SII-SWORD/CoKE huggingface dataset:
Pfam PF22359: Bacterial Ig-like domain (domain)
This entry represents bacterial domains that are structurally similar to an immunoglobulin-like domain of intimins. Members of this family include Surface layer protein from Geobacillus stearothermophilus.
Pfam PF19418: DEPDC5 protein C-terminal region (family)
This entry represents the C-terminal domain (CTD) (residues 1,291-1,603) of the DEPDC5 protein. It contains two structurally similar lobes and has a pseudo-2-fold rotational symmetry. Each half consists of a five-stranded beta-sheet, with an alpha-helix covering one side. The CTD is located in the core of DEPDC5 and contacts all the other domains of DEPDC5 except the NTD, making it the central organizer of this multi-domain protein.
Pfam PF17329: Family of unknown function (DUF5367) (family)
This bacterial family of proteins of unknown function is predicted to contain 3 or 4 trans-membrane regions.
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 PF15065: Lysosomal transcription factor, NCU-G1 (family)
NCU-G1 is a set of highly conserved nuclear proteins rich in proline with a molecular weight of approximately 44 kDa. Especially high levels are detected in human prostate, liver and kidney. NCU-G1 is a dual-function family capable of functioning as a transcription factor as well as a nuclear receptor co-activator by stimulating the transcriptional activity of peroxisome proliferator-activated receptor-alpha (PPAR-alpha).
Pfam PF04834: Early E3 14.5 kDa protein (family)
The E3B 14.5 kDa was first identified in Human adenovirus type 5. It is an integral membrane protein oriented with its C terminus in the cytoplasm.  It functions to down-regulate the epidermal growth factor receptor and prevent tumour necrosis factor cytolysis.  It achieves this through the interaction with E3 10.4 kDa protein.
Pfam PF04495: GRASP55/65 PDZ-like domain (domain)
GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system.  This region appears to be related to the PDZ domain.
Pfam PF19532: Transmembrane protein 131-like, second Ig-like domain (domain)
Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region. Using structure prediction models from AlphaFold, it has  been possible to identify the CHDs as Ig-like domains. This entry represents the second Ig-like domain of TMEM131L and the third in TMEM131. TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII.
Pfam PF14354: Restriction alleviation protein Lar (family)
This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli, [swissprot:P33229]. This protein modulates the activity of the Escherichia coli restriction and modification system.
Pfam PF00097: Zinc finger, C3HC4 type (RING finger) (domain)
The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF09017: Microbial transglutaminase (domain)
Microbial transglutaminase (MTG) catalyses an acyl transfer reaction by means of a Cys-Asp diad mechanism, in which the gamma-carboxyamide groups of peptide-bound glutamine residues act as the acyl donors. The MTG molecule forms a single, compact domain belonging to the alpha+beta folding class, containing 11 alpha-helices and 8 beta-strands. The alpha-helices and the beta-strands are concentrated mainly at the amino and carboxyl ends of the polypeptide, respectively. These secondary structures are arranged so that a beta-sheet is surrounded by alpha-helices, which are clustered into three regions.
Wikipedia: Transglutaminases are enzymes that in nature primarily catalyze the formation of an isopeptide bond between γ-carboxamide groups ( -(C=O)NH2 ) of glutamine residue side chains and the ε-amino groups ( -NH2 ) of lysine residue side chains with subsequent release of ammonia ( NH3 ). Lysine and glutamine residues must be bound to a peptide or a protein so that this cross-linking (between separate molecules) or intramolecular (within the same molecule) reaction can happen. Bonds formed by transglutaminase exhibit high resistance to proteolytic degradation (proteolysis). The reaction isGln-(C=O)NH2 + NH2-Lys → Gln-(C=O)NH-Lys + NH3
Pfam PF11298: Protein of unknown function (DUF3099) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02557: D-alanyl-D-alanine carboxypeptidase (family)
These proteins are metallopeptidases belonging to MEROPS peptidase family M15 (clan MD), subfamily M15B (vanY D-Ala-D-Ala carboxypeptidase).
