SII-SWORD/CoKE huggingface dataset:
Pfam PF23538: Teneurin antibiotic-binding-like domain (domain)
The Antibiotic-Binding-Like Domain (ABD) is a conserved structural motif identified in the teneurin family of proteins, characterized by its resemblance to bacterial proteins known to bind small-molecule antibiotics such as bleomycin and zorbamycin. In the crystal structure of chicken Ten2, the ABD comprises approximately 120 residues and is positioned immediately downstream of the shell exit site. Structural homology analyses reveal similarities between the ABD of chicken Ten2 and antibiotic-binding proteins found in bacteria. These bacterial proteins confer resistance to antibiotics by sequestering them, thereby preventing their activation by oxygen. The ABD of teneurins wraps around a long helix that leads into the most C-terminal domain, known as the ToxGHH domain.
Pfam PF06337: DUSP domain (domain)
The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet.
Wikipedia: Deubiquitinating enzymes (DUBs), also known as deubiquitinating peptidases, deubiquitinating isopeptidases, deubiquitinases, ubiquitin proteases, ubiquitin hydrolases, or ubiquitin isopeptidases, are a large group of proteases that cleave ubiquitin from proteins. Ubiquitin is attached to proteins in order to regulate the degradation of proteins via the proteasome and lysosome; coordinate the cellular localisation of proteins; activate and inactivate proteins; and modulate protein-protein interactions. DUBs can reverse these effects by cleaving the peptide or isopeptide bond between ubiquitin and its substrate protein. In humans there are nearly 100 DUB genes, which can be classified into two main classes: cysteine proteases and metalloproteases. The cysteine proteases comprise ubiquitin-specific proteases (USPs), ubiquitin C-terminal hydrolases (UCHs), Machado-Josephin domain proteases (MJDs) and ovarian tumour proteases (OTU). The metalloprotease group contains only the Jab1/Mov34/Mpr1 Pad1 N-terminal+ (MPN+) (JAMM) domain proteases.
Pfam PF24676: Domain of unknown function (DUF7656) (domain)
This domain is found in a group of uncharacterised eukaryotic proteins. It shares detectable similarity to the Thioredoxin-like SNTX domain ([pfam:PF18078]) 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.
Pfam PF16677: DNA-packaging protein gp3 (domain)
DNA-packaging protein gp3 (terminase small subunit) is involved in DNA packing in bacteriophage. it contains a channel where DNA is bound and passed to DNA-packaging protein gp2 (terminase large subunit).
Pfam PF17649: Vacuolar protein sorting 38 (family)
The class III phosphatidylinositol-3-kinase (PI3K) known as Vps34 (vacuolar protein sorting 34, encoded by PIK3C3) regulate intracellular membrane trafficking in endocytic sorting, cytokinesis and autophagy. Vps34 forms complexes with other proteins: Vps15 (encoded by PIK3R4, known as p150 in mammalian cells), Vps30 (encoded by VPS30/ATG6 in yeast, equivalent to mammalian Beclin 1, encoded by BECN1) and either Vps38 (UVRAG) or Atg14 (ATG14L). This family includes members such as Vps38 found in Saccharomyces cerevisiae [swissprot:Q05919]. Vps38 is characteristic of complex II and essential for vacuolar protein sorting. In mammalian cells, complex II is also involved in autophagy, receptor degradation and cytokinesis as well as signaling, recycling and lysosomal tubulation. Independently from complex I and II, Beclin 1 and UVRAG also play separate roles in endosome function and neuron viability. In complex I, Vps38/UVRAG is substituted with Atg14/ATG14L. Although the N-terminal domains of Vps30, Vps38 and Atg14 differ, the overall similarity of their domain organizations suggests that these proteins may have evolved from a common ancestor.
Pfam PF03963: Flagellar hook capping protein - N-terminal region (family)
FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum. It appears to act as a hook-capping protein to enable assembly of hook protein subunits.  FlgD regulates the assembly of the hook cap structure to prevent leakage of hook monomers into the medium and hook monomer polymerisation and also plays a role in determination of the correct hook length, with the help of the FliK protein.  This family represents the N-terminal conserved region of FlgD. A recent crystal structure showed that this region was likely to be flexible and was cleaved off during crystallisation.
Pfam PF17995: Endo-alpha-N-acetylgalactosaminidase N-terminal domain (domain)
This is the N-terminal domain found in Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase ([ec:3.2.1.97]) , a cell surface-anchored glycoside hydrolase from family GH101 involved in the breakdown of mucin type O-linked glycans. This is a twisted beta-sandwich domain composed of two sheets of six and seven antiparallel beta-strands. The domain appears to be missing the extended metal and carbohydrate-binding loops.
Wikipedia: Endo-α-N-acetylgalactosaminidase (EC 3.2.1.97, endo-α-acetylgalactosaminidase, endo-α-N-acetyl-D-galactosaminidase, mucinaminylserine mucinaminidase, D-galactosyl-3-(N-acetyl-α-D-galactosaminyl)-L-serine mucinaminohydrolase, endo-α-GalNAc-ase, D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase) is an enzyme with systematic name glycopeptide-D-galactosyl-N-acetyl-α-D-galactosamine D-galactosyl-N-acetyl-galactosaminohydrolase. This enzyme catalyses the following chemical reaction3-O-beta-D-galactosyl-N-acetyl-alpha-D-galactosaminyl-L-serine-[protein] + H2O  3-O-beta-D-galactosyl-N-acetyl-alpha-D-galactosamine + L-serine-[protein]
Pfam PF13518: Helix-turn-helix domain (domain)
This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.
Pfam PF11134: Phage stabilisation protein (family)
Members of this family are phage proteins that are probably involved with stabilising the condensed DNA within the capsid.
Pfam PF02446: 4-alpha-glucanotransferase (domain)
These enzymes [ec:2.4.1.25] transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan.
Wikipedia: In molecular biology, glycoside hydrolase family 77 is a family of glycoside hydrolases.
Pfam PF02986: Fibronectin binding repeat (conserved_site)
The ability of bacteria to bind fibronectin is thought to enable the colonisation of wound tissue and blood clots.  The fibronectin binding repeat is found in bacterial fibronectin binding proteins and serum opacity factor.  Bacterial fibronectin binding proteins are surface proteins that covalently link to the bacterial cell wall, mediate adherence of the bacteria to host cells and trigger the fibronectin/integrin-mediated uptake of bacteria by host cells. Each fibronectin binding repeat is an array of short motifs that bind to fibronectin type I domains. Fibronectin binding repeats are natively unfolded in the absence of fibronectin and are thought to adopt a well-defined conformation (tandem beta-zipper) upon binding.
Pfam PF09391: Protein of unknown function (DUF2000) (family)
This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold.
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 PF23641: YmcF-like (family)
This protein family includes Protein YmcF from Escherichia coli and similar sequences from gammaproteobacteria. YmcF is a 62-residues long cold shock-regulated micropeptide encoded by an small open reading frame (smORF).
Pfam PF22810: Lytic polysaccharide monooxygenase AA14 (family)
This entry represents the AA14 family of lytic polysaccharide monooxygenases (LPMOs). These enzymes cleave polysaccharides through an oxidative, instead of hydrolytic, mechanism. They fold into a globular structure, the core of which comprising largely an Ig-like beta-sandwich. The active site consists of two histidine and a tyrosine residue, forming the canonical histidine brace exposed at the surface.
Pfam PF21825: crAss001_48 related protein (family)
This entry represents a family of proteins that are present in crAss phage. AlphaFold predicts these short proteins to adopt an alpha helical hairpin structure. The function of these proteins is unknown.
Pfam PF02009: Rifin (family)
Plasmodium falciparum is the causative agent of deadly malaria disease. It encodes repetitive interspersed families of polypeptides (RIFINs), which are expressed on the surface of infected erythrocytes. All RIFIN sequences contain the PEXEL motif (a pentameric sequence RxLxE/Q/D, known as the Plasmodium export element) required for correct export and surface expression or host-targeting (HT) signal which plays a central role in the export of proteins into the host cell. It has been reported that PEXEL is preferably located 15-20 amino acids downstream of an N-terminal hydrophobic signal sequence. The RIFIN protein family can be divided into A and B types based on the presence or absence of a 25 amino acid motif located approximately 66 amino acids downstream of the PEXEL motif, with A- and B-types serving different roles in distinct parasite stages. The specific type B RIFIN variant (PF13_0006) is expressed on the surface of free merozoites, internally in developing gametocytes and on the surface of gametes at the point of emerging from activated, mature stage V gametocytes. While type A RIFIN are expressed on the infected erythrocyte surface, potentially contributing to the antigenic variation capacity of the parasite.
Pfam PF03219: TLC ATP/ADP transporter (family)
These proteins are members of the ATP:ADP Antiporter (AAA) family, which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers.
This family contains bacterial proteins as well as chloroplastic proteins found in plants.
Pfam PF17900: Peptidase M1 N-terminal domain (domain)
This domain is found at the N-terminus of aminopeptidases from the M1 family.
Pfam PF03642: MAP domain (domain)
This presumed 110 amino acid residue domain is found in multiple copies in MAP (MHC class II analogue protein) [swissprot:Q9Z4J2]. The protein has been found in a wide range of extracellular matrix proteins.
Pfam PF22651: AgamOBP47-like (domain)
This domain is found in the Anopheles gambiae odorant-binding protein AgamOBP47 and related proteins. OBP47 belongs a C-plus class OBP and possesses 13 cysteine residues. It folds into a eight helical structure instead of six as observed in the classical OBPs and no internal cavity.
Pfam PF18705: Family of unknown function (DUF5643) (domain)
This is an immunoglobulin-like domain 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 PF17595: Family of unknown function (DUF5491) (family)
This is a family of unknown function found in Myoviridae.
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 PF06784: Uncharacterised protein family (UPF0240) (family)
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 4 (NDUFAF4, also known as HRPAP20) is involved in the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) . It may be involved in cell proliferation and survival of hormone-dependent tumor cells .
Pfam PF20373: Family of unknown function (DUF6668) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 208 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 PF20187: Family of unknown function (DUF6550) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Firmicutes. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs at the C-terminal: FGW/I and I/VGxM.
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 PF04634: Immunity protein YezG-like (family)
This protein family includes the immunity protein YezG from Bacillus subtilis and similar sequences predominantly found in Firmicutes. YezG is the antitoxin component of a LXG toxin-antitoxin (TA) module that promote kin selection, mediate competition in biofilms, and drive spatial segregation of different strains, probably helping to avoid warfare between strains in biofilms. It shows an alpha/beta structure with an antiparallel beta-sheet.
Pfam PF18083: Proline utilization A N-terminal domain (domain)
This domain is found in Proline utilization A (PutA) proteins present in Geobacter sulfurreducens. PutA are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate and couple the oxidation of imported proline imported to the reduction of membrane-associated quinones. This domain is located at the N-terminus and is referred to as the alpha domain. The hydrocarbon tail of Zwittergent 3-12 binds to an exposed hydrophobic patch of the alpha domain which contains aromatic and nonpolar residues. The domain may be involved in membrane association.
Pfam PF19504: Family of unknown function (DUF6038) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000758) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a  protein from the capsular polysaccharide biosynthetic gene cluster  from Staphylococcus aureus.
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 PF20313: Family of unknown function (DUF6609) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are 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 PF07963: Prokaryotic N-terminal methylation motif (conserved_site)
This short motif directs methylation of the conserved phenylalanine residue.  It is most often found at the N-terminus of pilins and other proteins involved in secretion, see [pfam:PF00114], [pfam:PF05946], [pfam:PF02501] and [pfam:PF07596].
Pfam PF10394: Histone acetyl transferase HAT1 N-terminus (domain)
This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 ([pfam:PF00583]) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyse the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated.
Pfam PF11556: Erythrocyte binding antigen 175 (family)
EBA-175 is involved in the formation of a tight junction, a necessary step in invasion. This family represents the region VI which is a cysteine rich domain essential for EBA-175 trafficking. The structure is a homodimer that contains a five-alpha-helical core stabilised by four disulphide bridges.
Pfam PF06064: Host-nuclease inhibitor protein Gam (family)
The Gam protein inhibits RecBCD nuclease and is found in both bacteria and bacteriophage.
Pfam PF18429: Domain of unknown function (DUF5609) (domain)
This is a probable HAD-like (haloalkanoate dehalogenase) domain found in bacterial phosphoserine phosphatases.
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 PF10738: Probable lipoprotein LpqN (family)
This family is conserved in Mycobacteriaceae and is likely to be a lipoprotein.
Pfam PF20606: Domain of unknown function (DUF6799) (domain)
This domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes and it is approximately 50 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 PF09328: Domain of unknown function (DUF1984) (family)
Members of this family of functionally uncharacterised domains are found at the C-terminus of plant phytochelatin synthases.
Pfam PF19374: Family of unknown function (DUF5949) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide.
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 PF13053: Protein of unknown function (DUF3914) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: KFDIR and DLW.
Pfam PF13996: YobH-like protein (family)
The YobH-like protein family includes the YobH protein from E. coli [swissprot:Q2MB16] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: GYG and GLGL.
Pfam PF23974: Domain of unknown function (DUF7300) (domain)
This entry represents a small family of uncharacterised phage proteins. These proteins contain a small compact globular domain composed of a four stranded meander followed by a C-terminal alpha helix.
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 PF13472: GDSL-like Lipase/Acylhydrolase family (domain)
This family of presumed lipases and related enzymes are similar to [pfam:PF00657].
Pfam PF15254: Coiled-coil domain-containing protein 14 (coiled_coil)
This protein family, Coiled-coil domain-containing protein 14 (CCDC14) is a domain of unknown function. This family of proteins is found in eukaryotes. Proteins in this family are typically between 301 and 912 amino acids in length.