SII-SWORD/CoKE huggingface dataset:
Pfam PF20122: Family of unknown function (DUF6512) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 35 and 59 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 PF13448: Domain of unknown function (DUF4114) (family)
This is a repeated domain that is found towards the C-terminal of many different types of bacterial proteins. There are highly conserved glutamate and aspartate residues suggesting that this domain might carry enzymic activity.
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 PF09418: Protein of unknown function (DUF2009) (family)
This is a eukaryotic family of proteins with 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 PF16854: Vacuolar protein sorting-associated protein 53 C-terminus (repeat)
This is the C-terminal domain of vacuolar protein sorting-associated protein 53 (Vps53), a component of the Golgi-associated retrograde complex (GARP), involved in retrograde transport from early and late endosomes to late Golgi by linking the vesicle through the t-SNARE Tgl1 to the Golgi, leading to the membrane fusion between late Golgi and endosomal vesicles. This domain has a fold consisting of an alpha-helical bundle known as the CATCHR fold (complexes associated with tethering containing helical rods) which is shared by proteins of other tethering complexes, namely exocyst, COG and Dsl1.
Pfam PF14074: Protein of unknown function (DUF4257) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 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 PF12914: SH3 domain of SH3b2 type (domain)
This domain appears to be an SH3 domain of the SH3b2-type, and is the second SH3 domain to be found, downstream of an N-terminal domain that is probably the stabilising domain, for the structure from [swissprot:Q72DN3], PDB:3m1u, which is a four-domain protein.  The last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, [pfam:PF00877] (details derived from TOPSAN).
Pfam PF02735: Ku70/Ku80 beta-barrel domain (domain)
The Ku heterodimer (composed of Ku70 [swissprot:P12956] and Ku80 [swissprot:P13010]) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 [swissprot:P12956] and Ku80 [swissprot:P13010] proteins that form a DNA binding heterodimer.
Wikipedia: Ku is a dimeric protein complex that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to humans. The ancestral bacterial Ku is a homodimer. Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end. Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK. Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind, orienting the double-strand break for ligation.
Pfam PF16778: Phage tail assembly chaperone protein (domain)
Phage_tail_APC is a family of general phage tail assembly chaperone proteins from double-stranded DNA viruses with no RNA stage, many of which are unclassified.
Pfam PF05563: Salmonella plasmid virulence protein SpvD (family)
This family consists of several SpvD plasmid virulence proteins from different Salmonella species.The structure of the protein from Salmonella typhimurium has been solved and shows a papain-like fold, with a predicted catalytic triad of Cys73, His162 and Asp182. The protein has been shown to have deubiquitinating-like activity, releasing aminoluciferin (AML) from Ub-AML.
Pfam PF08769: Sporulation initiation factor Spo0A C terminal (domain)
The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain.  This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices.  The structure contains a helix-turn-helix and binds DNA.
Pfam PF24645: Domain of unknown function (DUF7639) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to adopt a globular structure composed of a three helical bundle.
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 PF21005: mRNA-capping enzyme catalytic subunit, GTase, OB fold (domain)
mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module ([pfam:PF03291]). The N-terminal module comprises a TPase domain ([pfam:PF10640]), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, [pfam:PF21004]) and OB fold (represented in this entry) domains. This domain contains an essential motif (RxxK) for GTase activity.
Pfam PF12953: Domain of unknown function (DUF3842) (domain)
This short protein is found mainly in firmicute bacteria. It is functionally uncharacterised.
Pfam PF04275: Phosphomevalonate kinase (family)
Phosphomevalonate kinase ([ec:2.7.4.2]) catalyses the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate,  an essential step in isoprenoid biosynthesis via the mevalonate  pathway. This family represents the animal type of the  enzyme. The other is the ERG8 type, found in plants and fungi, and some bacteria (see [pfam:PF00288]).
Pfam PF23852: Family of unknown function (DUF7215) (family)
This entry represents a domain of unknown function found in phage proteins, typically 45-60 amino acids in length. It is found in Streptomyces phages of the Caudoviricetes order, primarily in the Arquatrovirinae subfamily. The domain does not contain any conserved motifs or residues that provide hints about its function. A structure prediction shows that it is composed of two non-interacting alpha 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 PF19390: Family of unknown function (DUF5965) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF07398: MDMPI C-terminal domain (domain)
This domain is found at the C-terminus of the mycothiol maleylpyruvate isomerase enzyme (MDMPI). The structure of this protein has been solved. This domain appears weakly similar to [pfam:PF08608].
Pfam PF10173: Mitochondrial K+-H+ exchange-related (family)
The members of this family function as mitochondrial potassium-hydrogen exchange transporters. The family is part of a large mitochondrial KHE protein 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 PF19549: Family of unknown function (DUF6072) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000967) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the calyculin A  biosynthetic gene cluster from uncultured Candidatus  Entotheonella sp. and 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 PF23458: Domain of unknown function (DUF7130) (domain)
This domain is found in a group of uncharacterised proteins mainly from Halobacteria. It contains highly conserved cysteine residues arranged in two CxxC motifs that likely coordinate zinc. The first motif could be more broadly defined as a semi-conserved MWRCxxCGEM sequence motif. This domain is predicted to adopt a zinc ribbon fold with similarity to rubredoxin-like domains.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23888: Family of unknown function (DUF7240) (family)
This protein is found in uncharacterized proteins from various mycobacteriophages and bacterial species including Nocardia and Mycobacterium. The protein is typically around 100 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 PF23883: Family of unknown function (DUF7236) (family)
This entry represents a family of uncharacterised mycobacterium phage proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF07107: Wound-induced protein WI12 (domain)
This family consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum ([swissprot:Q9XES3]). Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development. This family seems partly related to the NTF2-like superfamily.
