SII-SWORD/CoKE huggingface dataset:
Pfam PF19986: Family of unknown function (DUF6422) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  lavendiol biosynthetic gene cluster from Streptomyces lavendulae.
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 PF01193: RNA polymerase Rpb3/Rpb11 dimerisation domain (domain)
The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer.  The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain ([pfam:PF01000]).  Some of the alpha subunits also contain iron-sulphur binding domains ([pfam:PF00037]).  Rpb11 is found as a continuous domain.  Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Pfam PF20377: Family of unknown function (DUF6672) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 134 and 164 amino acids in length. This family contains an N-terminal predicted transmembrane helix and a negatively charged C-terminus.
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 PF03107: C1 domain (domain)
This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in [pfam:PF00130], therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions.  The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol (A Bateman pers. obs.). This family are found in plant proteins.
Wikipedia: C1 domain binds an important secondary messenger diacylglycerol (DAG), as well as the analogous phorbol esters. Phorbol esters can directly stimulate protein kinase C, PKC.
Pfam PF23322: AH receptor-interacting protein, N-terminal FKBP-type PPIase (domain)
This is the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) domain of human AH receptor-interacting protein (AIP) and similar animal proteins. AIP may play a positive role in AHR-mediated (aromatic hydrocarbon receptor) signalling. This domain shows a typical FKBP fold with five antiparallel beta-strands forming a half beta-barrel wrapped around a central alpha-helix and an additional N-terminal alpha-helix and a rather long insert that covers the putative active site.
Pfam PF05426: Alginate lyase (repeat)
This family contains several bacterial alginate lyase proteins. Alginate is a family of 1-4-linked copolymers of beta -D-mannuronic acid (M) and alpha -L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyse the depolymerisation of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end.  This family adopts an all alpha fold.
Wikipedia: The enzyme mannuronate-specific alginate lyase catalyzes the degradation of alginate into various monosaccharide and polysaccharide products:Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-α-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and β-D-mannuronate at their reducing end.
Pfam PF25046: Domain of unknown function (DUF7790) (domain)
This domain is found in uncharacterised protein from Leptospira interrogans serogroup Icterohaemorrhagiae serovar Copenhageni and related bacterial proteins. Its structure was determined (PDB:6ULO) and shares a significant similarity to various methyltransferases.
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 PF21913: ORC6 second cyclin-like domain (domain)
The metazoan origin recognition complex subunit 6 (Orc6) contains two homologous domains that are arranged in tandem and both adopt a cyclin-like topology. This entry represents the second cyclin-like domain of Orc6.
Pfam PF03928: Haem degrading protein HbpS-like (family)
This entry includes haem degrading protein HbpS from Streptomyces reticuli (swiss:Q9RIM2) and and GlcG from Escherichia coli. HbpS is up-regulated in response to haemin- and peroxide-based oxidative stress. It interacts with the SenS/SenR two-component signal transduction system. Iron binds to surface-exposed lysine residues of an octomeric assembly of the protein. The structure of GlcG is composed of an alpha-beta(2)-alpha(3)-beta(2)-alpha fold, similar to the Roadblock/LC7 domain.
Pfam PF21534: Protein rolling stone (family)
This entry includes protein rolling stone (Rost) from fruit fly. It is a transmembrane protein involved in myoblast fusion.
Pfam PF10567: RNA-recognition motif (domain)
This conserved domain is found in fungal proteins and appears to be involved in RNA-processing. It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, copurifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in [swissprot:P39935] and [swissprot:P39936].
Pfam PF19150: Family of unknown function (DUF5832) (family)
This entry contains proteins of unknown function  found predominantly in the Phycodnaviridae,  Mimiviridae, Marseilleviridae and Iridoviridae  virus families.
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 PF11037: Insulin-resistance promoting peptide in skeletal muscle (family)
Musclin is a muscle derived secretory peptide which induces insulin resistance in vitro. It encodes a 130 amino acid sequence including a NH(2) terminal 30 amino acid signal sequence. Musclin expression level is tightly regulated by nutritional changes.
Pfam PF05587: Anthrax receptor extracellular domain (domain)
This region is found in the putatively extracellular N-terminal half of the anthrax receptor. It is  probably part of the Ig superfamily and most closely related to [pfam:PF01833] (personal obs: C Yeats).
Pfam PF06211: BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain (domain)
This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling.
Pfam PF17621: Family of unknown function (DUF5508) (family)
This is a family of unknown function found in Enterobacteriaceae.
