SII-SWORD/CoKE huggingface dataset:
Pfam PF10469: AKAP7 2'5' RNA ligase-like domain (domain)
AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains [pfam:PF02834]. Presumably this domain carried out some as yet unknown enzymatic function.
Pfam PF21917: N-terminal region of NMB0537 (domain)
This entry represents a pair of helices found at the N-terminus of some CBS domain proteins. A pair of these regions dimerise to form a four helical bundle. Proteins in this family have this region followed by two CBS domains and [pfam:PF03471].
Pfam PF14866: Long chain scorpion toxin, cysteine-stabilized alpha/beta domain (domain)
This entry includes long chain scorpion potassium channel toxins and and scorpine-like peptides, which exhibit strong antimicrobial effects as well as cytolytic activity against eukaryotic cells. Thi is the cysteine-stabilized alpha/beta (CS-alpha/beta) domain, which is more closely related to invertebrate defensins, than to the classical scorpion toxins. Its structure shows an alpha-helix along with one beta-sheet stabilized by three disulfide bridges folding into a CS-alpha/beta motif.
Pfam PF07939: Protein of unknown function (DUF1685) (family)
The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long.
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 PF09227: Bubble protein (domain)
Members of this family of fungal domains are functionally uncharacterised. They may act as toxins.
Pfam PF02583: Metal-sensitive transcriptional repressor (family)
This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression.
Pfam PF18480: Domain of unknown function (DUF5615) (domain)
This is a domain of unknown function found in potential toxin-antitoxin system component.
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 PF17306: Family of unknown function (DUF5355) (family)
This family of unknown function is found in Saccharomycetales.
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 PF21339: Vascular endothelial growth factor receptor 1-like, Ig-like domain (domain)
This domain is found in Vascular endothelial growth factor receptor 1 from humans (VEGFR-1) and similar proteins from animals. VEGFR-1 is a tyrosine kinase receptor for the placental growth factor (PlGF) that plays an essential role in the development of embryonic vasculature, the regulation of angiogenesis and other essential cellular processes. It consists of seven immunoglobulin-like (Ig-like) domains in its extracellular portion. This entry represents the second of these domains.
Pfam PF15776: Proline-rich protein family 22 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 420 amino acids in length.
Pfam PF17947: Four helical bundle domain (domain)
This domain is found in elongation factor 3A where it packs against the bottom of the concave face of the HEAT domain.
Pfam PF21536: Kelch-like protein 33-like, BTB/POZ domain (domain)
This entry represents the BTB/POZ domain found at the N-terminal of a group of Kelch repeats containing proteins, including KLHL33, whose function is not clear. The BTB/POZ domain is a common protein-protein interaction module.
Pfam PF18584: Synaptonemal complex 2 Spt16M-like domain (domain)
Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded beta-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD may be involved in chromatin binding.
Pfam PF14148: YhdB-like protein (family)
The YhdB-like protein family includes the B. subtilis YhdB protein [swissprot:O07530], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 82 amino acids in length. There are two conserved sequence motifs: LMVRT and FLHAY.
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 PF19691: Family of unknown function (DUF6192) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000713) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from from the ribostamycin biosynthetic gene cluster from Streptomyces ribosidificus. This family appears to be predominantly 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 PF11182: Alginate O-acetyl transferase AlgF (family)
AlgF is essential for the addition of O-acetyl groups to alginate, an extracellular polysaccharide. The presence of O-acetyl groups plays an important role in the ability of the polymer to act as a virulence factor.
Pfam PF14303: No apical meristem-associated C-terminal domain (family)
This domain is found in a number of different types of plant proteins including NAM-like proteins.
Pfam PF13656: RNA polymerase Rpb3/Rpb11 dimerisation domain (domain)
The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer.  The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain ([pfam:PF01000]).  Some of the alpha subunits also contain iron-sulphur binding domains ([pfam:PF00037]).  Rpb11 is found as a continuous domain.  Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.
Pfam PF20904: Antiactivator protein ExsD helical hairpin domain (domain)
The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC.
Pfam PF23629: MAP kinase-activating death domain protein death domain (domain)
This entry represents the death domain found in MAP kinase-activating death domain proteins.  The MADD family proteins function as guanyl-nucleotide exchange factors that regulate small GTPases of the Rab family, facilitating the conversion of GDP-bound inactive forms to GTP-bound active forms. ey targets include RAB27A, RAB27B, RAB3A, RAB3C, and RAB3D, which are crucial for synaptic vesicle exocytosis and secretion. The MADD family is involved in synaptic vesicle formation, vesicle trafficking at neuromuscular junctions, and up-regulating synaptic exocytosis in central synapses. They may interact with motor proteins like KIF1B and KIF1A for vesicle transport to presynaptic terminals. Additionally, they play roles in TNFA-mediated MAPK pathway activation, potentially linking TNFRSF1A with MAP kinase activation, and may regulate TNFA-induced apoptosis. In Caenorhabditis elegans, they are implicated in presynaptic activity regulation, dense-core vesicle trafficking, body muscle contractions, and fatty acid uptake by intestinal cells during the defecation motor program.
Wikipedia: The death domain (DD) is a protein interaction module composed of a bundle of six alpha-helices. DD is a subclass of protein motif known as the death fold and is related in sequence and structure to the death effector domain (DED) and the caspase recruitment domain (CARD), which work in similar pathways and show similar interaction properties. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats, caspase-like folds, kinase domains, leucine zippers, leucine-rich repeats (LRR), TIR domains, and ZU5 domains.