Pfam PF13036: Peptidoglycan-synthase activator LpoB (family)
This is a family of Gram-negative bacterial outer membrane lipoproteins. LpoB is required for the function of the major peptidoglycan synthase enzyme PBP1B. It interacts with PBP1B protein via the UvrB-like non-catalytic domain on that protein. LpoB has a 54-aa-long flexible N-terminal stretch followed by a globular domain with similarity to the N-terminal domain of the prevalent periplasmic protein TolB. The long, flexible N-terminal region of LpoB enables it to span the periplasm and reach its docking site in PBP1B.  Peptidoglycan is the essential polymer within the sacculus that surrounds the cytoplasmic membrane of bacteria.
Pfam PF24931: ACR9-like, ACT-like domain (domain)
This is the third ACT domain of ACT domain-containing protein ACR9 from Arabidopsis thaliana and similar sequences mainly from plants and proteobacteria. ACR9 may bind amino acids.
Pfam PF14002: YniB-like protein (family)
The YniB-like protein family includes the E. coli YniB protein [swissprot:P76208] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. This family of proteins are integral membrane proteins.
Pfam PF11584: Proteinaceous host-selective toxin ToxA (family)
ToxA is produced by particular Pyrenophora tritici-repentis races and is a proteinaceous host-selective toxin. It is necessary and sufficient to cause cell death in sensitive wheat cultivars.ToxA adopts a single-domain, beta-sandwich fold which has novel topology. The protein is directly involved in recognition events required for ToxA action. It is thought to be distantly related to FnIII proteins, gaining entry to the host via an integrin-like receptor.
Pfam PF11429: Colicin D (domain)
Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loop.
Pfam PF18661: Avirulence Effector AvrLm4-7 (domain)
AvrLm4-7 is found in Leptosphaeria maculans, an ascomycete fungus in the dothideomycete group which is responsible for stem canker (blackleg) of Brassica napus (oilseed rape, OSR) and other crucifers. AvrLm4-7 is one of six avirulence genes which encodes a small secreted protein strongly over-expressed at the onset of plant infection. This gene confers a dual recognition specificity by two distinct resistance genes of OSR, Rlm4 and Rlm7 and loss of AvrLm4 avirulence was demonstrated to be associated with a strong fitness cost. Structure and functional analysis of AvrLm4-7 protein show that it contains the motifs RAWG and RYRE, part of a well-structured protein region held together by disulfide bridges. Mutations in the RAWG motif or in the RYRE motif (especially mutations in both motifs) almost abolished the translocation of AvrLm4-7 into cells. Furthermore, loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein.
Pfam PF07737: Anthrax toxin lethal factor, N- and C-terminal domain (domain)
The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive.
Wikipedia: Anthrax toxin is a three-protein exotoxin secreted by virulent strains of the bacterium, Bacillus anthracis—the causative agent of anthrax. The toxin was first discovered by Harry Smith in 1954. Anthrax toxin is composed of a cell-binding protein, known as protective antigen (PA), and two enzyme components, called edema factor (EF) and lethal factor (LF). These three protein components act together to impart their physiological effects. Assembled complexes containing the toxin components are endocytosed. In the endosome, the enzymatic components of the toxin translocate into the cytoplasm of a target cell. Once in the cytosol, the enzymatic components of the toxin disrupt various immune cell functions, namely cellular signaling and cell migration. The toxin may even induce cell lysis, as is observed for macrophage cells. Anthrax toxin allows the bacteria to evade the immune system, proliferate, and ultimately kill the host animal. Research on anthrax toxin also provides insight into the generation of macromolecular assemblies, and on protein translocation, pore formation, endocytosis, and other biochemical processes.
Pfam PF12451: Vacuolar protein sorting protein 11 C terminal (family)
This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion.
Pfam PF04640: PLATZ transcription factor (family)
Plant AT-rich sequence and zinc-binding proteins (PLATZ) are zinc dependant DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression. Included in this family is the protein RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), a transcription factor that plays a central role in mediating RGF1 hormone peptide signalling, leading to the production of reactive oxygen species (ROS) in roots to modulate meristem size and root growth, probably via oxidative post-translational modification of the transcription factor PLETHORA.
Pfam PF14423: Immunity protein Imm5 (domain)
A predicted Immunity protein, with an all-alpha fold, present in bacterial polymorphic toxin systems as an immediate neighbor of the toxin .
Pfam PF13192: Thioredoxin domain (domain)
Several biological processes regulate the activity of target proteins through changes in the redox state of thiol groups (S2 to SH2), where a hydrogen donor is linked to an intermediary disulphide protein. Such processes include the ferredoxin/thioredoxin system, the NADP/thioredoxin system, and the glutathione/glutaredoxin system . Several of these disulphide proteins share a common structure, consisting of a three-layer Î±/Î²/Î± core.
Wikipedia: The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.
Pfam PF13338: Transcriptional regulator, AbiEi antitoxin (domain)
AbiEi_4 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is [pfam:PF13338].
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF21232: Yme1-like, N-terminal (repeat)
This domain is found at the N-terminal end of a group of proteins predominantly found in fungi, plants and basal metazoans, including Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 from Saccharomyces cerevisiae. This domain adopts a tetratricopeptide repeat fold.
Pfam PF23422: Family of unknown function (DUF7110) (family)
This family represents a group of proteins from halobacteria. Members are predicted to show an alpha-beta configuration.
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 PF21632: Helicase MOV-10, N-terminal (domain)
Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC). It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission. It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2. This entry represents the N-terminal domain of MOV-10, whose function is not known. According to structure predictions, it may consist in a helix-turn-helix domain which suggests a likely DNA-binding function.