SII-SWORD/CoKE huggingface dataset:
Pfam PF15784: G-protein pathway suppressor 2-interacting domain (family)
GPS2_interact is the more N-terminal domain of two co-repressor protein-families found in vertebrates. The domain is found in NCoR and SMRT proteins; N-CoR (nuclear receptor co-repressor) and SMRT (silencing mediator for retinoid and thyroid receptors) are related corepressors that mediate transcriptional repression by unliganded nuclear receptors and other classes of transcriptional repressors. GPS2 is a stoichiometric subunit of the N-CoR-HDAC3 complex. GPS2 links the complex to membrane receptor-related intracellular JNK (c-Jun amino-terminal kinase) signalling pathways.
Pfam PF14351: Domain of unknown function (DUF4401) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 357 and 735 amino acids in length. The family is found in association with [pfam:PF09925].  There is a single completely conserved residue K 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 PF10622: Energy-converting hydrogenase B subunit P (EhbP) (family)
Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane.  This family contains subunit P of Ehb.
Pfam PF05763: Protein of unknown function (DUF835) (family)
The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not 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 PF03098: Animal haem peroxidase (domain)
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions.

Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal haem peroxidases can be categorised as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin .
Wikipedia: Animal heme-dependent peroxidases is a family of peroxidases. Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, a number of animal heme peroxidases can be categorized as members of a superfamily: myeloperoxidase (MPO); eosinophil peroxidase (EPO); lactoperoxidase (LPO); thyroid peroxidase (TPO); prostaglandin H synthase (PGHS); and peroxidasin.
Pfam PF22127: NTD biosynthesis operon protein NtdA, N-terminal domain (domain)
This entry represents the N-terminal domain of NtdA, which is not found in other aminotransferases and consists of two-stranded parallel beta-sheet flanked by two alpha-helices. This domain may be involved in protein-protein interactions. NtdA is a sugar aminotransferase involved in the biosynthesis of kanosamine.
Pfam PF11864: Domain of unknown function (DUF3384) (family)
This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is typically between 422 to 486 amino acids in length. This domain is found associated with [pfam:PF02145].
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 PF08052: PyrBI operon leader peptide (family)
This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase. is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism.  In this mechanism, the concentration of UTP determines the extent of coupling between transcription and translation within the pyrBI leader region, hence determining the level of rho-independent transcriptional termination at an attenuator preceding the pyrB gene.
Pfam PF18344: Carbohydrate binding module family 32 (domain)
This domain is found in GH84C present in Clostridium perfringens. GH84C is a beta-N-acetylglucosaminidase. This domain is a family 32 carbohydrate binding module (CBM) which preferentially recognizes the non-reducing terminus of N-acetyllactosamine.
Pfam PF17404: Nrap protein domain 3 (domain)
Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localised in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript.
Pfam PF01813: ATP synthase subunit D (family)
This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase.
Pfam PF15938: Domain of unknown function (DUF4750) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 76 and 92 amino acids in length. There are two completely conserved W residues 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 PF13623: SurA-like N-terminal domain (domain)
This domain is found at the N-terminal of the chaperone SurA and related proteins such as PpiD and foldase PrsA. This is a helical domain that together with the C-terminal forms a domain containing substrate-binding sites. The C-terminal of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.
Pfam PF21853: Family of unknown function (DUF6912) (family)
This is a family of uncharacterized proteins.Their predicted structure shows some similarity to ADP-rybosylating toxins.
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 PF12854: PPR repeat (repeat)
This family matches additional variants of the PPR repeat that were not captured by the model for [pfam:PF01535]. The exact function is not known.
Pfam PF02123: Viral RNA-directed RNA-polymerase (family)
This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.
Pfam PF03347: Vibrio thermostable direct hemolysin (family)
Thermostable direct haemolysin (TDH) is considered an important virulence factor in Vibrio parahaemolyticus gastroenteritis and is a dimer composed of two identical subunit molecules of approximately 21kDa. The tetrameric form contains a central pore permitting entry and exit of water molecules. A number of biological properties have been attributed to TDH including haemolytic activity, enterotoxicity, cytotoxicity and cardiotoxicity .
Pfam PF09728: Myosin-like coiled-coil protein (coiled_coil)
Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed. It is a novel binding partner of several syntaxin family members and is possibly involved in Ca2+-dependent exocytosis in neuroendocrine cells. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localises to the nucleus in osteoblasts and dimerises with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription.
Pfam PF15452: Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter (family)
NYAP_C is a C-terminal family of eukaryotic proteins that are substrates of tyrosine kinase in the brain. When first identified, the family members were referred to as unconventional myosin XVI, or Myr 8. However, proteins have now been identified as being integrally involved in neuronal function and morphogenesis. The family is involved in both the activation of phosphoinositide 3-kinase (PI3K) and the recruitment of the downstream effector WAVE complex to the close vicinity of PI3K; it also appears to regulate the brain size and neurite outgrowth in mice.
Pfam PF01632: Ribosomal protein L35 (family)
This entry represents the large ribosomal subunit protein bL35, previously known as L35, a basic protein of 60 to 70 amino-acid residues . Like many basic polypeptides, it completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes . This family of ribosomal proteins includes proteins from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants .
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 PF04513: Baculovirus polyhedron envelope protein, PEP, C terminus (coiled_coil)
Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense  structure called the polyhedron envelope or polyhedron calyx.  The  polyhedron envelope (associated) protein PEP is thought to be an  integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper  formation of the periphery of polyhedra.  It is thought that PEP may  stabilise polyhedra and protect them from fusion or aggregation.
Pfam PF21176: RecR, helix-hairpin-helix (conserved_site)
The bacterial protein RecR is an important regulator oin the RecFOR homologous recombination pathway during DNA repair. It acts with RecF and RecO forming a complex that facilitates the loading of RecA  onto ssDNA. RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif ([pfam:PF02132]) and a Toprim domain ([pfam:PF13662]) and a C-terminal domain comprising a Walker B motif and a C-terminal helix ([pfam:PF21175]). This is the HhH motif found at the N-temrinal of RecR which is essential for DNA binding and association with RecO.
Pfam PF12743: Oestrogen-type nuclear receptor final C-terminal (domain)
This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localisation of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain.
Wikipedia: Estrogen receptors (ERs) are proteins found in cells that function as receptors for the hormone estrogen (17β-estradiol). There are two main classes of ERs. The first includes the intracellular estrogen receptors, namely ERα and ERβ, which belong to the nuclear receptor family. The second class consists of membrane estrogen receptors (mERs), such as GPER (GPR30), ER-X, and Gq-mER, which are primarily G protein-coupled receptors. This article focuses on the nuclear estrogen receptors.
Pfam PF07706: Aminotransferase ubiquitination site (conserved_site)
This segment contains a probable site of ubiquitination that ensures rapid  degradation of tyrosine aminotransferase in rats. The half life of the enzyme  in vivo is about  2-4 hours. In addition, unpublished information identifies at least 2 phosphorylation  sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at  S*QEECDK. This region of TAT is probably primarily related to regulatory events.   Most other transaminases are much more stable and are not phosphorylated.
Pfam PF21991: Cap-snatching endonuclease (domain)
The cap-snatching endonuclease family is a group of enzymes found in segmented negative strand RNA viruses of the arena-, bunya-, and orthomyxovirus families. The viruses use cap-snatching to transcribe viral mRNA, which involves cleaving the host mRNA near its 5' end and is accomplished by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. The cap-snatching ENs belong to the PD-D/ExK superfamily of cation-dependent nucleases and have an active site configuration that includes two divalent metal ions and a histidine residue. The available structures of the influenza orthomyxovirus and LACV orthobunyavirus show the canonical conformation of the active site, while the arenavirus ENs show differences in their active sites, such as the replacement of the metal-coordinating histidine with an acidic residue in arenavirus ENs. The Hantaan virus cap-snatching EN has been structurally characterized, revealing high endonuclease activity, while the Lassa virus endonuclease has low intrinsic activity due to its non-canonical coordination of the catalytic metal ions.
Pfam PF15545: Bacterial toxin 8 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold and HxR and HxxxH motifs and is usually exported by the type 2 and type 6 secretion system.
Pfam PF07606: Protein of unknown function (DUF1569) (family)
A family of hypothetical proteins identified in Rhodopirellula baltica.
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 PF19353: Family of unknown function (DUF5930) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in rhodobacteria. Proteins in this family are typically between 411 and 445 amino acids in length. The family is found to the N-terminus of [pfam:PF01551].
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 PF05887: Procyclic acidic repetitive protein (PARP) (disordered)
This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated.
Pfam PF20076: Domain of unknown function (DUF6472) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. The proteins contain 4 conserved cysteines.
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 PF05869: DNA N-6-adenine-methyltransferase (Dam) (family)
This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences.
Pfam PF04457: MJ1316 RNA cyclic group end recognition domain (domain)
RNA repair domain predicted to be involved specifically in the recognition of RNA 3' ends with 2'-3' cyclic phosphate groups.
Pfam PF14739: Domain of unknown function (DUF4472) (family)
This family is specific to the Chordates. Some members also carry Kinesin-motor domains at their N-terminus, Kinesin, [pfam:PF00225].
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 PF18569: Thioredoxin-like domain (domain)
This is a thioredoxin like domain found in AIMP2 proteins (Aminoacyl tRNA synthetase complex interacting multifunctional protein 2). Aimp2 is a component of human multi-tRNA synthetase complex (MSC). MSC is a macromolecular protein complex consisting of nine different ARSs and three ARS-interacting multifunctional proteins (AIMPs).
Wikipedia: Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes, including redox signaling. In humans, thioredoxins are encoded by TXN and TXN2 genes. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo. Although not entirely understood, thioredoxin is linked to medicine through their response to reactive oxygen species (ROS). In plants, thioredoxins regulate a spectrum of critical functions, ranging from photosynthesis to growth, flowering and the development and germination of seeds. Thioredoxins play a role in cell-to-cell communication.
Pfam PF07774: ER membrane protein complex subunit 1, C-terminal (domain)
This is the C-terminal domain of ER membrane protein complex subunit 1. ER membrane protein complex subunit 1 is a component of the ER membrane protein complex (EMC, composed of EMC1, EMC2, EMC3, EMC4, EMC5 and EMC6). In Saccharomyces cerevisiae, the EMC seems to be required for efficient folding of proteins in the endoplasmic reticulum (ER).
Pfam PF08500: Tombusvirus p33 (family)
Tombusviruses, which replicate in a wide range of plant hosts, replicate with the help of viral replicase protein including the overlapping p33 and p92 proteins which contain the domain described here.
Pfam PF05699: hAT family C-terminal dimerisation region (domain)
This dimerisation region is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation region forms extremely stable dimers in vitro.
Wikipedia: C7orf38 is a gene located on chromosome 7 in the human genome. The gene is expressed in nearly all tissue types at very low levels. Evolutionarily, it can be found throughout the kingdom animalia. While the function of the protein is not fully understood by the scientific community, bioinformatic tools have shown that the protein bares much similarity to zinc finger or transposase proteins. Many of its orthologs, paralogs, and neighboring genes have been shown to possess zinc finger domains. The protein contains a hAT dimerization domain nears its C-terminus. This domain is highly conserved in transposase enzymes.
Pfam PF24851: Domain of unknown function (DUF7725) (domain)
This domain is found in uncharacterised plan proteins. It has detectable similarity to winged helix HTH domains and it is predicted to adopt similar structure.
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.