SII-SWORD/CoKE huggingface dataset:
Pfam PF21371: Anaphase-promoting complex subunit 5, N-terminal domain (domain)
This domain is found at the N-terminal end of Anaphase-promoting complex subunit 5 from humans (Apc5), a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This domain has an alpha-helical fold. It is normally found in association with [pfam:PF12862].
Pfam PF21398: Putative peptidoglycan-binding domain (domain)
This entry represents a putative peptidoglycan binding domain.
Pfam PF20157: Glycosyltransferase Maf N-terminal domain (domain)
This entry represents the N-terminal Rossmann like domain from the flagellin glycosyltransferase Maf.
Pfam PF10453: FMR1-interacting protein 1 (NUFIP1) (family)
Proteins in this family have been implicated in the assembly of the large subunit of the ribosome and in telomere maintenance.  Some proteins in this family contain a CCCH zinc finger. This family contains a protein called human FMR1-interacting protein NUFIP1 which is known to bind RNA and is phosphorylated upon DNA damage.
Pfam PF21654: Cyclic GMP-AMP synthase DncV-like, nucleotidyltransferase domain (domain)
This is the nucleotidyltransferase domain of DncV from Vibrio cholerae (also known as Cyclic GMP-AMP synthase) and related proteins. DncV catalyses the synthesis of 3'3'-cyclic GMP-AMP (3'3'-cGAMP) from GTP and ATP. It is part of the CBASS (cyclic oligonucleotide-based antiphage signaling system) which provides immunity against bacteriophage. This protein is required for efficient V.cholerae intestinal colonization and and down-regulates the colonization-influencing process of chemotaxis.
Pfam PF06519: TolA C-terminal (family)
This family consists of several bacterial TolA proteins as well as two eukaryotic proteins of unknown function.  Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species (See [pfam:PF01024]). TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N-terminus, leaving most of the protein exposed to the periplasm.
Pfam PF01213: CAP N-terminal conserved motif (conserved_site)
This entry represents the N-terminal conserved motif of CAP proteins. CAPs consist of two domains separated by a proline-rich hinge. In budding and fission yeasts the CAP protein is a bifunctional protein whose N-terminal domain binds to adenylyl cyclase, and The C-terminal domain plays a role in recycling cofilin-bound, ADP-actin monomers.
Wikipedia: In molecular biology, the cyclase-associated protein family (CAP) is a family of highly conserved actin-binding proteins present in a wide range of organisms including yeast, flies, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium discoideum, CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly. In mammals, there are two different CAPs that share 64% amino acid identity.
Pfam PF09067: Erythropoietin receptor, ligand binding (domain)
Members of this family interact with erythropoietin (EPO), with subsequent initiation of the downstream chain of events associated with binding of EPO to the receptor, including EPO-induced erythroblast proliferation and differentiation through induction of the JAK2/STAT5 signaling cascade. The domain adopts a secondary structure composed of a short amino-terminal helix, followed by two beta-sandwich regions.
Pfam PF23753: WDR11 TPR domain (repeat)
This entry represents the TPR domain found at the C-terminal of WD repeat-containing protein 11 (WDR11) from animals and similar eukaryotic proteins. Members of this family share a domain architecture consisting of two beta-propellers followed by a TPR domain. WDR11 has been implicated in human developmental genetic disorders characterised by delayed puberty and infertility. WDR11 modulates the Hedgehog (Hh) signalling pathway and is essential for adequate ciliogenesis. WDR11 also interacts with EMX1, a homeodomain transcription factor involved in the development of olfactory neurons; and is involved in vesicle traffic as it binds TBC1D23, a vesicle-golgin adaptor required for endosome-to-Golgi trafficking.
Pfam PF15149: CATSPERB, C-terminal domain (domain)
This entry includes CATSPERB, an auxiliary subunit of the CatSper complex, a complex involved in sperm cell hyperactivation. This process is needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein; this entry represents the C-terminal domain which covers the Stem domain and the transmembrane helix, which are involved in the association with the channel domain.
Wikipedia: The cation channels of sperm also known as Catsper channels or CatSper, are ion channels that are related to the two-pore channels and distantly related to TRP channels. The four members of this family form voltage-gated Ca2+ channels that seem to be specific to sperm. As sperm encounter the more alkaline environment of the female reproductive tract, CatSper channels become activated by the altered ion concentration. These channels are required for proper fertilization. The study of these channels has been slow because they do not traffic to the cell membrane in many heterologous systems.
Pfam PF15302: P33 mono-oxygenase (family)
This family of proteins contains a flavine-containing mono-oxygenase motif. It may have a role in the regulation of neuronal survival, differentiation and axonal outgrowth.
Pfam PF17783: CvfB-like winged helix domain (domain)
This winged helix domain is found in RNA-binding proteins such as CvfB.
Pfam PF07069: Porcine reproductive and respiratory syndrome virus 2b (family)
This family consists of several Porcine reproductive and respiratory syndrome virus (PRRSV) ORF2b proteins. The function of this family is unknown however it is known that large amounts of 2b protein are present in the virion and it is thought that this protein may be an integral component of the virion.
Pfam PF11023: Zinc-ribbon containing domain (family)
This is a family of proteins conserved in the Bacillaceae family. Some members are annotated as being protein YgzB. The function is not known.
Pfam PF21216: Xaa-Pro dipeptidase, N-terminal domain (domain)
This domain is found in Xaa-Pro dipeptidase from Escherichia coli (PepQ), a metalloprotease that catalyse the cleavage of Xaa-Pro dipeptides. This protein is organised into N-terminal (this entry)  and C-terminal (usually [pfam:PF00557]) domains and adopts a dimeric configuration. This domain shows an alpha-beta structure with four helices, one pair flanking each side of the six-stranded mixed beta-sheet.
Pfam PF07325: Curtovirus V2 protein (family)
This family consists of several Curtovirus V2 proteins. The exact function of V2 is unclear but it is known that the protein is required for a successful host infection process.
Pfam PF05069: Phage virion morphogenesis family (family)
Protein S of phage P2 is thought to be involved in tail completion and stable head joining.
Pfam PF14155: Domain of unknown function (DUF4307) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 132 and 153 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24376: Family of unknown function (DUF7532) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an alpha-beta structure.
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 PF07404: Telomere-binding protein beta subunit (TEBP beta) (domain)
This domain represents the OB fold from several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialised protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognise and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.
Pfam PF10483: Elongator subunit Iki1 (family)
This family is a component of the RNA polymerase II elongator complex. This complex is involved in elongation of RNA polymerase II transcription and in modification of wobble nucleosides in tRNA.
Pfam PF08410: Domain of unknown function (DUF1737) (family)
This domain of unknown function is found at the N-terminus of bacterial and viral hypothetical 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 PF00364: Biotin-requiring enzyme (domain)
This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins.
Wikipedia: Biotin/lipoyl attachment domain has a conserved lysine residue that binds biotin or lipoic acid. Biotin plays a catalytic role in some carboxyl transfer reactions and is covalently attached, via an amide bond, to a lysine residue in enzymes requiring this coenzyme. Lipoamide acyltransferases have an essential cofactor, lipoic acid, which is covalently bound via an amide linkage to a lysine group. The lipoic acid cofactor is found in a variety of proteins.
Pfam PF03049: UL79 family (family)
Members of this family are functionally uncharacterised proteins from herpesviruses. This family groups together HSV-6 U52 [swissprot:P52469], HVS-1 18 [swissprot:Q01003] and HCMV UL79 [swissprot:P16752].
Pfam PF06640: P protein C-terminus (family)
This family represents the C-terminus of plant P proteins. The maize P gene is a transcriptional regulator of genes encoding enzymes for flavonoid biosynthesis in the pathway leading to the production of a red phlobaphene pigment, and P proteins are homologous to the DNA-binding domain of myb-like transcription factors. All members of this family contain the [pfam:PF00249] domain.
Pfam PF19659: Family of unknown function (DUF6162) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 190 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 PF20244: Family of unknown function (DUF6599) (family)
This entry represents a family of uncharacterised bacterial 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 PF21074: Glutamate dehydrogenase, C-terminal (domain)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation. This entry represents the helical C-terminal domain.
Pfam PF10030: Uncharacterized protein conserved in bacteria (DUF2272) (domain)
Members of this family of hypothetical bacterial proteins have no known function. However, given its similarity to the CHAP domain it seems likely that this is an enzyme involved in cleaving peptidoglycan.
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 PF15689: Nuclear receptor-interacting protein 1 repression 3 (family)
This domain is the third repression domain of nuclear receptor-interacting protein 1.
Wikipedia: Nuclear receptor-interacting protein 1 (NRIP1) also known as receptor-interacting protein 140 (RIP140) is a protein that in humans is encoded by the NRIP1 gene.
Pfam PF03014: Structural protein 2 nucleoplasmin-like domain (domain)
This family represents N-terminal domain of structural protein 2 of the hepatitis E virus.  The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation.
Pfam PF24528: Adhesion G-protein coupled receptor F3-like, Ig-like domain (domain)
This immunoglobulin-like (Ig-like) domain is found in human Adhesion G-protein coupled receptor F3 (ADGRF3) and similar proteins from vertebrates. ADGRF3 is an orphan receptor.
Pfam PF20553: Putative O-methyltransferase (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 312 and 330 amino acids in length. An AlphaFold model shows this family are similar to known O-methyltransferases.
Pfam PF12132: Protein of unknown function (DUF3587) (family)
This protein is found in viruses. Proteins in this family are typically between 209 and 248 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 PF04563: RNA polymerase beta subunit (family)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure.  This domain is also known as the protrusion domain.  The other lobe ([pfam:PF04561]) is nested within this domain.
Pfam PF01160: Vertebrate endogenous opioids neuropeptide (family)
Vertebrate endogenous opioid neuropeptides are released by post-translational proteolytic cleavage of precursor proteins. The precursors consist of the following components: a signal sequence that precedes a conserved region of about 50 residues; a variable-length region; and the sequence of the neuropeptide itself. Three types of precursor are known: preproenkephalin A (gene PENK), which is processed to produce 6 copies of Met-enkephalin, plus Leu-enkephalin; preproenkephalin B (gene PDYN), which is processed to produce neoendorphin, dynorphin, leumorphin, rimorphin and Leu-enkephalin; and prepronocipeptin (gene PNOC), whose processing produces nociceptin (orphanin FQ) and two other potential neuropeptides.

Sequence analysis reveals that the conserved N-terminal region of the precursors contains 6 cysteines, which are probably involved in disulphide bond formation. It is speculated that this region might be important for neuropeptide processing .
Wikipedia: Opioid peptides or opiate peptides are peptides that bind to opioid receptors in the brain; opiates and opioids mimic the effect of these peptides. Such peptides may be produced by the body itself, for example endorphins. The effects of these peptides vary, but they all resemble those of opiates. Brain opioid peptide systems are known to play an important role in motivation, emotion, attachment behaviour, the response to stress and pain, control of food intake, and the rewarding effects of alcohol and nicotine.
Pfam PF09223: ZinT (YodA) periplasmic lipocalin-like zinc-recruitment (domain)
ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families [pfam:PF01297],[pfam:PF00950], [pfam:PF00005], regulated by the transcription-regulator FUR, [pfam:PF01475]. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), [pfam:PF01297].  Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination.
Wikipedia: In molecular biology, ZinT is a family of protein domains found in prokaryotes. The domain contains a single binding site that can accommodate a divalent cation, with a geometry suggestive of zinc binding. This family was first thought to be part of the bacterial response to a toxic heavy metal cadmium by binding to the metal to ensure its elimination; however, more recent work has suggested a role in zinc homeostasis.
Pfam PF13018: Extended Signal Peptide of Type V secretion system (conserved_site)
This conserved domain is called ESPR for Extended Signal Peptide Region. It is present at the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems, including the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (TAAs). So far, the ESPR is present only in Gram-negative bacterial proteins originating from the classes Beta- and Gamma-proteobacteria. ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation. Deletion of ESPR causes mis-folding of the TAAs passenger domain in the periplasm , substantially impairing its translocation across the outer membrane.
Wikipedia: In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion. TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful and infective to the host organism.
Pfam PF21889: TPR1-like, CTLH-containing domain (domain)
This domain is found in Protein TPR1 from Oryza sativa, also known as Topless-related protein 2, and in similar sequences predominantly found in plants and some fungal species. TPR1 is thought to be a downstream regulator of strigolactones signalling. This entry represents the second part of the N-terminal domain of TPR1, which contains the C-terminal to LisH (CTLH) motif, responsible for the binding to the auxin-responsive protein 12 (IAA12). This domain shows an all-alpha configuration.
Pfam PF05767: Poxvirus virion envelope protein A14 (family)
This family consists of several Poxvirus virion envelope protein A14 like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression.
Pfam PF05842: Euplotes octocarinatus mating pheromone protein (family)
This family consists of several mating pheromone proteins from Euplotes octocarinatus. Cells of the ten mating types of the ciliate Euplotes octocarinatus communicate by pheromones before they enter conjugation. The pheromones induce homotypic pairing when applied to mating types that do not secrete the same pheromone(s). Heterotypic pairs (i.e., those between cells of different mating types) are formed only when both mating types in a mixture secrete a pheromone that the other does not. The genetics of mating types is based on four codominant mating type alleles, each allele determining production of a different pheromone. The pheromones not only induce pair formation but also attract cells.
Pfam PF15569: Immunity protein 40 (family)
A predicted immunity protein with an alpha+beta fold and conserved phenylalanine and tryptophan residues and a GGD motif. 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 Ntox19 family.
Pfam PF21527: Putative adhesin Stv domain (domain)
This entry represents a putative adhesin domain found in gram negative bacteria.
Pfam PF22513: Antitoxin FitA-like, ribbon-helix-helix (domain)
This domain is found in Antitoxin FitA from Neisseria gonorrhoeae and similar bacterial sequences. FitA is the antitoxin component of a type II toxin-antitoxin (TA) system. It binds DNA through its ribbon-helix-helix motif (this entry).
Pfam PF01594: AI-2E family transporter (family)
This family includes four different proteins from  E. coli alone. One of them, YdgG or TqsA, has been shown to mediate transport of the quorum-sensing signal autoinducer 2 (AI-2). It is not clear if TqsA enhances secretion of AI-2 or inhibits AI-2 uptake. By altering the intracellular concentration of AI-2, TqsA affects gene expression in biofilms and biofilm formation. TsqA belongs to the AI-2 exporter (AI-2E) superfamily.