SII-SWORD/CoKE huggingface dataset:
Pfam PF21992: Domain of unknown function (DUF6927) (domain)
This domain is found C-terminal in uncharacterised bacterial proteins. It is probably remotely related to PemK-like, MazF-like toxins and is predicted to adopt SH3-like fold.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15571: Immunity protein 44 (family)
A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI1, Tox-URI2 or Tox-ParBL1 families. The gene for this toxin is also found in heterogeneous poly-immunity loci that show variations in structure even between closely related strains.
Pfam PF09246: PHAT (repeat)
The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding.
Pfam PF20468: Hermansky-Pudlak syndrome 6 protein C-terminal domain (repeat)
This entry represents the C-terminal alpha solenoid domain of the HPS6 protein.
Wikipedia: Hermansky–Pudlak syndrome 6 (HPS6), also known as ruby-eye protein homolog (Ru), is a protein that in humans is encoded by the HPS6 gene.
Pfam PF10529: Histidine-rich Calcium-binding repeat region (repeat)
This is a histidine-rich calcium binding repeat which appears in proteins called histidine-rich-calcium binding proteins (HRC). HRC is a high capacity, low affinity Ca2+-binding protein, residing in the lumen of the sarcoplasmic reticulum. HRC binds directly to triadin. This binding interaction occurs between the histidine-rich region of HRC and multiple clusters of charged amino acids, named as the KEKE motifs, in the lumenal domain of triadin. The region in which this repeat is found in many copies is long and variable but is the acidic region of the protein. There is also a cysteine-rich region further towards the C-terminus. HRC may regulate sarcoplasmic reticular calcium transport and play a critical role in maintaining calcium homeostasis and function in the heart. HRC as a candidate regulator of sarcoplasmic reticular calcium uptake.
Pfam PF04979: Protein phosphatase inhibitor 2 (IPP-2) (family)
Protein phosphotase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells.
Pfam PF21473: Single-stranded DNA binding protein Ssb-like, OB fold (domain)
This entry represents the OB fold of single-stranded DNA binding protein Ssb from archaea and its homologues from mammals and plants. Members of this entry have a simple domain organisation consisting of a single DNA-binding OB fold coupled to a flexible C-terminal tail. The ssDNA recognition is modulated by base-stacking of three key aromatic residues in archaeal Ssb, in contrast with the OB domain of the human homologue hSSB1.
Pfam PF07749: Endoplasmic reticulum protein ERp29, C-terminal domain (domain)
ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals.  ERp29 is comprised of two domains. This domain, the C-terminal domain, has an all helical fold. ERp29 is thought to form part of the thyroglobulin folding complex.
Pfam PF19206: Family of unknown function (DUF5878) (family)
This is a family of uncharacterised proteins of unknown function 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 PF10323: Serpentine type 7TM GPCR chemoreceptor Srv (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF07386: Protein of unknown function (DUF1499) (family)
This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. 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 PF08140: Crustacean cuticle protein repeat (family)
This family consists of the cuticle proteins from the Cancer pagurus and the Homarus americanus. These proteins are isolated from the calcified regions of the crustacean and they contain two  copies of an 18 residue sequence motif, which thus far has been  found only in crustacean calcified exoskeletons.
Pfam PF06154: CbeA_antitoxin, type IV, cytoskeleton bundling-enhancing factor A (family)
CbeA_antitoxin is a family of cognate antitoxins to the CbtA toxins that act by inhibiting the polymerisation of cytoskeletal proteins, see [pfam:PF06755]. These are classified as a type IV toxin-antitoxin system. The family includes three proteins from E. coli YagB, YeeU and YfjZ, which act not by forming a complex with CbtA but through acting as antagonists to the CbtA toxicity, by stabilising the CbtA target proteins. For example, YeeU binds directly to both MreB and FtsZ and enhances the bundling of their filaments in vitro.  YeeU is also able to neutralise the toxicity caused by other MreB and FtsZ inhibitors, such as A22 [S-(3, 4-dichlorobenzyl)isothiourea] for MreB, and SulA and DicB for FtsZ. Thus CbeA, for cytoskeleton bundling-enhancing factor A, is proposed as a general name for all of these antitoxin proteins.
Pfam PF19636: Family of unknown function (DUF6139) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: EATN and KGYAI.
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 PF09635: MetRS-N binding domain (domain)
The MetRS-N domain binds an Arc1-P domain in a tetrameric complex resembling a classical GST homo-dimer. Domain-swapping between symmetrically related MetRS-N and Arc1p-N domains generates a 2:2 tetramer held together by van der Waals forces. This domain is necessary for formation of the aminoacyl-tRNA synthetase complex necessary for tRNA nuclear export and shuttling as part of the translational apparatus. The domain is associated with [pfam:PF09334].
Pfam PF17853: GGDEF-like domain (domain)
This domain is distantly related to the GGDEF domain, suggesting these may by diguanylate cyclase enzymes.
Pfam PF01808: AICARFT/IMPCHase bienzyme (family)
This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide  ribonucleotide formyltransferase [ec:2.1.2.3] (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. This is catalysed by a pair of C-terminal deaminase fold domains in the protein, where the active site is formed by the dimeric interface of two monomeric units. The last  step is catalysed by the N-terminal IMP (Inosine monophosphate)  cyclohydrolase domain [ec:3.5.4.10] (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP.
Pfam PF17930: LpxI N-terminal domain (domain)
This entry represents the N-terminal domain of the LpxI enzyme that is involved in biosynthesis of lipid A. Specifically it carried out the hydrolysis of UDP-2,3-diacyl- glucosamine. This step is either carried out by LpxI or LpxH. This domain has a Rossmann fold.
Pfam PF05357: Phage Coat Protein A (domain)
Infection of Escherichia coli by filamentous bacteriophages is mediated  by the minor phage coat protein A and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA.  These two receptors are contacted in a sequential manner, such that  binding of TolA by the extreme N-terminal domain is conditional on a  primary interaction of the second coat protein A domain with the F'  pilus.
Pfam PF20014: GTPase-associated protein 1, middle domain (domain)
Middle domain found in the multidomain  GTPase-associated protein 1 (GAP1) of the GTPase-centric systems, a class of NTP-dependent biological conflict systems.
Pfam PF04504: Glabrous-enhancer-binding protein-like family, DBD domain (domain)
This entry represents the DNA binding domain (DBD) present in GLABROUS1 enhancer-binding protein (GeBP) and GeBP-like proteins, such us storekeeper and storekeeper-like (STKL) transcription factors. GeBP and GeBP-like proteins play a redundant role in cytokinin hormone pathway regulation. Storekeeper was identified as a B-box motif binding factor that regulates expression of patatin, a storage protein in potato. Storekeeper-like transcription factors STKL1 and STKL2 function as transcription factors in the glucose signalling pathway. The overall predicted structure of this DNA binding domain (DBD) reveals a bundle of four helices, with helices alpha1 to alpha3 making up a single myb-type helix-turn-helix (HTH) domain.
Pfam PF22883: Consortin, N-terminal domain (domain)
Consortin is a trans-Golgi network cargo receptor involved in targeting connexins to the plasma membrane. This entry represents a helical domain found towards its N-terminal.
Pfam PF02219: Methylenetetrahydrofolate reductase (domain)
This family includes the 5,10-methylenetetrahydrofolate reductase [ec:1.7.99.5] from bacteria and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known to be a TIM barrel.
Pfam PF14283: Mobile element protein CD1107-like (family)
This family includes the mobile element protein CD1107 from Clostridioides difficile ([swissprot:Q18AV9],) and similar proteins mainly found in firmicutes.
Pfam PF01782: RimM N-terminal domain (domain)
The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes.  This N-terminal domain is found associated with a PRC-barrel domain.
Pfam PF16539: Flagellar assembly protein T, middle domain (domain)
FlgT_M is the middle region of a family of flagellar proteins that make up part of the basal body of the flagellum.  The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures.  FlgT-N and FlgT-M are thought to be involved in the H-ring and the T-ring formation, respectively. and FlgT-M is also required for the stable association of FlgT with the basal body.
Pfam PF16855: Small outer capsid protein (domain)
This protein attaches to and stabilises the bacteriophage capsid.
Pfam PF17734: Spermatogenesis-associated protein 46 (family)
This family is found in chordata . Functional characterization studies showed that the deletion of Spata46 in mice resulted in subfertility with abnormal sperm head shape and a failure of sperm-egg fusion. Spata46 has also been shown to localize to the nuclear membrane by a transmembrane region in the N-terminal.
Pfam PF06459: Ryanodine Receptor TM 4-6 (family)
This region covers TM regions 4-6 of the ryanodine receptor 1 family.
Pfam PF05063: MT-A70 (family)
MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A  methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs.
Pfam PF06832: Penicillin-Binding Protein C-terminus Family (family)
This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit ([pfam:PF00905]). It is predicted by PROF to be an all beta fold.
Pfam PF03216: Rhabdovirus nucleoprotein (family)
This is a family of Rhabdovirus nucleocapsid proteins. These proteins undergo phosphorylation.
Pfam PF11145: Protein of unknown function (DUF2921) (family)
This eukaryotic family of 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 PF11138: Protein of unknown function (DUF2911) (family)
This bacterial family of 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 PF01627: Hpt domain (family)
The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined. The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to  contain a binding surface for Ssk1p (response regulator receiver domain containing protein [pfam:PF00072]).
Wikipedia: Histidine phosphotransfer domains and histidine phosphotransferases are protein domains involved in the "phosphorelay" form of two-component regulatory systems. These proteins possess a phosphorylatable histidine residue and are responsible for transferring a phosphoryl group from an aspartate residue on an intermediate "receiver" domain, typically part of a hybrid histidine kinase, to an aspartate on a final response regulator.
Pfam PF09933: Predicted small integral membrane protein (DUF2165) (family)
This domain, found in various hypothetical prokaryotic 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 PF14347: Domain of unknown function (DUF4399) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 135 and 1079 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 PF07554: FIVAR domain (domain)
This domain is found in a wide variety of contexts, but mostly occurring in cell wall associated proteins. A lack of conserved catalytic residues suggests that it is a binding domain. From context, possible substrates are hyaluronate or fibronectin (personal obs: C Yeats). This is further evidenced by. Possibly the exact substrate is N-acetyl glucosamine. Finding it in the same protein as [pfam:PF05089] further supports this proposal. It is found in the  C-terminal part of [swissprot:O82833], which is removed during maturation  (). Some of the proteins it is found in (e.g. [swissprot:Q9RL69]) are  involved in methicillin resistance (). The name FIVAR derives from Found In Various Architectures.
Pfam PF09398: FOP N terminal dimerisation domain (domain)
Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures.  This domain includes a Lis-homology motif.  It forms an alpha helical bundle and is involved in dimerisation.
Pfam PF13641: Glycosyltransferase like family 2 (domain)
Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis.
Pfam PF16725: Nucleolin binding domain (domain)
This domain adopts a three helix fold resembling part of a winged helix motif. It binds nucleolin.
Pfam PF06734: UL97 (family)
This family represents a conserved region within viral UL97 phosphotransferases. UL97 participates in the phosphorylation of the nucleoside analog ganciclovir (GCV) to produce GCV-monophosphate.
Pfam PF02155: Glucocorticoid receptor (family)
Steroid or nuclear hormone receptors (NRs) constitute an important super- family of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner . In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.

NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed "orphan" receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.

The glucocorticoid receptor consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain is unique to the glucocorticoid receptors; it spans the first 440 residues, and is primarily responsible for transcriptional activation. The smaller (around 65 residues), highly-conserved central portion of the protein is the DNA binding domain, which plays a role in DNA binding specificity, homo- dimerisation and in interactions with other proteins. The hormone binding domain comprises approximately 250 residues at the C terminus of the receptor. This domain mediates receptor activity via interaction with heat shock proteins and cyclophilins, or with hormone.
Pfam PF14408: Ribosomally synthesised peptide in actinomycetes (family)
Ribosomally synthesised peptide that is usually in the gene neighbourhood of a RimK-like ATP-grasp and an aspartyl-O-methylase. Gene contexts suggest that it is further modified by the ATP-grasp  and the methylase. It might function in defence or development, or  as a peptide antibiotic.
Pfam PF13501: Sulfur oxidation protein SoxY (domain)
This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family [pfam:PF01880]. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme. The structure of this domain shows an Ig-like fold.
Pfam PF09852: Predicted membrane protein (DUF2079) (family)
This domain, found in various hypothetical prokaryotic 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 PF17941: Polyphosphate kinase C-terminal domain 1 (domain)
Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains.