SII-SWORD/CoKE huggingface dataset:
Pfam PF23936: ELP1 three-helix bundle (domain)
This entry represents the helical bundle domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia. The C-terminal dimerization domain consists of 28 alpha-helices organised in three domains: an elongated alpha-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28). ELP1 self-association contributes to its stability and is important for Elongator assembly. ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling.
Pfam PF18835: Beta helix repeat of Inulin fructotransferase (repeat)
This region contains a right-handed parallel beta helix repeat unit found in Inulin fructotransferase. This Pfam entry includes sequences not found by [pfam:PF13229].
Pfam PF18445: PR zinc knuckle motif (conserved_site)
This is a zinc knuckle motif found in PRDM4 (Schwann cell factor 1, SC-1), a member of the PR protein family. PRDM4 is a transcriptional regulator that has been implied in transduction of nerve growth factor signals via the p75 neurotrophin receptor and in cell growth arrest. The short motif is also present in several other PR proteins including human PRDM6 (PRISM), PRDM7, PRDM9 (meisetz), PRDM10 (tristanin), PRDM11, and PRDM15. The conservation of cysteine and histidine residues suggested that this 20 amino acid motif binds zinc, hence the name 'PR zinc knuckle' to distinguish it from the longer (30 amino acid) C2H2-like zinc fingers that are located C-terminally of the PR domain. The PR zinc knuckle fold is similar to that of Gag-knuckles (a beta-hairpin providing two zinc ligands followed by a short helix or a loop providing the other two zinc ligands) and zinc ribbons (two beta-hairpins, each providing two zinc ligands).
Pfam PF09281: Taq polymerase, exonuclease (domain)
Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase.
Wikipedia: Taq polymerase is a thermostable DNA polymerase I named after the thermophilic eubacterial microorganism Thermus aquaticus, from which it was originally isolated by Chinese scientist Alice Chien et al. in 1976. Its name is often abbreviated to Taq or Taq pol. It is frequently used in the polymerase chain reaction (PCR), a method for greatly amplifying the quantity of short segments of DNA.
Pfam PF03300: Tenuivirus non-structural, movement protein NS4 (family)
NS4 (also known as pc4) transports viral genome to neighbouring plant cells directly through plasmosdesmata, without any budding. It allows efficient cell to cell propagation, by bypassing the host cell wall barrier .
Pfam PF22848: Alpha-L-arabinofuranosidase 1 domain (domain)
This domain is found in Alpha-L-arabinofuranosidase 1 from Arabidopsis thaliana (ASD1), which may be involved in the coordinated dissolution of the cell wall matrix during abscission and in the secondary cell wall formation in xylem vessels. This domain is often found associated to [pfam:PF06964].
Pfam PF04217: Protein of unknown function, DUF412 (family)
This family consists of bacterial proteins, including yfbV  from E. coli. YfbV is a membrane protien involved in  insulating the chromosome from the TerR macrodomain.
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 PF13977: BetI-type transcriptional repressor, C-terminal (domain)
This family comprises the C-terminal portion of proteins that belong to the TetR family of transcriptional regulators. The C terminus represents the regulatory region, and does not include the DNA binding helix-turn-helix domain. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. One of the target proteins is BetI, an osmoprotectant which controls the choline-glycine betaine pathway in E.coli.
Pfam PF23078: Chromodomain-helicase-DNA-binding protein 6-9, tri-helical (domain)
This domain is found in human Chromodomain-helicase-DNA-binding protein 6-9 (CHD6-9), DNA-dependent ATPases that play a role in chromatin remodelling and transcriptional regulation. CHD8 acts as a transcription repressor by remodelling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity. It also acts as a negative regulator of Wnt signalling pathway by regulating beta-catenin (CTNNB1) activity. CHD6 regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. CHD9 acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. This domain is predicted to form a tri-helical structure, with a three-membered alpha-helical bundle and a two-stranded antiparallel beta-sheet.
Pfam PF18989: Family of unknown function (DUF5722) (family)
This is a family of unknown function mainly found in bacteria.
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 PF08264: Anticodon-binding domain of tRNA ligase (domain)
This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA ligase.
