SII-SWORD/CoKE huggingface dataset:
Pfam PF07979: Intimin C-type lectin domain (domain)
This domain is found at the C-terminus of intimin. Its structure has been solved and shown to have a C-lectin type of structure. Intimin is a bacterial adhesion molecule involved in intimate attachment of enteropathogenic and enterohemorrhagic Escherichia coli to mammalian host cells. Intimin targets the translocated intimin receptor (Tir), which is exported by the bacteria and integrated into the host cell plasma membrane.
Wikipedia: Intimin is a virulence factor (adhesin) of EPEC and EHEC E. coli strains. It is an attaching and effacing (A/E) protein, which with other virulence factors is necessary and responsible for enteropathogenic and enterohaemorrhagic diarrhoea.
Pfam PF04672: S-adenosyl methyltransferase (family)
This family contains a SAM (S-adenosyl methyltransferase) domain, with a central beta sheet with 3 alpha-helices on both sides. Crystal packing analysis of the structure PDB:3giw from [swissprot:Q82L35] suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met22 . The UNL is likely to be a phenylalanine or phenylalanine-like molecule. (details derived from TOPSAN).
Pfam PF23756: HPS5 beta propeller (repeat)
This entry represents the beta-propeller domain found in HPS5, a component of the biogenesis of lysosome-related organelles complex-2 (BLOC-2) and which has a role in the endo-lysosomal dynamics of skin fibroblasts. Its mutation or absence has been linked to eye-colour mutations in insects and Hermansky-Pudlak type 5 syndrome (HPS-5) in mammals, a disease characterized by defects in lysosome-related organelles such as melanosomes and platelet dense granules. This entry also represents the beta-propeller domain found in the tectonin beta-propeller repeat-containing protein 2 (TCPR2).
Pfam PF18289: CCDC81 eukaryotic HU domain 2 (domain)
This is the second of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules.
Pfam PF11630: Anti-lipopolysaccharide factor/Scygonadin (family)
Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus.
Pfam PF00743: Flavin-binding monooxygenase-like (family)
This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases.
Wikipedia: The flavin-containing monooxygenase (FMO) protein family specializes in the oxidation of xeno-substrates in order to facilitate the excretion of these compounds from living organisms. These enzymes can oxidize a wide array of heteroatoms, particularly soft nucleophiles, such as amines, sulfides, and phosphites. This reaction requires an oxygen, an NADPH cofactor, and an FAD prosthetic group. FMOs share several structural features, such as a NADPH binding domain, FAD binding domain, and a conserved arginine residue present in the active site. Recently, FMO enzymes have received a great deal of attention from the pharmaceutical industry both as a drug target for various diseases and as a means to metabolize pro-drug compounds into active pharmaceuticals. These monooxygenases are often misclassified because they share activity profiles similar to those of cytochrome P450 (CYP450), which is the major contributor to oxidative xenobiotic metabolism. However, a key difference between the two enzymes lies in how they proceed to oxidize their respective substrates; CYP enzymes make use of an oxygenated heme prosthetic group, while the FMO family utilizes FAD to oxidize its substrates.
Pfam PF23586: NWD2 C-terminal beta-propeller (repeat)
This entry represents the beta-propeller found at the C-terminal of NACHT and WD repeat domain-containing protein 2 (NWD2) from human and similar eukaryotic proteins. The function of these proteins is not yet known.
Pfam PF21326: KDM6, GATA-like (domain)
Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY (also known as KMD6C). This entry represents the Zn2+-coordinated GATA-like (GATAL) domain, which seems to be sensitive to redox environment. It is involved in substrate binding.
Pfam PF07912: ERp29, N-terminal domain (domain)
ERp29 ([swissprot:P52555]) is a ubiquitously expressed endoplasmic reticulum protein, and is involved in  the processes of protein maturation and protein  secretion in this organelle. The protein exists as a homodimer, with each monomer being  composed of two domains. The N-terminal domain  featured in this family is organised into a  thioredoxin-like fold that resembles the a domain  of human protein disulphide isomerase (PDI). However, this domain lacks the C-X-X-C motif  required for the redox function of PDI; it is  therefore thought that ERp29's function is similar  to the chaperone function of PDI. The N-terminal domain is exclusively responsible for the homodimerisation of the protein, without covalent linkages or additional contacts with other domains.
Pfam PF04627: Mitochondrial ATP synthase epsilon chain (family)
This family constitutes the mitochondrial ATP synthase epsilon subunit.  This is not to be confused with the bacterial epsilon subunit, which is homologous to the mitochondrial delta subunit ([pfam:PF00401] and [pfam:PF02823]) The epsilon subunit is located in the extrinsic membrane section F1, which is the catalytic site of ATP synthesis.  The epsilon subunit was not well ordered in the crystal structure of bovine F1, but it is known to be located in the stalk region of F1. E subunit is thought to be involved in the regulation of ATP synthase, since a null mutation increased oligomycin sensitivity and decreased inhibition by inhibitor protein IF1.
Wikipedia: ATP synthase F1 subunit epsilon, mitochondrial is an enzyme that in humans is encoded by the ATP5F1E gene. The protein encoded by ATP5F1E is a subunit of ATP synthase, also known as Complex V. Variations of this gene have been associated with a condition called mitochondrial complex V deficiency, nuclear 3 (MC5DN3) and papillary thyroid cancer.
Pfam PF21360: PylC-like, N-terminal domain (domain)
This domain is found in 3-methyl-D-ornithine--L-lysine ligase from Methanosarcina barkeri (PylC) and similar sequences from prokaryotes. PylC is required for the biosynthesis of pyrrolysine. This ATP-grasp enzyme is composed of three domains. This entry represents the N-terminal domain, which is composed of a central four-stranded beta-sheet that is faced on both sides by two helices. It shows an adenine binding pocket that has not been observed in any homologous structure determined before.
Pfam PF16137: Domain of unknown function (DUF4845) (family)
This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Pseudomonas species. Distant homology analysis suggests that proteins from this family are related to pilin type IV proteins from the Bundlin (PF05307) family, this prediction is however not confirmed by any experimental evidence
Pfam PF14217: Domain of unknown function (DUF4327) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 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 PF24990: ERT1/acuK family PAS domain (domain)
This entry represents a C-terminal PAS domain found in ART1/acuK family proteins.  The ERT1/acuK family consists of transcription factors that play a crucial role in regulating nonfermentable carbon utilization. These proteins act as activators of gluconeogenetic genes, facilitating the conversion of non-carbohydrate substrates into glucose. Members of this family are involved in various metabolic pathways, including gluconeogenesis and the tricarboxylic acid (TCA) cycle. Some proteins in this family also participate in processes such as drug resistance and cell wall remodeling. The family includes proteins that bind specific DNA sequences in promoter regions, thereby influencing gene expression. Additionally, certain members are involved in iron acquisition and metabolism, contributing to the organism's virulence and adaptation to glucose starvation conditions.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF01283: Ribosomal protein S26e (family)
This family represents the small ribosomal subunit protein eS26 (previously known as S26) which is found mainly in eukaryotes and includes mammalian S26 ; Octopus S26 ; Drosophila S26 (DS31) ; plant cytoplasmic S26; and fungal S26 . S26 may be involved in the attachment of eIF3 and poly (U) . Disruption of RPS26, the gene encoding a homologue of ribosomal protein small subunit S26 in yeast (S. cerevisiae), resulted in the formation of micro-colonies, suggesting that it is important for the normal cell growth of S. cerevisiae . This entry also includes uncharacterised archaeal sequences.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF03321: GH3 family N-terminal domain (domain)
The GH3 IAA-amido conjugating enzyme family consists of proteins that catalyze the synthesis of amino acid conjugates with indole-3-acetic acid (IAA) or jasmonate (JA), which are plant hormones. This entry represents the N-terminal domain of these enzymes. These enzymes play a crucial role in regulating plant hormone levels by conjugating excess IAA and JA to amino acids, thus providing a mechanism for plants to maintain hormonal homeostasis. The conjugation process is ATP-dependent and involves the adenylation of the hormone followed by the transfer to an amino acid. This family is involved in various plant physiological processes including disease resistance, stamen and carpel differentiation, floret fertility, and response to environmental stresses such as wounding and pathogen attack. Some members also exhibit activity towards synthetic auxins and may confer resistance to herbicides. The family's broad substrate specificity includes various amino acids and analogs of IAA, contributing to the complexity of hormone regulation in plants.
Pfam PF05916: GINS complex protein helical bundle domain (domain)
This entry represents the C-terminal alpha helical bundle domain. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication.  It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family.  The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase.
Pfam PF11992: TgpA N-terminal domain (domain)
This domain can be found at the N terminus of TgpA from Pseudomonas aeruginosa. TgpA is a transglutaminase that plays a critical role in the viability of Pseudomonas aeruginosa. This domain is composed of 5 transmembrane helices.
Pfam PF22614: Calcium-activated potassium channel slowpoke-like RCK domain (domain)
This entry includes calcium-activated potassium channels, known as BK channels or Slowpoke homologues (Slo1-3) which includes calcium-activated potassium channel slowpoke from Drosophila (Slo) and its homologues from vertebrates KCMA1, KCNT1/2 and KCNU1. This entry represents the C-terminal regulator of K+ conductance (RCK) domains which appear as tandem domains in these proteins. The RCK domain has a Rossmann-fold topology with unique positions that compose a well-conserved salt bridge and a hydrophobic dimer interface. This domain is also presents in prokaryotic K+ channels.