Wikipedia: In molecular biology, VanY are protein domains found in enzymes named metallopeptidases. They are vital to bacterial cell wall synthesis and antibiotic resistance.
Pfam PF14447: Prokaryotic RING finger family 4 (family)
RING finger family domain found sporadically in bacteria. The finger is fused to an N-terminal alpha-helical domain, ROT/Trove-like repeats and a C-terminal TerD domain. The architecture suggests a possible role in an RNA-processing complex.
Pfam PF08132: S-adenosyl-l-methionine decarboxylase leader peptide (family)
This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzymes in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5' leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism.
Pfam PF00355: Rieske [2Fe-2S] domain (domain)
The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein.
Wikipedia: Rieske proteins are iron–sulfur protein (ISP) components of cytochrome bc1 complexes and cytochrome b6f complexes and are responsible for electron transfer in some biological systems. John S. Rieske and co-workers first discovered the protein and in 1964 isolated an acetylated form of the bovine mitochondrial protein. In 1979, Trumpower's team isolated the "oxidation factor" from bovine mitochondria and showed it was a reconstitutively-active form of the Rieske iron-sulfur protein.
It is a unique [2Fe-2S] cluster in that one of the two Fe atoms is coordinated by two histidine residues rather than two cysteine residues. They have since been found in plants, animals, and bacteria with widely ranging electron reduction potentials from -150 to +400 mV.
Pfam PF14096: Domain of unknown function (DUF4274) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 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 PF06018: CodY GAF-like domain (domain)
This domain is a GAF-like domain found at the N-terminus of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. This domain is involved in GTP binding and also branched chain amino acids (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Wikipedia: In molecular biology, the CodY protein family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk.
Pfam PF00395: S-layer homology domain (repeat)
S-layers are paracrystalline mono-layered assemblies of (glyco)proteins which coat the surface of bacteria . Several S-layer proteins and some other cell wall proteins contain one or more copies of a domain of about 50-60 residues, which has been called SLH (for S-layer homology). Although it was originally proposed that SLH domains bind to peptidoglycan, it is now evident that pyruvylated secondary cell wall polymers (SCWPs), which are either teichoic acids, teichuronic acids, lipoteichoic acids or lipoglycans, serve as the anchoring structures for SLH motifs in the Gram-positive cell wall . However, the study of S-layer protein SbpA of Bacillus sphaericus revealed that SLH motifs are not sufficient for specific binding to SCWPs. Thus, the molecular basis explaining SLH affinity and specificity of interaction with cell wall polymers are not completely elucidated .
Pfam PF01012: Electron transfer flavoprotein domain (domain)
This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein.
Wikipedia: An electron transfer flavoprotein (ETF) or electron transfer flavoprotein complex (CETF) is a flavoprotein located on the matrix face of the inner mitochondrial membrane and functions as a specific electron acceptor for primary dehydrogenases, transferring the electrons to terminal respiratory systems such as electron-transferring-flavoprotein dehydrogenase. They can be functionally classified into constitutive, "housekeeping" ETFs, mainly involved in the oxidation of fatty acids, and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates.
Pfam PF07660: Secretin and TonB N terminus short domain (family)
This is a short domain found at the N-terminus of the Secretins of the bacterial type II/III secretory system as well as the TonB-dependent receptor proteins. These proteins are involved in TonB-dependent active uptake of selective substrates.
Pfam PF09046: AvrPtoB E3 ubiquitin ligase (domain)
The E3 ubiquitin ligase domain found in the bacterial protein AvrPtoB inhibits immunity-associated programmed cell death (PCD) when translocated into plant cells, probably by recruiting E2 enzymes and transferring ubiquitin molecules to cellular proteins involved in regulation of PCD and targeting them for degradation. The structure of this domain reveals a globular fold centred on a four-stranded beta-sheet that packs against two helices on one face and has three very extended loops connecting the elements of secondary structure, with remarkable homology to the RING-finger and U-box families of proteins involved in ubiquitin ligase complexes in eukaryotes.
Pfam PF09060: L27_N (domain)
The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation.
Wikipedia: The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein. The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.
The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer.
Pfam PF07683: Cobalamin synthesis protein cobW C-terminal domain (domain)
This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF12529: Xylosyltransferase C terminal (family)
This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with [pfam:PF02485]. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans.
Pfam PF22865: Small protein MgtS-like (family)
This family includes Small protein MgtS from Escherichia coli and similar sequences mainly found in gammaproteobacteria. MgtS, also known as YneM, is the product of a small open reading frame (smORF). This 31-amino-acid protein modulates intracellular magnesium levels to maintain cellular integrity. It forms a single transmembrane helix.
Pfam PF02286: Dehydratase large subunit (domain)
This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.
Pfam PF06552: Plant specific mitochondrial import receptor subunit TOM20 (repeat)
This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria.
Wikipedia: The translocase of the outer membrane (TOM) is a complex of proteins found in the outer mitochondrial membrane of the mitochondria. It allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion. Most of the proteins needed for mitochondrial function are encoded by the nucleus of the cell. The outer membrane of the mitochondrion is impermeable to large molecules greater than 5000 daltons. The TOM works in conjunction with the translocase of the inner membrane (TIM) to translocate proteins into the mitochondrion. Many of the proteins in the TOM complex, such as TOMM22, were first identified in Neurospora crassa and Saccharomyces cerevisiae. Many of the genes encoding these proteins are designated as TOMM (translocase of the outer mitochondrial membrane) complex genes.
Pfam PF23365: Family of unknown function (DUF7090) (family)
This entry represents a family of proteins from halobacteria. Members of this family, often annotated as ATPases, are predicted to show a central beta-sheet with alpha-helices in both sides.
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 PF12019: Type II transport protein GspH (domain)
GspH is involved in bacterial type II export systems. Like all pilins, GspH has an N terminus alpha helix. This helix is followed by nine beta strands forming two beta sheets, one of five antiparallel strands and one of four antiparallel strands. GspH is a minor pseudopilin; it is expressed much less than other pseudopilins in the type II secretion pilus (major pilins).  The function and localisation of minor pseudo-pilins are still to be fully unraveled. It has been suggested that some minor pseudopilins may assemble either into the base or the tip of pili, or both. They function as initiators or regulators of pilus biogenesis and dynamics, and/or as adaptors between various pseudopilin component and other members of the T2SS.
Pfam PF14230: Domain of unknown function (DUF4333) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 255 amino acids in length. There are two completely conserved C residues that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14578: Elongation factor Tu domain 4 (domain)
Elongation factor Tu consists of several structural domains, and this is usually the fourth.
Pfam PF04624: Dec-1 repeat (repeat)
The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown.  Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats.
Pfam PF05820: Baculoviridae AC81 (family)
This family consists of several highly related Baculovirus proteins and includes Autographa californica multiple nucleopolyhedrovirus (AcMNPV) protein AC81, which is required for nucleocapsid envelopment. Ac81 contains a functional hydrophobic transmembrane (TM) domain, whose deletion resulted in a phenotype similar to that of Ac81 knockout.
Pfam PF16090: Domain of unknown function (DUF4819) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 82 and 99 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 PF02450: Lecithin:cholesterol acyltransferase (family)
Lecithin:cholesterol acyltransferase (LCAT) is involved in extracellular metabolism of plasma lipoproteins, including cholesterol.
Wikipedia: In enzymology, a phospholipid:diacylglycerol acyltransferase is an enzyme that catalyzes the chemical reactionphospholipid + 1,2-diacylglycerol  lysophospholipid + triacylglycerol
Pfam PF19181: Family of unknown function (DUF5863) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF13033: Protein of unknown function (DUF3894) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 79 amino acids in length. There are two conserved sequence motifs: FNIC and MALLNLT.
Pfam PF12306: Inclusion body protein (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein.