SII-SWORD/CoKE huggingface dataset:
Pfam PF21500: DNA polymerase III subunit delta', AAA+ ATPase lid domain (domain)
DNA polymerase III subunit delta' is part of the beta sliding clamp loading complex, which hydrolyses ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex. It consists of three domains, of which the N-terminal domain contains a nonfunctional nucleotide binding site. This entry represents the lid domain (or domain 2 in).
Pfam PF20915: Viral genome-linked protein (domain)
This family represents Viral genome-linked protein (VPg) from Caliciviruses such as Feline calicivirus (FCV). VPg plays a key role in translation initiation from genomic and subgenomic RNAs and is thought to function as a cap substitute for ribosomal recruitment. It interacts with the initiation factor eIF4E. This protein shows a compact helical structure flanked by flexible N and C terminal ends.
Pfam PF23007: STICHEL, DnaA_N-like alpha-beta domain (domain)
This domain is found in protein STICHEL (STI) from Arabidopsis thaliana and related proteins mainly from plants. STICHEL acts as a key regulator of trichome branching through an endoreduplication-independent pathway. The domain represented by this entry is predicted to adopt a globular alpha/beta structure with significant similarity to domains belonging to Ribosome-binding factor A, RbfA superfamily including ribosomal protein eS7. It has a significant sequence similarity to DnaA N-terminal domain. This domain is topologically very similar to KH type II domains but it lacks their characteristic KH-motif.
Pfam PF01614: Bacterial transcriptional regulator IclR C-terminal (domain)
This entry includes bacterial transcriptional regulators, such as glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this domain covers the C-terminal region that binds to regulatory substrates including Glyoxylate, allantoin/ate, indole, aromatic hydrocarbons, sugar acids, succinic semialdehyde, benzoate derivatives, ascorbic acid, glycerol-3-phosphate, glyceraldehyde-3-phosphate and pyruvate.
Pfam PF13842: DDE_Tnp_1-like zinc finger (domain)
This zinc-finger domain is frequently found at the C-terminal of proteins derived from transposable elements.
Pfam PF10494: Serine-threonine protein kinase 19 (family)
This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulfonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP.
Pfam PF10739: Protein of unknown function (DUF2550) (family)
This family is conserved in Corynebacterineae. The function is not known though most members are annotated as either secreted, or membrane, 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 PF24968: Domain of unknown function (DUF7770) (domain)
This entry represents a domain found in  uncharacterized proteins. It is predicted to adopt a globular structure that resembles the conserved core of the PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes) which consists of thiol peptidases with a circularly permuted papain-like fold. This domain is found either standalone or in combination with other domains.
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 PF21876: C381 turret protein 2nd galactose-binding domain-like (domain)
This entry represents the Sulfolobus turreted icosahedral virus (STIV) turret protein second jelly roll domain. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions.
Pfam PF03729: Short repeat of unknown function (DUF308) (repeat)
Family of short repeats that occurs in a limited number of membrane proteins. It may divide further in short repeats of around 7-10 residues of the pattern G-#-X(2)-#(2)-X (#=hydrophobic).
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 PF02681: Divergent PAP2 family (family)
This family is related to the [pfam:PF01569] family (personal obs: C Yeats).
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 PF24394: TMEM62 C-terminal domain (domain)
This domain is found C-terminal in the human Transmembrane protein 62 (TMEM62), uncharacterised At3g03305 protein from Arabidopsis thaliana and related eukaryotic proteins. TMEM62 has been identified as a potential therapeutic target to enhance survival from high-grade serous carcinomas. The domain represented by this entry is likely transmembrane and composed of alpha-helices. It is frequently found associated with [pfam:PF00149] and PF24384.
Pfam PF16297: Domain of unknown function (DUF4939) (family)
This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other  diseases. But the specific function of this family is still unknown.
Pfam PF08572: pre-mRNA processing factor 3 domain (domain)
This domain is found in U4/U6 and U4/U5/U6-small nuclear ribonucleoprotein Prp3, part of the tri-RNA complex that form the spliceosome. Prp3 plays a key role in the recognition of the snRNA duplex. The pre-mRNA processing factor 3 (PRP3) domain, responsible for the binding to stem II of the snRNA duplex, is highly conserved among eukaryotes and is found N-terminal to [pfam:PF06544]. The human PRP3 has been implicated in autosomal retinitis pigmentosa.
Pfam PF12193: Sulfolobus virus coat protein C terminal (domain)
This domain family is found in viruses, and is approximately 70 amino acids in length. It is the C terminal of a coat protein in sulfolobus viruses.
Pfam PF08809: Phage related hypothetical protein (DUF1799) (domain)
Members of this family are about 100 amino acids in length and are uncharacterised.
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 PF17996: Carbohydrate esterase 2 N-terminal (domain)
This is the N-terminal beta-sheet domain with jelly roll topology found in CE2 acetyl-esterase from the bacterium Clostridium thermocellum. This enzyme displays dual activities, it catalyses the deacetylation of plant polysaccharides and also potentiates the activity of its appended cellulase catalytic module through its noncatalytic cellulose binding function. This N-terminal jelly-roll domain appears to extend the substrate/cellulose binding cleft of the catalytic domain in C.thermocellum.
Pfam PF10066: Uncharacterized conserved protein (DUF2304) (family)
Members of this family of hypothetical archaeal 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 PF09337: H2C2 zinc finger (domain)
This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters.
Pfam PF01395: PBP/GOBP family (domain)
The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors. This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with pheromone-sensitive neurons and general-odorant binding proteins (GOBP).
Wikipedia: Odorant-binding proteins (OBPs) are small soluble proteins secreted by auxiliary cells surrounding olfactory receptor neurons, including the nasal mucus of many vertebrate species and in the sensillar lymph of chemosensory sensilla of insects. OBPs are characterized by a specific protein domain that comprises six α-helices joined by three disulfide bonds. Although the function of the OBPs as a whole is not well established, it is believed that they act as odorant transporters, delivering the odorant molecules to olfactory receptors in the cell membrane of sensory neurons.
Pfam PF14594: Siphovirus ReqiPepy6 Gp37-like protein (family)
This family includes numerous phage proteins from Siphoviruses. The function of this protein is uncertain, but it is related to [pfam:PF06605]. In Rhodococcus phage ReqiPepy6 this protein is called Gp37.
Pfam PF15239: Cilia-and flagella-associated protein 96 (family)
This family (previously DUF4586) represents Cilia- and flagella-associated protein 96 (CFAP96, also known as C4orf47). CFAP96 is an axonemal microtubule-associated protein (MAP). The EM structure of sperm DMTs shows that CFAP96 binds to tubulin and, similarly to other axonemal wedge-MAPs, binds deeper into the inter-protofilament cleft making extensive contacts with flanking protofilaments.
Pfam PF13912: C2H2-type zinc finger (domain)
This entry represents the classical C2H2 zinc finger domain.
C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short Î²-hairpin and an Î±-helix (Î²/Î²/Î± structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 . C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes . Transcription factors usually contain several Znf's (each with a conserved Î²/Î²/Î± structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short Î±-helix in the Znf, the Znf spanning 3-4 bases of the DNA . C2H2 zinc fingers can also bind to RNA and protein targets .
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
Pfam PF14861: Plant antimicrobial peptide (domain)
This family includes plant antimicrobial peptides. They adopt an alpha-helical hairpin fold stabilised by two disulphide bonds.
Pfam PF05292: Malonyl-CoA decarboxylase C-terminal domain (domain)
This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK).
Pfam PF03695: Uncharacterised protein family (UPF0149) (domain)
The protein in this family are about 190 amino acids long.  The function of these proteins is unknown.
Pfam PF04166: Pyridoxal phosphate biosynthetic protein PdxA (family)
In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesised  de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by  the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Pfam PF17839: C-terminal domain of cyclic nucleotide phosphodiesterase (domain)
This is the C-temrinal domain found in Listeria monocytogenes, Lmo2642 cyclic nucleotide phosphodiesterase. The auxiliary C-terminal domain, consists of five alpha-helices forming a long helical bundle, and is connected to the catalytic domain [pfam:PF00149] by two loop segments. It is suggested that this auxiliary domain of Lmo2642 might confer functional specificity to the protein through the interactions with unknown factors or involving the substrate recognition.
Pfam PF14357: Domain of unknown function (DUF4404) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved residues (P and G) 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 PF01386: Ribosomal L25p family (domain)
Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis [swissprot:P14194], which is induced by stress.
Pfam PF23334: VWC2L-like domain (domain)
This domain is found in human von Willebrand factor C domain -containing protein 2-like (VWC2L) and similar proteins predominantly found in vertebrates. VWC2L may play a role in neurogenesis, bone differentiation and matrix mineralisation. This domain is predicted to adopt an all-beta configuration.
Pfam PF24651: Domain of unknown function (DUF7644) (domain)
This entry represents a small family of uncharacterised staphylococcal phage proteins. Structure prediction suggests they form a compact domain composed of a three stranded beta sheet packed against 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 PF05382: Bacteriophage peptidoglycan hydrolase (family)
At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 [swissprot:O03979] has been shown to be a N-acetylmuramoyl-L-alanine amidase. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids.  This family appears to be related to [pfam:PF00877].
Wikipedia: In enzymology, a N-acetylmuramoyl-L-alanine amidase is an enzyme that catalyzes a chemical reaction that cleaves the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
Pfam PF05474: Semenogelin (family)
This family consists of several mammalian secreted seminal proteins  including semenogelin I and II. Freshly ejaculated human semen has  the appearance of a loose gel in which the predominant structural  protein components are the seminal vesicle secreted semenogelins (Sg). This family also includes seminal vesicle secretory protein 3A  from mouse, which has been shown to be involved in the coagulation  of semen resulting in the formation of the copulatory plug.
Pfam PF21382: Integrator IntS9, C-terminal domain (domain)
IntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS9 which interacts with the C-terminal of IntS11 (responsible for endonuclease activity of INT), a crucial interaction for the role of INT in snRNA 3'-end processing.
Pfam PF04976: DMSO reductase anchor subunit (DmsC) (family)
The terminal electron transfer enzyme Me2SO reductase of Escherichia coli is a heterotrimeric enzyme composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC).
Pfam PF06821: Serine hydrolase (domain)
Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile. This family has an alpha-beta hydrolase fold. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family.
Pfam PF21397: Alpha-11 giardin annexin domain (domain)
This entry represents the fourth annexin domain of of Alpha-11 giardin, an unusual annexin from Giardia lamblia. Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids.
Pfam PF01067: Calpain large subunit, domain III (domain)
The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions.
Pfam PF00586: AIR synthase related protein, N-terminal domain (domain)
This family includes Hydrogen expression/formation protein  HypE [swissprot:P24193], AIR synthases [swissprot:P08178] [ec:6.3.3.1], FGAM synthase [swissprot:P35852] [ec:6.3.5.3] and selenide, water dikinase [swissprot:P16456] [ec:2.7.9.3]. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain.
Pfam PF22804: F1F0 ATP synthase subunit ASA5 (family)
This entry represents the homologues of mitochondrial F1F0 ATP synthase subunit ASA5. F0 has six transmembrane helices and four long, membrane-intrinsic helices, which form the two helical hairpins of the conserved alpha subunit. Of the six transmembrane helices, two belong to ASA6 and one each to ASA5, ASA8, ASA9, and ASA10.
Pfam PF17942: Morc6 ribosomal protein S5 domain 2-like (domain)
This domain is found in MORC6 proteins in eukaryotes. Arabidopsis microrchidia (MORC) ATPase family proteins are conserved among plants and animals and are involved in transcriptional silencing. In Arabidopsis, MORC6/DMS11 was reported to function in the condensation of pericentromeric heterochromatin, thereby facilitating transcriptional silencing. Further studies demonstrate that MORC6 and its homologs MORC1 and MORC2 form a complex which associates with SUVH9, required for Pol V occupancy in the RdDM (RNA-directed DNA methylation) pathway.
Pfam PF01944: Stage II sporulation protein M (family)
SpoIIM is on e of four stage II sporulation proteins that is necessary for the forespore inside the mother-cell to be properly internalised through the breakdown of peptidoglycans trapped between the membranes of the septum separating the forespore and the mother-cell. The four proteins working in sequence are SpoIIB, [pfam:PF05036], SpoIIM, SpoIIP, [pfam:PF07454], and finally SpoIID, [pfam:PF08486]. D, M and P are in a complex with each other and the complex assembles in a hierarchical manner such that M, which serves as a membrane anchor, recruits P to the septum and P, in turn, recruits D to the septum.