Wikipedia: An aminoacyl-tRNA synthetase, also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. It does so by catalyzing the transesterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
Pfam PF01623: Carlavirus putative nucleic acid binding protein (family)
This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF. These proteins may function as viral transcriptional regulators. The carlavirus family includes garlic latent virus and potato virus S and M, these viruses are positive strand, ssRNA with no DNA stage.
Pfam PF15493: Domain of unknown function, YrpD (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 236 and 351 amino acids in length. The member from Bacillus subtilis, UniProtKB:O05411, is named YrpD.
Pfam PF02391: MoaE protein (family)
This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.
Pfam PF02276: Photosynthetic reaction centre cytochrome C subunit (family)
Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake  of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidised electron donor.
Wikipedia: Photosynthetic reaction centre proteins are main protein components of photosynthetic reaction centres (RCs) of bacteria and plants. They are transmembrane proteins embedded in the chloroplast thylakoid or bacterial cell membrane.
Pfam PF20750: Poly(A) polymerase nucleotidyltransferase domain (domain)
In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA.  The N-terminal catalytic domain of Poly(A) polymerase is a member of the nucleotidyltransferase superfamily.
Pfam PF15729: Cation channel sperm-associated targeting subunit tau (domain)
Cation channel sperm-associated targeting subunit tau (CTSRT, also known as Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 11 and C2 calcium-dependent domain-containing protein 6) has been identified in mice as an auxiliary component of the CatSper complex, which is involved in sperm cell hyperactivation. Sperm cell hyperactivation is required for sperm motility, essential late in the preparation of sperm fertilisation. This protein is key for CatSper flagellar targeting and trafficking into the quadrilinear nanodomains as it links the channel-carrying vesicles ans motor proteins in elongating flagella.
Pfam PF10787: Uncharacterised protein from bacillus cereus group (family)
This family is conserved in the Bacillus cereus group. Several members are called YfmQ but the function is not known.
Pfam PF23285: Domain of unknown function (DUF7078) (domain)
This domain is found in uncharacterised proteins mainly from fungi. This domain is predicted to adopt a globular structure consisting of a four helical bundle and having structural similarity to the alpha-helical domain inserted in the third Ig domain of the Trs130 component of the TRAPPII complex.
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 PF22606: Cdc6/ORC-like, ATPase lid domain (domain)
This entry represents the AAA+ ATPase lid domain of eukaryotic Cdc6/ORC proteins and its homologues from archaea.
Pfam PF09174: Maf1 regulator (family)
Maf1 is a negative regulator of RNA polymerase III.  It targets the initiation factor TFIIIB.
Pfam PF18822: CdvA-like coiled-coil domain (coiled_coil)
A coiled coil region domain related to the CdvA-like proteins.
Pfam PF06933: Special lobe-specific silk protein SSP160 (family)
This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species.
Pfam PF17095: Spectrin-binding region of Ca2+-Calmodulin (family)
CAMSAP_CC1 is the conserved region on calmodulin-regulated spectrin-associated proteins in eukaryotes that binds spectrin. CAMSAPs are vertebrate microtubule-binding proteins, representatives of a family of cytoskeletal proteins that arose in animals. This conserved CC1 region binds to both spectrin and Ca2+/calmodulin in vitro, although the binding of Ca2+/calmodulin inhibited the binding of spectrin. CC1 appears to be a functional region of CAMSAP1 that links spectrin-binding to neurite outgrowth.
Pfam PF15173: FAM180 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 182 amino acids in length. There are two conserved sequence motifs: ELAS and DFE. The function of this family is unknown.
Pfam PF11803: UDP-glucuronate decarboxylase N-terminal (family)
The N-terminus of the UDP-glucuronate decarboxylases may be involved in localisation to the perinuclear Golgi membrane.
Pfam PF24854: Domain of unknown function (DUF7728) (domain)
This domain is found in uncharacterised fungal proteins. It is predicted to fold into a beta-sandwich. It contains highly conserved cysteine residues that are predicted to form a disulfide bond.
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 PF12384: Ty3 transposon peptidase (family)
Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species.
Pfam PF16219: Domain of unknown function (DUF4879) (domain)
family of short proteins of bacterial proteins of phage origin, exemplified by protein SPBc2p013 from Bacillus phage SPBc2, found in various Bacillus and Pseudomonas species. Structure show unexpected structural similarity to greek key beta barrels from the E-set domain, especially to domains involved in carbohydrate and protein- protein binding. However functional consequences of this similarity are not confirmed.
Pfam PF06022: Plasmodium variant antigen protein Cir/Yir/Bir (family)
This family consists of several Cir, Yir and Bir proteins from the Plasmodium species P.chabaudi, P.yoelii and P.berghei.
Pfam PF23295: Armadillo-like repeats (repeat)
This entry represents a region of armadillo-like repeats found in human WD repeat and FYVE domain-containing protein 3 (WDFY3) and similar eukaryotic sequences. WDFY3 is required for selective macroautophagy (aggrephagy). It is important for normal brain development.
Pfam PF13395: HNH endonuclease (domain)
This HNH nuclease domain is found in CRISPR-related proteins.
Pfam PF00046: Homeodomain (domain)
This entry represents the homeodomain (HD), a protein domain of approximately 60 residues that usually binds DNA. It is encoded by the homeobox sequence , which was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates , as well as plants , fungi  and some species of lower eukaryotes. Many members of this group are transcriptional regulators, some of which operate differential genetic programs along the anterior-posterior axis of animal bodies . This domain folds into a globular structure with three Î±-helices connected by two short loops that harbour a hydrophobic core. The second and third form a helix-turn-helix (HTH) motif, which make intimate contacts with the DNA: while the first helix of this motif helps to stabilise the structure, the second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. One particularity of the HTH motif in some of these proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the Î²-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.
Wikipedia: A homeobox is a DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of the full-grown organism.
Pfam PF13949: ALIX V-shaped domain binding to HIV (domain)
The binding of the LYPxL motif of late HIV p6Gag and EIAV p9Gag to this domain is necessary for viral budding.This domain is generally central between an N-terminal Bro1 domain, [pfam:PF03097] and a C-terminal proline-rich domain. The retroviruses thus used this domain to hijack the ESCRT system of the cell.
Pfam PF07097: Protein of unknown function (DUF1359) (family)
This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. 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 PF18412: Outer-membrane lipoprotein Wza C-terminal domain (domain)
This is the C-terminal domain found in Wza, an integral outer membrane lipoprotein, which is essential for group 1 capsule export in Escherichia coli. The domain is exposed on the cell surface and is suggested to mimic antimicrobial peptide pore formation.
Pfam PF02269: Transcription initiation factor IID, 18kD subunit (domain)
This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold
Wikipedia: The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Pfam PF03140: Plant protein of unknown function (family)
The function of the plant proteins constituting 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 PF05600: CDK5 regulatory subunit-associated protein 3 (family)
This family contains several eukaryotic sequences such as CDK5RAP3 (also known as C53 or LZAP) which serves as a probable tumour suppressor. Initially identified as a CDK5R1 interactor controlling cell proliferation. It negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation. It also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint. It has been shown to bind Wip1 and stimulates its phosphatase activity.
Pfam PF11494: Ta0938 (domain)
Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein.
Pfam PF12039: Protein of unknown function (DUF3525) (family)
This family of proteins is functionally uncharacterised. This protein is found in viruses. Proteins in this family are about 360 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 PF23543: DUF6688 C-terminal domain (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 360 and 412 amino acids in length. This entry corresponds to the alpha-helical C-terminal domain.
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 PF21410: Microtubule-associated protein 6 (family)
Microtubule-associated protein 6 (MAP6, previously named STOP proteins) is a calmodulin binding protein that is involved in microtubule stabilisation. MAP6 is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. It regulates axonal growth during neuron polarization, which is controlled by a palmitoylation cycle. MAP6 interacts with TMEM106B, and this interaction is crucial for controlling dendritic trafficking of lysosomes, presumably by acting as a molecular brake for retrograde transport. This protein stabilize cold-resistant microtubules, which is essential for neuronal development, maintenance, and function.
Pfam PF21456: Baseplate wedge protein gp7, domain VI (domain)
This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 and similar proteins predominantly found in tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain VI, which forms a ribbon-like structure that interacts with N-terminal region of the protein Gp10.
Pfam PF02929: Beta galactosidase small chain (domain)
This domain comprises the small chain of dimeric beta-galactosidases [ec:3.2.1.23].  This domain is also found in single chain beta-galactosidase.