Pfam PF24474: Domain of unknown function (DUF7579) (domain)
This domain is centrally located in a group of uncharacterised plant proteins. It is often found associated to [pfam:PF12371]
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 PF23880: Domain of unknown function (DUF7233) (domain)
This domain is found in the phages infecting Mycobacterium and Gordonia. The domain is around 70-100 amino acids long.
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 PF20994: CENPU protein (family)
This protein is part of the yeast kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules. This protein is a component of the inner kinetochore COMA complex, which connects centromere-associated proteins and the outer kinetochore.
Pfam PF14690: zinc-finger of transposase IS204/IS1001/IS1096/IS1165 (domain)
This entry represents a zinc-finger domain found in transposases for insertion sequence IS204, IS1001, IS1096 and IS1165.
Pfam PF15752: Domain of unknown function (DUF4688) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 331 and 596 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 PF20517: Transmembrane protein 127 (family)
TMEM127 modulates mTOR function in the endolysosome. Its interaction with early endosomal GTPase Rab5 to inhibit mTOR signalling seems to be related with its tumour-suppressing properties.
Pfam PF21487: Tas3, C-terminal helical domains (domain)
RNA-induced transcriptional silencing complex protein tas3 (Tas3) plays a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. It is part of the RNA-induced transcriptional silencing (RITS) complex which provides a physical tether between the RNAi and heterochromatin assembly pathways. This entry represents the C-terminal alpha-helical domain which self-associates into a helical polymer and is required for cis spreading of RITS in centromeric DNA regions.
Pfam PF04239: YetF C-terminal domain (domain)
This domain is found at the C-terminal end of the YetF protein, which contains three N-terminal transmembrane helices.
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 PF22763: NrS-1 polymerase HBD domain (domain)
This entry represents the helix bundle domain (HBD) domain of NrS-1 polymerase which together with the N-terminal Prim/Pol domain, is responsible for DNA polymerization and de novo primer synthesis activities. This domain is critical for the primer synthesis activity of NrS-1 polymerase.
Pfam PF20333: Family of unknown function (DUF6628) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 140 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 PF23809: Bacteriophage holin (family)
This entry represents a family of bacteriophage holin proteins. Holins are small membrane proteins that control the timing of host cell lysis during the phage lytic cycle. Holins typically have 2-4 transmembrane helices. The exact mechanism of how holins trigger cell lysis is not fully understood. The holin family is found in phages that infect Actinobacteria, primarily Mycobacteria and Gordonia species.
Pfam PF08263: Leucine rich repeat N-terminal domain (family)
Leucine Rich Repeats [pfam:PF00560] are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF03473: MOSC domain (domain)
The MOSC (MOCO sulfurase C-terminal) domain is a  superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms such as [swissprot:P32157], or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters.
Pfam PF02247: Large coat protein (domain)
This family contains the large coat protein (LCP) of the comoviridae viral family.
Pfam PF09458: H-type lectin domain (domain)
The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain [pfam:PF00754].
Pfam PF13418: Galactose oxidase, central domain (repeat)
Wikipedia: The Kelch motif is a region of protein sequence found widely in proteins from bacteria and eukaryotes. This sequence motif is composed of about 50 amino acid residues which form a structure of a four stranded beta-sheet "blade". This sequence motif is found in between five and eight tandem copies per protein which fold together to form a larger circular solenoid structure called a beta-propeller domain.
Pfam PF04254: Protein of unknown function (DUF432) (family)
Archaeal protein of unknown 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 PF20720: Novel STAND NTPase 3 (domain)
This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems and in metazoan TRADD-N associated counter-invader proteins.
Pfam PF24286: Family of unknown function (DUF7474) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt a mainly alpha-helical 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.
Pfam PF12218: N terminal extension of bacteriophage endosialidase (repeat)
This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. This domain is found in the bacteriophage protein endosialidase. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain. The endosialidase protein complexes to form homotrimeric molecules.
Pfam PF17719: Family of unknown function (DUF5564) (family)
This is a family of unknown function found in chordata.
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 PF23759: Galactose binding domain-like (domain)
This entry represents a Galactose binding domain-like domain that is found in a variety of bacterial cell surface proteins that usually have a C-terminal type 9 secretion signal domain. The domain contains four conserved cysteines. AlphaFold models suggest that the first and third form one disulphide bond and the second and fourth form a second disulphide bond.
Pfam PF02395: Immunoglobulin A1 protease (domain)
This entry represents the N-terminal domain found in serine protease autotransporters Pic, sepA, espP and espC and immunoglobulin A1 protease autotransporter (IgA1) from bacteria. These proteins have been found in virulent strains and are considered virulence factors. Pic and other bacterial autotransporters confer serum resistance even although they do not degrade immunoglobulin as in the case of IgA1. This domain has protease activity.
Pfam PF19337: BMP and activin membrane-bound inhibitor homolog C-terminus (domain)
This family represents the C-terminal domain of BMP and activin membrane-bound inhibitor homolog (BAMBI) which contains the transmembrane domain and a short intracellular domain that, unlike all other known TGF-beta type I or type II receptors, does not encode a serine/threonine-kinase domain. However, it shares sequence homology with the E6 and catalytic loops of receptor serine/threonine kinases. BAMBI is an essential regulator of cell proliferation and differentiation that represses transforming growth factor-beta and enhances Wnt/beta-catenin signalling in various cell types. It stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling.
Pfam PF02461: Ammonia monooxygenase (family)
Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons.
Wikipedia: Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes.