SII-SWORD/CoKE huggingface dataset:
Pfam PF06689: ClpX C4-type zinc finger (domain)
The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known.
Pfam PF06929: Rotavirus VP3 protein (family)
This family consists of several Rotavirus specific VP3 proteins. VP3 is known to be a viral guanylyltransferase and is thought to posses methyltransferase activity and therefore VP3 is a predicted multifunctional capping enzyme.
Pfam PF05061: Poxvirus A11 Protein (family)
Family of conserved Chordopoxvirinae A11 family proteins. Conserved region spans entire protein in the majority of family members.
Pfam PF18778: Novel AID APOBEC clade 1 (family)
A distinct family of AID/APOBEC-like deaminases found in ray-finned fishes, the coelacanth, amphibians, lizards, and marsupials.
Pfam PF06004: Bacterial protein of unknown function (DUF903) (family)
This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. 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 PF19762: Domain of unknown function (DUF6249) (domain)
This domain family is found in bacterial proteins, functionally uncharacterised. Proteins in this family are typically between 174 and 239 amino acids in length. This domain is thought to contain transmembrane regions. This family is distantly related to [pfam:PF11239].
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 PF01473: Putative cell wall binding repeat (repeat)
These repeats are characterised by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins.  The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in [swissprot:P15057] might be responsible for the specific recognition of choline-containing cell walls. Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding as well as in the related dextransucrases of Leuconostoc mesenteroides.  Repeats also occur in toxins of Clostridium difficile and other clostridia, though the ligands are not always known.
Pfam PF09304: Cortexillin coiled-coil region (coiled_coil)
This entry represents the coiled-coil oligomerization domain found in cortexillin I, an actin-bundling protein. The domain forms a parallel two-stranded alpha-helical coiled coil approximately 18 heptad repeats in length. The structure reveals novel types of ionic coiled-coil interactions including distinct interhelical salt bridge patterns. A key feature is the presence of a 14-residue trigger site (residues 311-324) that is essential for proper coiled-coil formation. This region contains an elaborate network of interhelical and intrahelical salt bridges that are crucial for dimer assembly and stability. The domain shows several unusual features including charged residues at core a and d heptad positions that participate in stabilizing salt bridge networks.
Pfam PF24971: SAMD1 small helical domain (domain)
This domain is found in the human Sterile alpha motif domain-containing protein 1 (SAMD1) and related proteins. SAMD1 directly recognizes and binds unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. SAMD1 acts as a transcriptional repressor and chromatin regulator.
Pfam PF11722: CCCH zinc finger in TRM13 protein (domain)
This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.
Pfam PF08801: Nup133 N terminal like (repeat)
Nup133 is a nucleoporin that is crucial for nuclear pore complex (NPC) biogenesis. The N terminal forms a seven-bladed beta propeller structure. This family now contains other sized nucleoporins, including Nup155, Nup8, Nuo132, Nup15 and Nup170.
Wikipedia: Nucleoporins are a family of proteins which are the constituent building blocks of the nuclear pore complex (NPC). The nuclear pore complex is a massive structure embedded in the nuclear envelope at sites where the inner and outer nuclear membranes fuse, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm. Nuclear pores enable the passive and facilitated transport of molecules across the nuclear envelope. Nucleoporins, a family of around 30 proteins, are the main components of the nuclear pore complex in eukaryotic cells. Nucleoporin 62 is the most abundant member of this family. Nucleoporins are able to transport molecules across the nuclear envelope at a very high rate. A single NPC is able to transport 60,000 protein molecules across the nuclear envelope every minute.
Pfam PF13266: Protein of unknown function (DUF4057) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 279 and 322 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 PF04078: Cell differentiation family, Rcd1-like (repeat)
Two of the members in this family have been characterised as being  involved in regulation of Ste11 regulated sex genes. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation.
Pfam PF23060: M02D8_5-like, first CUB domain (domain)
This entry represents the first occurrence of the CUB domain in a family of uncharacterised proteins present in nematodes. Consecutive repetitions of this domain are common in this protein family. The CUB domain (for complement C1r/C1s, Uegf, Bmp1) is a structural motif of approximately 110 residues found predominantly in extracellular and plasma membrane-associated proteins, many of which undergo developmental regulation. CUB domains appear to be involved in oligomerisation and/or recognition of substrates and binding  partners.
Pfam PF22273: Domain of unknown function (DUF6956) (domain)
This domain is found in uncharacterised bacterial proteins either as standalone or in combination with other domains. It is predicted to adopt an alpha-beta structure with ferredoxin-like 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 PF14766: Replication protein A interacting N-terminal (family)
This family of proteins represents the N-terminal domain of replication protein A (RPA) interacting protein.  RPA interacting protein is involved in the import of RPA into the nucleus. The N-terminal domain is responsible for interaction with importin beta.
Pfam PF03103: Domain of unknown function (DUF243) (family)
This family of uncharacterised proteins is only found in fly proteins. It is found associated with YLP motifs [pfam:PF02757] in some proteins.
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 PF05727: Uncharacterised protein family (UPF0228) (family)
This small family of proteins is currently restricted Methanosarcina species.  Members of this family are about 200 residues in length, except for [swissprot:Q8TMK1] that has two copies of this region.  Although the function of this region is unknown the pattern of conservation suggests that this may be an enzyme, including multiple conserved aspartate and glutamate residues (Bateman A. pers. obs.). The most conserved motif in these proteins is NEL/MEXNE/D, where X can be any amino acid, which is found at the C-terminus of these proteins.
Pfam PF21953: NAD nucleotidase, C-terminal domain (domain)
This is the C-terminal domain of a family of Zn2+-dependent 5'-nucleotidases. This domain has a four-layered structure with a five-stranded beta-sheet forming the core.
Pfam PF15783: Fibrous sheath-interacting protein 2 (family)
FSIP2, fibrous sheath-interacting protein 2, is the C-terminal portion of a family of proteins found in mammals. The function is not known but the domain appears to be repeated up to 10 times in some members.
Pfam PF18973: Putative Chitin binding like (family)
This family includes host-selective toxins such as SnTox1 found in S. nodorum. SnTox1 is a necrotrophic effector contains 6 cysteine residues, a common feature for some fungal avirulence effectors such as the Avr and ECP effectors from Cladosporium fulvum. The high content of cysteine residues and high stability suggest that SnTox1 may function in the plant apoplastic space which is abundant in plant defense components. Protein sequence analysis indicate that SnTox1 contains a C-terminal chitin binding (CB) like motif. Three-dimensional (3D) structure-based sequence alignment suggested that the putative CB motif in SnTox1 was more similar to those of plant-specific ChtBDs than to Avr4 proteins, which are related to invertebrate ChtBDs. Furthermore, SnTox1 contained all secondary-structure-related residues including the strictly conserved b-strand-forming 'CCS' motif found only in plant-specific ChtBD1 proteins.
Pfam PF13906: C-terminus of AA_permease (domain)
This is the C-terminus of AA-permease enzymes that is not captured by the models [pfam:PF00324] and [pfam:PF13520].
Pfam PF24500: Domain of unknown function (DUF7589) (domain)
This domain is found in uncharacterised proteins mainly from plants. It is predicted to fold into a six-stranded beta-barrel. Inserted in this barrel is an alpha-helix that packs on the barrel side and it is enriched with positively charged residues which may have a functional importance.
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 PF23997: Domain of unknown function (DUF7315) (domain)
This domain is found in uncharacterised archaeal proteins. It is predicted to fold into an alpha-helical hairpin and it is likely associated with the membrane.
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 PF16875: Glycosyl hydrolase family 36 N-terminal domain (domain)
This domain is found at the N-terminus of many family 36 glycoside hydrolases. It has a beta-supersandwich fold.
Pfam PF10031: Small integral membrane protein (DUF2273) (family)
Members of this family of hypothetical bacterial proteins have 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 PF00282: Pyridoxal-dependent decarboxylase conserved domain (domain)
Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). Pyridoxal 5'-phosphate (PLP) is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy .

PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the Îµ-amino group of an active site lysine residue on the enzyme. The Î±-amino group of the substrate displaces the lysine Îµ-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalysed reactions, enzymatic and non-enzymatic .
A number of pyridoxal-dependent decarboxylases share regions of sequence similarity, particularly in the vicinity of a conserved lysine residue, which provides the attachment site for the pyridoxal-phosphate (PLP) group . Among these enzymes are aromatic-L-amino-acid decarboxylase (L-dopa decarboxylase or tryptophan decarboxylase), which catalyses the decarboxylation of tryptophan to tryptamine ; tyrosine decarboxylase, which converts tyrosine into tyramine; histidine decarboxylase, which catalyses the decarboxylation of histidine to histamine ; L-aspartate decarboxylase, which converts aspartate to beta-alanine ; and phenylacetaldehyde synthase that catalyses the decarboxylation of L-phenylalanine to 2-phenylethylamine . These enzymes belong to the group II decarboxylases .
Wikipedia: In molecular biology, group II pyridoxal-dependent decarboxylases are a family of enzymes including aromatic-L-amino-acid decarboxylase EC 4.1.1.28 that catalyse the decarboxylation of tryptophan to tryptamine, tyrosine decarboxylase EC 4.1.1.25 that converts tyrosine into tyramine and histidine decarboxylase EC 4.1.1.22 that catalyses the decarboxylation of histidine to histamine.
Pfam PF04602: Mycobacterial cell wall arabinan synthesis protein (family)
Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol.
Wikipedia: An arabinosyltransferase is a transferase enzyme acting upon arabinose.
This enzyme is involved in polymerisation of arabinogalactan. Mycobacterially, the more precise term is arabinofuranosyltransferase, since the arabinose residues occur only in a furanose form.
Pfam PF20216: Family of unknown function (DUF6576) (family)
This presumed domain is functionally uncharacterised. This domain family corresponds to the C-terminal domain of proteins that are thought to belong to the rhomboid family. It is approximately 40 amino acids in length and it is found mainly in Bacteroidetes. It contains the conserved sequences DxILDKI, GYxxL and EKxxL.
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 PF14607: N-terminus of Esterase_SGNH_hydro-type (domain)
This domain lies upstream of SGNH hydrolase, but its function is not known. There is a highly conserved GxDLY sequence-motif.
Pfam PF18408: C2H2 Hakai zinc finger domain (domain)
This is the C2H2 zinc finger domain found in E3 ubiquitin ligase Hakai. Hakai targets tyrosine-phosphorylated E-cadherin. It carries a Tyr(P)-binding domain, coined the HYB domain for Hakai phosphotyrosine (Tyr(P)) binding. HYB domain structure illustrates that it forms a zinc-coordinated homodimer in an antiparallel, intertwined configuration, utilizing residues from the Tyr(P)-binding region of two Hakai monomers. The C-terminal region of the HYB domain, which harbors the atypical zinc-coordination motif and key residues involved in the Tyr(P) interaction, plays an important role in the dimerization observed in the HYB domain.
Pfam PF11537: Nitrosopumilus output domain 5 (domain)
NitrOD5 (Nitrosopumilus output domain 5) is found in thaumarchaea, either in stand-alone form or in combination with the Response_reg [pfam:PF00072] domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems).
Pfam PF02298: Plastocyanin-like domain (domain)
This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family (eg  [swissprot:P93328]) may not bind copper due to the lack of key residues.
Pfam PF14543: Xylanase inhibitor N-terminal (domain)
This domain is found N-terminal in some aspartic proteinases and in xylanase inhibitors. The activity of these proteins is vital for plant-survival as xylanase produced by phytopathogens destroys plant cells.
Pfam PF03407: Nucleotide-diphospho-sugar transferase (family)
Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases.
Pfam PF21050: LisH domain-containing protein ARMC9, ARM repeats (repeat)
ARMC9 is localised to the basal body of a cilium and is upregulated during ciliogenesis. It is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length. This entry represents the armadillo repeats found towards the C-terminal ARMC9.
Pfam PF17285: PRMT5 TIM barrel domain (domain)
This domain corresponds to the N-terminal TIM barrel domain from PRMT5 proteins..
Pfam PF06720: Bacteriophage phi-29 early protein GP16.7 (family)
This family consists of several bacteriophage phi-29 early protein GP16.7 sequences of around 130 residues in length. The function of this family is unknown.
Pfam PF13458: Periplasmic binding protein (family)
This family includes a diverse range of periplasmic binding proteins.
Pfam PF23296: Domain of unknown function (DUF7079) (domain)
This is a presumed domain found in a set of bacterial sequences, whose function 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 PF08006: HAAS transmembrane region (domain)
This entry represents the transmembrane region fused to HAAS (HTH-associated alpha-helical signaling) domain (Preprint https://doi.org/10.1101/2020.09.24.301986).
Pfam PF14510: ABC-transporter N-terminal (domain)
This domain is found at the N-terminus of ABC-transporter proteins from fungi, plants to higher eukaryotes. It is predicted to be an intracellular domain.
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF24005: Domain of unknown function (DUF7320) (domain)
This entry represents an uncharacterized protein found in T4-like bacteriophages. It is found between the cd and pseT genes in the T4 phage genome. The function of this protein is unknown. Structure prediction suggests these proteins have a compact fold composed of five 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 PF10823: Protein of unknown function (DUF2568) (family)
One member in this family is annotated as yrdB which is part of a four gene operon however currently 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 PF22975: EPS8 spectrin-like domain (domain)
This entry represents a spectrin-like domain is the EPS8 protein. Epidermal growth factor receptor kinase substrate 8 (EPS8) is a signalling adapter that possesses actin binding, bundling, and barbed-end capping activities. It forms a complex with Sos-1, Abi1 and the lipid kinase phosphoinositide 3-kinase (PI3-K) to regulate Rac activation that leads to actin cytoskeletal remodeling. It is critical for dendritic cell migration. It is involved in the initial growth of stereocilia in both inner hair cells and outer hair cells. It also regulates axonal filopodia in hippocampal neurons in response to brain-derived neurotrophic factor (BDNF). It has been linked to proliferation, metastasis and prognosis of many malignant tumours.
Pfam PF09247: TATA box-binding protein binding (domain)
Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription.