SII-SWORD/CoKE huggingface dataset:
Pfam PF15549: PGC7/Stella/Dppa3 domain (family)
The domain belongs to a fast evolving family known only from the placental mammals. The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization. This suggests that it might bind methylated DNA sequences directly. The conserved core includes a postively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion. Most placental mammals contain 3-6 paralogs of this domain family. The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins.
Wikipedia: Developmental pluripotency-associated protein 3 is a protein that in humans is encoded by the DPPA3 gene.
Pfam PF19851: Family of unknown function (DUF6326) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 159 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 PF04843: Herpesvirus tegument protein, N-terminal conserved region (family)
All herpesviruses contain a Ubiquitin (Ub)-specific cysteine protease (USP) domain embedded within their large tegument protein. The herpesvirus tegument ubiquitin (Ub)-specific protease (htUSP) domain of ~200 amino acids adopts an Î±-Î²-Î± sandwich fold that features a central catalytic cleft, ideally suited to accommodate the C-terminal stretch of Ub. The catalytic triad Cys-His-Asp is strictly conserved, along with a putative oxyanion hole-forming Gln residue. The htUSP domain is a member of peptidase family C76 of clan CA .
Pfam PF21501: Protein LANA1-like, DNA-binding domain (domain)
Latency-associated nuclear antigen (LANA) is a multifunctional protein that plays a role in the replication and long-term persistence of the viral episomal genome in dividing cells. It binds to mitotic chromosomes via its N-terminal region and to a 16-bp imperfect palindrome within the origin of replication (oriP) located in the viral terminal repeat (TR) through its C-terminal. It also plays a role in the repression of host NF-kappa-B activity upon TNF-alpha stimulation by promoting the proteasomal degradation of host RELA. This entry represents the DNA-binding domain of LANA from murine gammaherpesvirus 68, which is homologous to that of Kaposi's sarcoma-associated herpesvirus (KSHV).
Pfam PF15515: MvaI/BcnI restriction endonuclease family (domain)
This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends.
Pfam PF02419: PsbL protein (family)
This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. The function of this small  protein is unknown. Interestingly the mRNA for this protein requires a post-transcriptional modification of an ACG triplet to form an AUG initiator codon.
Pfam PF21564: Lactococcus phage p2, Receptor binding protein, neck domain (domain)
This domain is found centrally located in Receptor binding protein from Lactococcus phage p2 (RBP, also known as Gp18) and similar proteins from closely related lactococcal phages. RBP shows three domains: the N-terminal shoulder domain ([pfam:PF20747]), which is attached to the phage, the neck domain (this entry) and the C -terminal receptor-recognition head domain ([pfam:PF08931]). The central domain folds into four beta-strands, which interlace with the beta-strands of two other subunits to form an equilateral triangular prism around the three-fold axis of a triple-stranded beta-helix.
Pfam PF08627: CRT-like, chloroquine-resistance transporter-like (family)
This family represents the Plasmodium falciparum chloroquine resistance transporter (CRT) and homologous proteins. CRT regulates other transporters, like Na-H antiporter or nonselective cation transporters. The Arabidopsis homologues are involved in thiol transport from the plastid to the cytosol, playing a significant role in regulating GSH levels and the redox potential of the cytosol. Homologues from Dictyostelium discoideum are also included in this family.
Pfam PF20135: Family of unknown function (DUF6525) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 69 and 100 amino acids in length. There are two conserved sequence motifs: AALPWSP and RAE.
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 PF12337: Protein of unknown function (DUF3637) (family)
This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF00073], [pfam:PF08935].
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 PF09303: KCNMB2, ball and chain domain (domain)
Members of this family are found in the cytoplasmic N-terminus of KCNMB2, the beta-2 subunit of large conductance calcium and voltage-activated potassium channels. They are responsible for the fast inactivation of these channels.
Wikipedia: Calcium-activated potassium channel subunit beta-2 is a protein that in humans is encoded by the KCNMB2 gene.
Pfam PF06156: Initiation control protein YabA (family)
YabA is involved in initiation control of chromosome replication. It interacts with both DnaA and DnaN, acting as a bridge between these two proteins.
Pfam PF06245: Protein of unknown function (DUF1015) (family)
Family of proteins with unknown function found in archaea and 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 PF24726: Domain of unknown function (DUF7678) (domain)
This entry represents a conserved domain of unknown function (DUF7678) found in various bacterial species. The domain is approximately 75-100 amino acids in length and contains several highly conserved residues.  The function of this domain remains to be determined. Structure prediction suggests this domain is composed of a 6 stranded beta sheet with an Alpha helix packed on one side.
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 PF02957: TT viral ORF2-like (domain)
This entry represents a domain found in ORF2 from Torque teno virus (TTV) and related viruses. This domain contains a set of conserved cysteine and histidine residues suggesting a zinc binding domain and has been implicated in kinases regulation. TTV, isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals, and numerous prevalence studies have raised questions about its role in unexplained hepatitis. This domain is also present in the VP2 protein from the chicken anaemia virus which is a gyrovirus. Gyroviruses are small circular single stranded viruses.
Pfam PF10728: Domain of unknown function (DUF2520) (domain)
This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases.
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 PF16124: RecQ zinc-binding (domain)
This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ.
Pfam PF17711: Family of unknown function (DUF5556) (family)
This is a family of unknown function found in primates.
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 PF07148: Maltose operon periplasmic protein precursor (MalM) (family)
This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown.
Pfam PF06177: QueT transporter (family)
This family includes the queT gene encoding a hypothetical integral membrane protein with 5 predicted transmembrane regions. The queT genes in Firmicutes are often preceded by the PreQ1 (7-aminomethyl-7-deazaguanine) riboswitches of two distinct classes, suggesting involvement of the QueT transporters in uptake of a queuosine biosynthetic intermediate.
Pfam PF18252: Copper(I)-binding protein CorA-like (domain)
This domain is found in CorA present in Methylomicrobium album. CorA is a copper repressible surface associated copper(I)-binding protein. CorA can bind one copper ion per protein molecule. The overall fold of CorA is similar to M. capsulatus protein MopE, including the unique copper(I)-binding site and most of the secondary structure elements.
Pfam PF22296: bAvd-like (family)
This protein family includes accessory variability determinant bAvd protein from Bordetella phage BPP-1 and similar sequences from tailed bacteriophages and proteobacterial prophages. bAvd proteins are encoded by diversity-generating retroelements (DGR). They transfer coding information from a template region through an RNA intermediate to a protein-encoding variable region and generates protein sequence variation to provide the phage with the capacity to adapt to its host. The reverse transcription by the DGR is carried out by a complex of reverse transcriptase bRT and bAvd proteins. bAvd forms a positively charged pentameric, barrel-shaped structure, with one end narrower than the other.
Pfam PF17863: AAA lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.
Pfam PF13985: YbgS-like protein (family)
This family of proteins is functionally uncharacterised. The family includes the YbgS protein from E. coli [swissprot:P0AAV6]. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. Some members of this family are annotated as homeobox protein, but this annotation cannot be verified.
Pfam PF16377: Domain of unknown function (family)
This family around 150 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown.
Pfam PF05362: Lon protease (S16) C-terminal proteolytic domain (domain)
The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.
Wikipedia: In molecular biology, the Lon protease family is a family of enzymes that break peptide bonds in proteins resulting in smaller peptides or amino acids. They are found in archaea, bacteria and eukaryotes. Lon proteases are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16. In the eukaryotes the majority of the Lon proteases are located in the mitochondrial matrix. In yeast, the Lon protease PIM1 is located in the mitochondrial matrix. It is required for mitochondrial function, it is constitutively expressed but is increased after thermal stress, suggesting that PIM1 may play a role in the heat shock response. Lon proteases have two specific subfamilies: LonA and LonB, differentiated by the number of AAA+ domains found in the protein.
Pfam PF00136: DNA polymerase family B (family)
This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Wikipedia: A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.
These enzymes catalyze the chemical reactiondeoxynucleoside triphosphate + DNAn ⇌ pyrophosphate + DNAn+1.
Pfam PF21541: CATSPER protein subunit beta protein 1st domain (domain)
This entry represents the N-terminal domain from the Cation channel sperm-associated protein subunit beta protein.
Pfam PF09596: MamL-1 domain (domain)
The MamL-1 domain is a polypeptide of up to 70 residues, numbers 15-67 of which adopt an elongated kinked helix that wraps around ANK and CSL forming one of the complexes in the build-up of the Notch transcriptional complex for recruiting general transcription factors..
Wikipedia: In molecular biology, there are a number of neurogenic proteins referred to as mastermind-like proteins (MAMLs) of which this domain is the N-terminal region. Mastermind-like proteins act as critical transcriptional co-activators for Notch signaling.
Pfam PF03859: CG-1 domain (domain)
CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin -binding domain and ankyrins (ANK) motifs.
Pfam PF13183: 4Fe-4S dicluster domain (domain)
Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.
Pfam PF13251: Domain of unknown function (DUF4042) (repeat)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 180 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 PF23010: PHLPP protein RA domain (domain)
This entry represents the N-terminal RA domain found in the PHLPP family proteins are serine/threonine phosphatases that play a crucial role in the regulation of cellular signaling pathways. They are involved in the dephosphorylation of the AGC kinase family members, including AKT1, AKT2, AKT3, PRKCA, and PRKCB, which are key regulators of cell survival, apoptosis, and proliferation. The family members act as tumor suppressors by triggering apoptosis through the dephosphorylation of specific serine residues on these kinases. They also regulate cap-dependent translation by dephosphorylating RPS6KB1 and control the activity of STK4 and RAF1 kinases, influencing apoptosis and kinase activity, respectively. Additionally, they have roles in long-term memory formation, circadian rhythm consolidation, and T-cell development and function. PHLPP2 contains a Ras-associating (RA) domain followed by a PH domain, leucine-rich repeats and protein phosphatase 2C (PP2C) domain. The presence of a PH domain is important for interaction with some of their substrates. This domain is also found in fungal adenylate cyclases (also known as ATP pyrophosphate-lyase) such as CYR1 from yeast, the orthologues of PHLPP2. They play essential roles in regulation of cellular metabolism by catalysing the synthesis of a second messenger, cAMP.
Pfam PF21318: BRCA2, OB2 (domain)
BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. t stimulates the displacement of Replication protein A (RPA), and also facilitates filament formation. This entry represents the second OB fold (OB2) from the C-terminal ssDNA binding domain (DBD) which has three OB folds. OB2 and OB3 are arranged in tandem  and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B.
Pfam PF07137: VDE lipocalin domain (domain)
This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage.
Pfam PF12872: OST-HTH/LOTUS domain (domain)
A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn-  helix fold and bind RNA with a potential specificity for dsRNA.In  eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.
Wikipedia: Oskar may refer to:
Pfam PF19080: Family of unknown function (DUF5772) (family)
This is a family of proteins of unknown function found in viruses which appears to contain transmembrane proteins inferred from homology.
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 PF20441: Terminase large subunit, endonuclease domain (domain)
This is the endonuclease domain of Terminase large subunit TerL, a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain ([pfam:PF03354]) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly. This nuclease domain has a RNAse H-like fold and it has been proposed to utilise a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases.