:PF00152]). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule [ec:6.1.1.-]. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pfam PF01500: Keratin, high sulfur B2 protein (family)
High sulfur proteins are cysteine-rich proteins synthesised during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments. This family has been divided up into four regions, with the second region containing 8 copies of a short repeat. This family is also known as B2 or KAP1.
Pfam PF15423: FLYWCH-type zinc finger-containing protein (family)
This family is the N-terminus of some FLYWCH-zinc-finger proteins, found in eukaryotes. The family is found in association with [pfam:PF04500]. There are two conserved sequence motifs: EQE and QEPS.
Pfam PF07173: Glycine-rich domain-containing protein-like (family)
This entry includes Arabidopsis Glycine-rich domain- containing protein 1 and 2 (GRDP1/2). They are involved  in development and stress responses.
Pfam PF18844: Bacterial archaeo-eukaryotic release factor family 2 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. This family contains a well-conserved 'FP' motif in the catalytic loop.