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 PF18572: Trehalose-6-phosphate phosphatase N-terminal helical bundle domain (domain)
This is the N-terminal domain found in trehalose-6-phosphate phosphatase (T6PP, EC 3.1.3.12) from parasitic nematodes such as Brugia malayi. In the model nematode Caenorhabditis elegans, T6PP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate. T6PP has also been shown to be essential in Mycobacterium tuberculosis. The N-terminal domain composed of a three-helix bundle is similar in topology to the Microtubule Interacting and Transport (MIT) domains of the Vps4-like ATPases from Sulfolobus acidocaldarius. MIT domains are protein-interacting domains typically associated with multivesicular body formation, cytokinetic abscission, or viral budding. Mutational analysis indicate that deletion or mutation of the MIT-like domain is highly destabilizing to the enzyme.
Pfam PF18637: Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain (domain)
The enzyme aldos-2-ulose dehydratase/isomerase (AUDH) participates in carbohydrate secondary metabolism, catalyzing the conversion of glucosone and 1,5-d-anhydrofructose to the secondary metabolites cortalcerone and microthecin, respectively. Crystal structure analysis revealed that the enzyme subunit is built up of three domains, an N-terminal seven-bladed propeller, a bicupin and a C-terminal lectin domain. This entry describes the second Cupin domain (residues 574-739) composed of two antiparallel sheets that build up the jellyroll sandwich fold formed from four and five beta-strands. This cupin domain in AUDH is found to contain a zinc binding site where the metal site is located at the bottom of the cleft formed by the beta-sandwich, as observed in many cupins.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF13917: Zinc knuckle (domain)
The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag  proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.
Pfam PF04963: Sigma-54 factor, core binding domain (domain)
This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain.
Pfam PF24355: Domain of unknown function (DUF7514) (domain)
This domain is found in uncharacterised eukaryotic proteins. It is predicted to adopt a globular structure composed of 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 PF23436: RabGAP TBC domain (domain)
The TBC1 domain family is characterized by a conserved domain that confers GTPase-activating protein (GAP) activity towards various Rab family proteins, which are small GTPases involved in intracellular vesicle trafficking. Members of this family play diverse roles in cellular processes such as endocytosis, vesicular recycling, autophagy, cell cycle progression, and cytokinesis. They are involved in the regulation of membrane trafficking events, including endosome-to-Golgi transport, insulin-stimulated glucose uptake, and cilium biogenesis. Some family members also participate in signaling pathways, acting as modulators of small G protein signaling or as inhibitors of the Ras signaling pathway. The TBC1 domain typically contains arginine and glutamine fingers critical for the GAP activity, which facilitates the conversion of active GTP-bound Rab proteins to their inactive GDP-bound state, thereby regulating various stages of vesicle formation, movement, and fusion.
Pfam PF24703: Domain of unknown function (DUF7666) (domain)
This entry represents an uncharacterised protein domain that is sometimes found associated with [pfam:PF01469]. The family also includes an N-terminal domain found in the Pseudomonas syringae InaZ ice nucleation protein.
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 PF12326: N-glycosylation protein (family)
This family is not required for survival of S.cerevisiae, but its deletion leads to heightened sensitivity to oxidative stress. It appears to be involved in N-glycosylation, and resides in the endoplasmic reticulum.
Pfam PF12619: Mini-chromosome maintenance protein 2 (family)
This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with [pfam:PF00493]. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function.
Pfam PF05242: Glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1) (family)
This family consists of the lactophorin precursors proteose peptone component 3 (PP3) and glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1). GlyCAM-1 functions as a ligand for L-selectin, a  saccharide-binding protein on the surface of circulating leukocytes, and mediates the trafficking of blood-born lymphocytes into secondary lymph  nodes. In this context, sulphatation of the carbohydrates of GlyCAM-1 has  been shown to be a critical structural requirement to be recognised by  L-selectin. GlyCAM-1 is also expressed in pregnant and lactating mammary glands of mouse and in an unknown site in the lung, in the bovine uterus  and rat cochlea.
Pfam PF05535: Chromadorea ALT protein (family)
This family consists of several ALT protein homologues found in nematodes. Lymphatic filariasis is a major tropical disease caused by the mosquito borne nematodes Brugia and Wuchereria. About 120 million people are infected and at risk of lymphatic pathology such as acute lymphangitis and elephantiasis. Expression of alt-1 and alt-2 is initiated midway through development in the mosquito, peaking in the infective larva and declining sharply following entry into the host. ALT-1 and the closely related ALT-2 have been found to be strong candidates for a future vaccine against human filariasis.
Pfam PF17579: Family of unknown function (DUF5482) (family)
This is a family of unknown function found in Saccharomycetales.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00699: Urease beta subunit (domain)
This subunit is known as alpha in Heliobacter.
Pfam PF22498: FKBP-like, N-terminal domain (domain)
This entry represents a N-terminal FKBP-like domain of a putative methyltransferase from Thermoplasma acidophilum (PDB:1yb2).
Pfam PF07834: RanGAP1 C-terminal domain (domain)
Ran-GTPase activating protein 1 (RanGAP1, [swissprot:P46061]) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localisation at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1, [swissprot:Q93068]). This domain is composed almost entirely of helical substructures that are organised into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation.
Pfam PF22401: Cell-shape determining Csd6 N-terminal dimerization domain (domain)
This entry represents the dimerization domain found at the N-terminal of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in deglycosylation of the flagellar protein FlaA.
Pfam PF10071: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310) (family)
Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined.
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 PF15708: Proline-rich protein family 20 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 73 and 221 amino acids in length. There is a conserved AYV sequence motif.
Pfam PF09025: YopR, type III needle-polymerisation regulator (domain)
The YopR core domain, predominantly found in the Gammaproteobacteria virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR. YopR controls the selective access of early (YscF, YscI and YscP) substrates to the type III secretion machines of yersiniae and other Gammaproteobacteriae. YopR is a mobile regulatory component thought to function as a checkpoints probing the completion of discrete intermediary stages in the assembly of the type III injection pathway. The location of secreted YopR (into the medium) is directly controlling the secretion of YscF, the polymerised needle protein [pfam:PF09392], thereby impacting the assembly of type III machines.
Wikipedia: In molecular biology, YopR is a protein domain commonly found in gram negative bacteria, in particular Yersinia and is a core domain. Proteins in this entry are type III secretion system effectors. They are named differently in different species and in Yersinia has been designated YopR which is encoded by the YscH gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.
A hallmark of Yersinia type III machines is the presence of needles extending from the bacterial surface. Needles perform two functions, firstly, as a channel to export effectors into the immune cells and secondly as a sensor.
Pfam PF12816: Vps8 central TPR (repeat)
Vps8 is one of the Golgi complex components necessary for vacuolar sorting. Eukaryotic cells contain a highly dynamic endo-membrane system, in which individual organelles keep their identity despite continuous vesicle generation and fusion. Vesicles that bud from a donor membrane are targeted and delivered to each individual organelle, where they release their cargo after fusion with the acceptor membrane. Vps8 is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering).  Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. Late endosomes form intralumenal vesicles, and the resulting multivesicular bodies fuse with the vacuole to release their cargoes. Vps8 consists of a beta-propeller at the N-terminal ([pfam:PF23410]), a central TPR-like region and a RING finger at the C-terminal. This entry represents a central TPR segment after the beta-propeller.
Pfam PF17902: SH3 domain (domain)
This entry represents an SH3 domain.
Pfam PF08845: Toxin SymE, type I toxin-antitoxin system (domain)
SymE (SOS-induced yjiW gene with similarity to MazE ) is an SOS-induced toxin. It inhibits cell growth, decreases protein synthesis and increases RNA degradation. It may play a role in the recycling of RNAs damaged under SOS response-inducing conditions. It is predicted to have an AbrB fold, similar to that of the antitoxin MazE. Its translation is repressed by the antisense RNA SymR, which acts as an antitoxin.
Wikipedia: The SymE-SymR toxin-antitoxin system consists of a small symbiotic endonuclease toxin, SymE, and a non-coding RNA symbiotic RNA antitoxin, SymR, which inhibits SymE translation. SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems.
Pfam PF09824: ArsR transcriptional regulator (family)
Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Pfam PF13384: Homeodomain-like domain (domain)
Wikipedia: A homeobox is a DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of the full-grown organism.
Pfam PF04940: Sensors of blue-light using FAD (domain)
The BLUF domain has been shown to bind FAD in the AppA protein ([swissprot:Q53119]). AppA is  involved in the repression of photosynthesis genes in response to blue-light.
Wikipedia: In molecular biology, the BLUF domain is a FAD-binding protein domain. They are present in various proteins, primarily from bacteria, for example a BLUF domain is found at the N-terminus of the AppA protein from Rhodobacter sphaeroides. The BLUF domain is involved in sensing blue-light using FAD and is similar to the flavin-binding PAS domains and cryptochromes. The predicted secondary structure reveals that the BLUF domain has a novel FAD-binding fold.