SII-SWORD/CoKE huggingface dataset:
Pfam PF09235: Ste50p, sterile alpha motif (domain)
The fungal Ste50p SAM domain consists of five helices, which form a compact, globular fold. It is required for mediation of homodimerisation and heterodimerisation (and in some cases oligomerisation) of the protein.
Wikipedia: In molecular biology, the protein domain Sterile alpha motif is a putative protein interaction module present in a wide variety of proteins involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins, nevertheless with a low affinity constant.
Pfam PF23740: Zona pellucida sperm-binding protein 2, Ig-like domain (domain)
This domain is found in human Zona pellucida sperm-binding protein 2 (ZP2) and similar proteins from vertebrates. ZP2 is a component of the zona pellucida, an extracellular matrix surrounding oocytes which mediates sperm binding, induction of the acrosome reaction and prevents post-fertilisation polyspermy. This domain is predicted to adopt a two-layer beta sandwich configuration.
Pfam PF18906: Phage tail tube protein (family)
This family of proteins are tube proteins which polymerise to form the phage tails.
Pfam PF05629: Nanovirus component 8 (C8) protein (family)
This family consists of a group of 17.4 kDa nanovirus proteins which are highly related to the faba bean necrotic yellows virus component 8 protein whose function is unknown.
Pfam PF09571: XcyI restriction endonuclease (family)
This family includes the XcyI (recognises and cleaves C^CCGGG) restriction endonucleases.
Pfam PF14394: Domain of unknown function (DUF4423) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 170 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 PF16796: Microtubule binding (domain)
This motor homology domain binds microtubules and lacks an ATP-binding site.
Pfam PF17434: Family of unknown function (DUF5413) (family)
This is a family of unknown function found in Bradyrhizobiaceae. Family members contain 3 or 4 predicted 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 PF24182: Gene 1 ring forming protein (domain)
This entry represents an uncharacterised family of bacteriophage proteins annotated as gene 1. These proteins form a pair of alpha helices that interact with each other.  These proteins are predicted to form large ring structures, with 13-15 subunits having the highest predicted scores. Once the rings are formed they have a strongly negatively charged exterior.
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 PF20098: Family of unknown function (DUF6488) (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.
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 PF07566: Domain of Unknown Function (DUF1543) (domain)
This domain is found as 1-2 copies in a small family of proteins 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 PF01549: ShK domain-like (domain)
This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges.  The domain is found in the potassium channel inhibitor ShK in sea anemone.
Wikipedia: Stichodactyla toxin is a 35-residue basic peptide from the sea anemone Stichodactyla helianthus that blocks a number of potassium channels. Related peptides form a conserved family of protein domains known as the ShkT domain. Another well-studied toxin of the family is BgK from Bunodosoma granulifera.
Pfam PF12434: Malate dehydrogenase enzyme (family)
This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF00390], [pfam:PF03949], [pfam:PF01515]. There is a conserved AAL sequence motif.  There is a single completely conserved residue R that may be functionally important. Malate dehydrogenase is one of the enzymes involved in the citric acid cycle in mitochondria. It converts malate to oxaloacetate using NAD as a cofactor.
Pfam PF07984: Nucleotidyltransferase (domain)
This family contains many hypothetical proteins. It also includes four nematode prion-like proteins. This domain has been identified as part of the nucleotidyltransferase superfamily.
Pfam PF11215: Protein of unknown function (DUF3010) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF11266: Long-chain fatty aldehyde decarbonylase (domain)
This cyanobacterial family of fatty aldehyde decarbonylases acts on  mainly C16 and C18 substrates to form hydrocarbons and carbon  monoxide. Note that the corresponding EC number ([ec:4.1.99.5]) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase.
Pfam PF00775: Dioxygenase (domain)
This entry represents the C-terminal domain common to several intradiol ring-cleavage dioxygenases.
Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (IPR000486) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) . These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues.

Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (1.13.11.1); protocatechuate 3,4-dioxygenase (3,4-PCD) (1.13.11.3); and chlorocatechol 1,2-dioxygenase (1.13.11.1) .
Wikipedia: Dioxygenases are oxidoreductase enzymes. Aerobic life, from simple single-celled bacteria species to complex eukaryotic organisms, has evolved to depend on the oxidizing power of dioxygen in various metabolic pathways. From energetic adenosine triphosphate (ATP) generation to xenobiotic degradation, the use of dioxygen as a biological oxidant is widespread and varied in the exact mechanism of its use. Enzymes employ many different schemes to use dioxygen, and this largely depends on the substrate and reaction at hand.
Pfam PF02271: Ubiquinol-cytochrome C reductase complex 14kD subunit (family)
The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex.
Wikipedia: The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain, playing a critical role in biochemical generation of ATP. Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial and the nuclear genomes. Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most bacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits, 2 core proteins and 6 low-molecular weight proteins.
Pfam PF14885: Hypothetical glycosyl hydrolase family 15 (family)
GHL15 is a family of hypothetical glycoside hydrolases.
Pfam PF05876: Phage terminase large subunit gpA, ATPase domain (domain)
This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, TerL (gpA), products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA during the DNA packaging process. TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal (represented in this entry) reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity.
Pfam PF09873: Uncharacterized protein conserved in archaea (DUF2100) (family)
This domain, found in various hypothetical archaeal proteins, has no known 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 PF22443: FbpC-like, regulatory domain (domain)
This entry represents the regulatory domain (RD) of Fe(3+) ions import ATP-binding protein FbpC, the nucleotide-binding domain of the iron-uptake ABC transporter FbpABC from Neisseria gonorrhoeae. This domain adopts two OB-folds per monomer.
Pfam PF14198: Transposon-encoded protein TnpV (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 114 and 125 amino acids in length.
Pfam PF11751: Type IX secretion system membrane protein PorP/SprF (family)
This entry describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Cytophaga johnsonae (Flavobacterium johnsoniae), that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss of the rapid gliding phenotype.
Pfam PF11560: Lamina-associated polypeptide 2 alpha (family)
LAPs are components of the nuclear lamina which supports the nuclear envelope.LAP2alpha is a non-membrane-associated member of the LAP family which is unique. This family of proteins is the C terminal domain of LAP2alpha which consists of residues 459-693 and constitutes a dimeric structure with an antiparallel coiled coil. LAP2alpha is involved in cell-cycle regulation and chromatin organisation and preferentially binds to lamin A/C.
Pfam PF06384: Beta-catenin-interacting protein ICAT (family)
This family consists of several eukaryotic beta-catenin-interacting (ICAT) proteins. Beta-catenin is a multifunctional protein involved in both cell adhesion and transcriptional activation. Transcription mediated by the beta-catenin/Tcf complex is involved in embryological development and is upregulated in various cancers. ICAT selectively inhibits beta-catenin/Tcf binding in vivo, without disrupting beta-catenin/cadherin interactions.
Pfam PF00594: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain (domain)
This  domain is  responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).
Wikipedia: Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain is a protein domain that contains post-translational modifications of many glutamate residues by vitamin K-dependent carboxylation to form γ-carboxyglutamate (Gla). Proteins with this domain are known informally as Gla proteins. The Gla residues are responsible for the high-affinity binding of calcium ions.
Pfam PF23485: YBR230W-A (family)
This protein family includes the uncharacterised protein YBR230W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF).
Pfam PF06575: Protein of unknown function (DUF1132) (family)
This family consists of several hypothetical proteins from Neisseria meningitidis. The function of this family is unknown.
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 PF17789: Macroglobulin domain MG4 (domain)
This domain is MG4 found in complement C3 and C5 proteins.
Pfam PF01124: MAPEG family (family)
This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyses the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity.
Wikipedia: In molecular biology the MAPEG  family of proteins are a group of membrane associated proteins with highly divergent functions. Included are the 5-lipoxygenase-activating protein, leukotriene C4 synthase, which catalyzes the production of leukotriene C4 (LTC4) from leukotriene A4 (LTA4), and microsomal glutathione S-transferase II (GST-II), which also produces LTC4 from LTA4.
Pfam PF15772: UPF0688 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 176 and 243 amino acids in length.
Pfam PF25010: UBP24/USP9X/USP9Y ARM repeat (repeat)
This entry represents an ARM-repeats domain found in ubiquitin carboxyl-terminal hydrolases (UCHs), such as UBP24, UBP34, USP9X and USP9Y and the orthologues from Drosophila. UCHs are thiol proteases that recognise and hydrolyse the peptide bond at the C-terminal glycine of ubiquitin. UBP24 regulates cell survival in various contexts through modulating the protein stability of some of its substrates including DDB2, MCL1 or TP53. USP9X and USP9Y are involved in deubiquitination of target proteins.
Pfam PF10303: Protein of unknown function (DUF2408) (family)
This is a family of proteins conserved in fungi. The function is unknown.
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 PF03612: Sorbitol phosphotransferase enzyme II N-terminus (family)
Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man family is unique in several respects among PTS permease families.


 * It is the only PTS family in which members possess a IID protein.
 * It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
 * Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.


The Gut family consists only of glucitol-specific permeases, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein.

This entry represents the N-terminal conserved region of the IIBC component.
Pfam PF17375: Family of unknown function (DUF5397) (family)
This is a family of unknown function found in Proteobacteria.
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 PF20677: Herpesvirus envelope glycoprotein gp350 N-terminal C domain (domain)
This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C-terminal that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A, B and C) which organise into an "L-shape" structure. This is domain C.
Pfam PF18701: Family of unknown function (DUF5641) (domain)
This presumed domain is found in a range of retrotransposon polyproteins.
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 PF09899: Putative amidoligase enzyme (DUF2126) (family)
Members of this family of bacterial domains are predominantly found in transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown, but they are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes).
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 PF17153: Periplasmic sensor domain, extracellular (family)
CHASE9 is a conserved extracellular (periplasmic) sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases, methyl-accepting chemotaxis proteins, adenylate cyclases and protein serine phosphatases, including the c-di-GMP phosphodiesterases PdeI (YliE) of Escherichia coli.
Pfam PF17047: Synaptotagmin-like mitochondrial-lipid-binding domain (domain)
SMP is a proposed lipid-binding module, ie a synaptotagmin-like mitochondrial-lipid-binding domain found in eukaryotes. The SMP domain has a beta-barrel structure like protein modules in the tubular-lipid-binding (TULIP) superfamily. It dimerises to form an approximately 90-Angstrom-long cylinder traversed by a channel lined entirely with hydrophobic residues. The following two C2 domains then form arched structures flexibly linked to the SMP domain. The SMP domain is a lipid-binding domain that links the ER with other lipid bilayer-membranes within the cell.
Pfam PF13284: Domain of unknown function (DUF4072) (family)
This short domain is normally found at the very N-terminus of Hyrdrolases [pfam:PF00702].
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 PF04069: Substrate binding domain of ABC-type glycine betaine transport system (family)
Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation.  This domain is often fused to the permease component of the transporter complex.  Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport.  Choline is necessary for the biosynthesis of glycine betaine.  L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).