Pfam PF19364: Family of unknown function (DUF5940) (family)
This presumed domain is functionally uncharacterised. This domain family is found mainly in firmicutes, and is approximately 170 amino acids in length. The family is found in association with [pfam:PF08545].
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 PF03683: Uncharacterised protein family (UPF0175) (family)
This family contains small proteins of unknown function.
Pfam PF17542: Uncharacterized RP853 (family)
This is a family of unknown function found in Rickettsia. Family members are predicted to contain one trans-membrane region.
Pfam PF21068: MvdD pre-ATP grasp domain (domain)
The pair of ATP-grasp proteins MvdD and MvdC (microviridin D and C), as well as an acetyltransferase, produce microviridin K, an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide). Microviridins are peptidase inhibitors. This domain represents the pre-ATP grap domain.
Pfam PF18765: Polymerase beta, Nucleotidyltransferase (domain)
A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins.
Pfam PF20545: Domain of unknown function (DUF6759) (domain)
This presumed domain family is functionally uncharacterised. This domain is found in bacteria and is typically 100 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 PF05175: Methyltransferase small domain (domain)
This domain is found in ribosomal RNA small subunit methyltransferase C (eg [swissprot:P44453]) as well as other methyltransferases (eg [swissprot:Q53742]).
Pfam PF15535: Bacterial toxin 37 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an all-beta fold and a conserved glutamate residue, and [KR] and Hx[DH] motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion systems.
Pfam PF09805: Nucleolar protein 12 (25kDa) (family)
Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export.
Pfam PF02499: Probable DNA packing protein, C-terminus (domain)
This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is found at the C-terminus of the protein.
Pfam PF04633: Herpesvirus BMRF2 protein (family)
This is a family of unknown function found in the Herpes viruses.
Pfam PF19246: Family of unknown function (DUF5894) (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 PF12143: Chloroplastic Polyphenol Oxidase C-terminal domain (domain)
This domain family is found at the C-terminus of a family of tyrosinase enzymes [pfam:PF00264].  The tyrosinase family proteins are chloroplastic enzymes that catalyze the oxidation of mono- and o-diphenols to o-diquinones. These reactions are crucial in the formation of melanin and other pigment compounds in plants. The enzymatic activity of these proteins is essential for the browning process in damaged or ripe fruits and vegetables, and plays a role in plant defense mechanisms.
Pfam PF13925: con80 domain of Katanin (domain)
The con80 domain of katanin is the C-terminal region of the protein that binds to the N-terminal domain of katanin-p60, the catalytic ATPase. The complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of p60 to the spindle poles.  The assembly and function of the mitotic spindle requires the activity of a number of microtubule-binding proteins. Katanin, a heterodimeric microtubule-severing ATPase, is found localized at mitotic spindle poles. A proposed model is that katanin is targeted to spindle poles through a combination of direct microtubule binding by the p60 subunit and through interactions between the WD40 domain and an unknown protein.
Pfam PF02724: CDC45 (family)
CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae ([swissprot:Q08032]), forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus ([swissprot:Q99107]) among others. It also has a role in minichromosome maintenance. It is a core component of the CMG helicase (Cdc45-MCM-GINS), required for DNA synthesis during genome duplication. Structures of CDC45 confirmed that it is evolutionary related to bacterial RecJ nuclease.
Pfam PF09692: Argonaute siRNA chaperone (ARC) complex subunit Arb1 (family)
Arb1 is required for histone H3 Lys9 (H3-K9) methylation, heterochromatin, assembly and siRNA generation in fission yeast.
Pfam PF12704: MacB-like periplasmic core domain (domain)
This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein. Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter.
Pfam PF04280: Tim44-like domain (domain)
Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane.  Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region.  This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast.  This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane.
Pfam PF12093: Betacoronavirus NS8 protein (family)
This family of proteins includes the accessory proteins encoded by the ORF8 in coronaviruses, also known as accessory protein 8, or non-structural protein 8 (NS8). This is distinct from NSP8, which is encoded on the replicase polyprotein. Proteins in this family are typically between 39 to 121 amino acids in length. This protein has two conserved sequence motifs: EDPCP and INCQ. It may modulate viral pathogenicity or replication in favour of human adaptation. ORF8 was suggested as one of the relevant genes in the study of human adaptation of the virus. This entry includes the NS8a and NS8b proteins from human SARS coronavirus (SARS-CoV). Recently, the the structure of SARS-CoV-2 ORF has been determined and revealed a core of approximately 60 residues similar to SARS-CoV ORF7a, the Ig-like fold, with the addition of two dimerisation interfaces unique to SARS-CoV-2 ORF8. It forms a covalent disulfide-linker dimer through an N-terminal sequence specific to SARS-CoV-2 and a separate non-covalent interface is formed by another SARS-CoV-2 specific sequence. The presence of these interfaces shows that SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.