SII-SWORD/CoKE huggingface dataset:
Pfam PF00060: Ligand-gated ion channel (family)
This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
Wikipedia: Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are activated by the neurotransmitter glutamate. They mediate the majority of excitatory synaptic transmission throughout the central nervous system and are key players in synaptic plasticity, which is important for learning and memory. iGluRs have been divided into four subtypes on the basis of their ligand binding properties (pharmacology) and sequence similarity: AMPA receptors, kainate receptors, NMDA receptors and delta receptors.
Pfam PF21608: V-cyclin, C-terminal domain (domain)
This domain is found at the C-terminal end of V-cyclin from Murid herpesvirus 4 (MuHV-4) and similar proteins predominantly from gamma-herpesvirus. This domain shows an all-alpha fold structure. It is usually associated with [pfam:PF00134].
Pfam PF20183: Family of unknown function (DUF6546) (family)
This entry represents a family of uncharacterised proteins. Some of these contain an N-terminal F-box domain [pfam:PF00646].
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 PF12248: Farnesoic acid 0-methyl transferase (domain)
This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyses the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH).
Pfam PF10397: Adenylosuccinate lyase C-terminus (domain)
This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions, Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide, the eighth step of the de novo pathway, and the formation of adenosine monophosphate (AMP) from adenylosuccinate, the second step in the conversion of inosine monophosphate into AMP.
Pfam PF02367: Threonylcarbamoyl adenosine biosynthesis protein TsaE (domain)
This family of proteins is involved in the synthesis of threonylcarbamoyl adenosine (t(6)A).
Pfam PF09278: MerR, DNA binding (domain)
Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold.
Pfam PF19346: Family of unknown function (DUF5924) (family)
This family of uncharacterised proteins is found in bacteria. This entry represents a likely integral membrane region with six transmembrane helices. The family is found in association with [pfam:PF11141].
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 PF24602: Domain of unknown function (DUF7622) (domain)
This domain is found several times in a group of uncharacterised proteins from nematodes. It is predicted to adopt a mainly beta configuration.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22984: Mediator of RNA polymerase II transcription subunit 14, RM6 (repeat)
This entry represents an alpha/beta motif that is found tandemly repeated in the homologues of human Mediator of RNA polymerase II transcription subunit 14 (Med14). Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Med14 along with Med17 are scaffold subunits in nucleating Mediator. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents repeat RM6.
Pfam PF21586: DraIII (family)
This protein family includes DraIII from Deinococcus radiophilus, a type IIP restriction endonuclease that recognises a gapped double-stranded DNA sequence and nicks creating a double strand break with a three base 3' overhang. DraIII adopts a homodimeric configuration. Each monomer shows a beta-beta-alpha-metal fold in the C terminus, where the HNH active site is located. It also has two zinc- and one magnesium-binding sites.
Pfam PF15382: Domain of unknown function (DUF4609) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 139 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 PF18423: Zinc binding domain (domain)
This is N-terminal domain containing a mononuclear metal center for zinc binding found in copper chaperone CopZ proteins.
Pfam PF12703: Toxin of toxin-antitoxin type 1 system (family)
This family is the toxin of a type 1 toxin-antitoxin system which is found in a relatively widespread range of bacterial species. The species distribution suggests frequent horizontal gene transfer.  In a type 1 system, as characterised for the plasmid-encoded E coli hok/sok system, the toxin-encoding stable mRNA encodes a protein which rapidly leads to cell death unless the translation is suppressed by a short-lived small RNA. The plasmid-encoded module prevents the growth of plasmid-free offspring, thus ensuring the persistence of the plasmid in the population. Plasmid-free cells arising after cell-division will be killed because the stable mRNA toxin is present while the comparably unstable anti-toxin is rapidly degraded. Where the system is transcribed chromosomally, the mechanism is poorly understood.
Wikipedia: PtaRNA1 is a family of non-coding RNAs.
Homologs of PtaRNA1 can be found in the bacterial families, Betaproteobacteria and Gammaproteobacteria. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene. In Xanthomonas campestris pv. vesicatoria, this gene is annotated as XCV2162 and is included in the plasmid toxin family of proteins.
Pfam PF14220: Domain of unknown function (DUF4329) (family)
This domain is functionally uncharacterised.  It is found in bacteria and eukaryotes, and is approximately 130 amino acids in length. It is often found in association with [pfam:PF05593] and [pfam:PF03527]. There is a single completely conserved residue D and a highly conserved HTH motif which 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 PF06265: Putative antitoxin YutD-like (family)
This family contains a group of uncharacterised bacterial proteins, including YutD from Bacillus subtilis (PDBe:2kl5), a probable antitoxin component of a putative type VII toxin-antitoxin (TA) system, that probably neutralises cognate toxin YutE.
Pfam PF10780: 39S ribosomal protein L53/MRP-L53 (family)
MRP-L53 is also known as Mrp144. It is part of the 39S ribosome.
Pfam PF16081: Mycobacterial 2 TMS Phage Holin (M2 Hol) Family (family)
Phage_holin_8_1 is a family of two transmembrane mycobacteriophage holins, small hydrophobic proteins that effect lysis of host mycobacterial cells in conjunction with a mycobacteria-specific lysin, lysB. The product of lysB gene targets the mycobacteria outer membrane, the last barrier to bacteriophage release.
Pfam PF21833: Family of unknown function (DUF6893) (family)
This entry represents a small protein that has a likely signal peptide that takes up most of the sequence. Thus a small peptide might be released from these proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09949: Phosphatidate phosphatase APP1, catalytic domain (domain)
This entry represents a conserved region found in Phosphatidate phosphatase APP1 from yeast, which contains the catalytic motif DXDX(T/V), present in other Mg+2-dependent phosphatases. This domain has a weak sequence similarity to the haloacid dehalogenase-like domain. APP1 catalyses the dephosphorylation of phosphatidate to yield diacylglycerol and may play a role in vesicular trafficking through its phosphatidate phosphatase activity at cortical actin patches.
Pfam PF15710: Break repair meiotic recombinase recruitment factor 1 (disordered)
Brme1 (also known as Meiok21) is a component of meiotic recombination bridges involved in meiotic double-strand break repair. The C-terminal domain of Brme1 physically interacts with the N-terminal domain of HSF2BP. BRME1 facilitates the loading of RAD51 and DMC1 recombinases onto DSBs (DNA double-strand breaks) through interaction with MEILB2/HSF2BP and replacing ssDNA binding proteins. Brme1 is highly expressed in mice testes and fetal ovaries. Knockout of Brme1 results in male mice infertility.
Pfam PF07895: Protein of unknown function (DUF1673) (family)
This family contains hypothetical proteins of unknown function expressed by two archaeal species.
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 PF11702: Protein of unknown function (DUF3295) (family)
This family is conserved in fungi but the function is not 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 PF01217: Clathrin adaptor complex small chain (domain)
Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer .
This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species . The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly .
Wikipedia: Clathrin adaptor proteins, also known as adaptins, are vesicular transport adaptor proteins associated with clathrin. The association between adaptins and clathrin are important for vesicular cargo selection and transporting. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Therefore, adaptor proteins are responsible for the recruitment of cargo molecules into a growing clathrin-coated pits. The two major types of clathrin adaptor complexes are the heterotetrameric vesicular transport adaptor proteins (AP1-5), and the monomeric GGA adaptors. Adaptins are distantly related to the other main type of vesicular transport proteins, the coatomer subunits, sharing between 16% and 26% of their amino acid sequence.
Pfam PF25125: Domain of unknown function (DUF7817) (domain)
This domain is found towards the C terminus of human NEDD4 -binding protein 2 (N4BP2), which has 5'-polynucleotide kinase and nicking endonuclease activity and may play a role in DNA repair or recombination. This domain is often found N-terminal to [pfam:PF25124] and [pfam:PF08590].
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 PF20604: Domain of unknown function (DUF6798) (domain)
This presumed domain is functionally uncharacterised. This domain family is mainly found in bacteria and archaea, and is approximately 60 amino acids in length. There is a conserved WxxR sequence  motif and a conserved Lys residue. Members of this entry may be transmembrane proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF04454: Encapsulating protein for peroxidase (family)
The Linocin_M18 is found in eubacteria and archaea. These proteins, referred to as encapsulins, form nanocompartments within the bacterium which contain ferritin-like proteins or peroxidases, enzymes involved in oxidative-stress response. These enzymes are targeted to the interior of encapsulins via unique C-terminal extensions.
Wikipedia: The encapsulins are a family of bacterial proteins that serve as the main structural components of encapsulin nanocompartments. There are several different encapsulin proteins, including EncA, which forms the shell, and EncB, EncC, and EncD, which form the core. They are found in bacteria and archaea. They serve as intracellular structures that compartmentalize specific biochemical reactions. They are highly versatile systems and protect cargo proteins from environmental damage and optimize the efficiency of enzymatic processes.
Pfam PF21820: Family of unknown function (DUF6886) (family)
This is a family of proteins whose function is unknown. They may be distantly related to ADP-ribosylating toxins.
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 PF05142: Domain of unknown function (DUF702) (family)
Members of this family are found in various putative zinc finger proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15137: Exosomal polycystin 1 interacting protein (family)
This family includes the exosomal polycystin 1 interacting protein (also known as C21orf62 or CU062 in human), which is a small glycoprotein that can oligomerize with itself and interact with PC1 protein polycystin-1 (PC1). It may have a role in the identification of senescent mitochondria and their extrusion in extracellular vesicles.
Pfam PF21092: FACT complex subunit SSRP1, C-terminal domain (domain)
FACT (facilitates chromatin transactions) is a general chromatin factor that acts to reorganise nucleosomes. SSRP1 is a subunit of this complex that is conserved among higher eukaryotes. This entry represents the C-terminal domain of SSRP1, which is highly likely to be disordered.
Pfam PF02934: GatB/GatE catalytic domain (domain)
This domain is found in the GatB and GatE proteins.
Pfam PF23545: HMPTM N-terminal zinc ribbon domain (domain)
This domain is found in 7,8-dihydro-6-hydroxymethylpterin dimethyltransferase (HMPTM) and related proteins. HMPTM is involved in catalysing the methylation at C-7 and C-9 of 7,8-dihydro-6-hydroxymethylpterin, a common intermediate in both folate and MPT biosynthesis. The domain represented by this entry is predicted to adopt a zinc beta-ribbon fold. It contains three invariant cysteines and one histidine arranged in two CxxC and CxxH sequence motifs.
Pfam PF01276: Orn/Lys/Arg decarboxylase, major domain (domain)
Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates . One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group. Ornithine decarboxylase is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. Arginine decarboxylase catalyzes the decarboxylation of arginine and lysine decarboxylase catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life .
Wikipedia: In molecular biology, group III pyridoxal-dependent decarboxylases are a family of bacterial enzymes comprising ornithine decarboxylase EC 4.1.1.17, lysine decarboxylase EC 4.1.1.18 and arginine decarboxylase EC 4.1.1.19.
Pfam PF20826: PhD finger domain (domain)
PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains.  Several PHD fingers have been identified as binding modules of methylated histone H3.
Wikipedia: The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain proteins HAT3.1 in Arabidopsis and maize ZmHox1a. 
The PHD zinc finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.
Pfam PF00863: Peptidase family C4 (family)
This peptidase is present in the nuclear inclusion protein of potyviruses.
Pfam PF15430: Single domain von Willebrand factor type C (family)
SVWC is a family of single-domain von Willebrand factor type C proteins from lower eukaryotes. The canonical pattern of most von Willebrand factor type C (VWC) domains is of ten cysteines, however this family, largely but not exclusively of arthropod proteins, contains only eight. SVWC family proteins respond to environmental challenges, such as bacterial infection and nutritional status. They also are involved in anti-viral immunity, and all of these functions seem linked to SVWC expression being induced by Dicer2.
Pfam PF14895: Protein phosphatase 1 inhibitor (family)
This family of proteins interacts with and inhibits the phosphatase activity of protein phosphatase 1 (PP1) complexes.
Pfam PF08581: Tup N-terminal (domain)
The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor.
Pfam PF24600: RavZ catalytic domain (domain)
The intracellular pathogen Legionella pneumophila interferes with autophagy by delivering an effector protein, cysteine protease RavZ, into the host cytosol. This effector protein cleaves membrane-conjugated Atg8/LC3 proteins from pre-autophagosomal structures. RavZ is a two domain protein consisting of an N-terminal catalytic domain, which is represented in this entry, and a C-terminal phosphatidylinositol 3-phosphate (PI3P)-binding domain ([pfam:PF22225]).
Pfam PF15875: Domain of unknown function (DUF4731) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 37 and 78 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 PF08408: DNA polymerase family B viral insert (family)
This viral domain is found between the exonuclease domain of the DNA polymerase family B ([pfam:PF03104]) and the [pfam:PF00136] domain, connecting the two.
Pfam PF24154: Tis1 immunity protein (family)
Tas1 is a type VI secretion effector in the pathogen Pseudomonas aeruginosa that synthesizes (p)ppApp. Its cognate immunity protein Tis1 is represented by this entry. Binding of the immunity protein probably neutralises Tas1-mediated toxicity by inducing structural rearrangement in the acceptor nucleotide binding site of the enzyme.
Pfam PF21239: Ribosomal RNA large subunit methyltransferase M, N-terminal (domain)
This is the THUMP-like domain of Ribosomal RNA large subunit methyltransferase M (RLMM), adjacent the ferredoxin-like domain ([pfam:PF18125]), which together constitutes the N-terminal domain. RlmM specifically catalyses the 2'-O-methylation of nucleotide C2498 in the peptidyl transferase loop of 23S rRNA.