SII-SWORD/CoKE huggingface dataset:
Pfam PF17009: Domain of unknown function (DUF5090) (family)
This is a microsporidial-specific family of proteins of unknown function. The family is likely to be of four transmembrane domains.
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 PF07436: Curtovirus V3 protein (family)
This family consists of several Curtovirus V3 proteins of around 90 residues in length. The function of this family is unknown.
Pfam PF11179: Protein of unknown function (DUF2967) (family)
This family of proteins with unknown function appears to be restricted to Drosophila.
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 PF18528: RNA editing 3' terminal uridylyl transferase 2 middle domain (domain)
Post-transcriptional RNA editing in Trypanosomatids (pathogenic protozoa) is catalyzed by a large multiprotein complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl transferase 2 (TUTase 2; RET2) catalyzes the uridylate addition reaction.  RET2 structure consists of three domains: the N-terminal domain (NTD), the middle domain (MD) and the C-terminal domain (CTD). This MD domain is mainly composed of six helices and a four-stranded antiparallel beta-sheet. structural comparison reveals that the fold of this MD is topologically similar to the binding domains of several RNA-binding proteins such as the RNA-binding domain of the U1A spliceosomal protein, the RRM domain of the human La protein and the CTD of an archaeal CCA-adding enzyme. The CTD of the archaeal CCA-adding enzyme has been shown to bind double-stranded tRNA stem substrate through the alpha-helices regions. Hence it is suggested that this domain might be an RNA-binding domain.
Pfam PF24354: Neuron-derived neurotrophic factor, N-terminal domain (domain)
This domain is found N-terminal in the human Neuron-derived neurotrophic factor (NDNF) and related proteins. NDNF is a secretory protein that plays a role in various cellular processes. It acts as a chemorepellent on gonadotropin-releasing hormone expressing neurons regulating their migration to the hypothalamus. It also promotes neuron migration, growth and survival as well as neurite outgrowth and is involved in the development of the olfactory system. The domain represented by this entry is predicted to fold into a beta-sandwich that has some similarity to Nucleoplasmin-like fold.
Pfam PF02206: Domain of unknown function (family)
This domain has no known function and is found in Caenorhabditis elegans proteins normally at the N-terminal.
Pfam PF00525: Alpha crystallin A chain, N terminal (family)
The crystallins are water-soluble structural proteins that occur in high concentration in the cytoplasm of eye lens fibre cells. Four major groups of crystallin have been distinguished on the basis of size, charge and immunological properties: alpha-, beta-and gamma-crystallins occur in all vertebrate classes (though gamma-crystallins are low or absent in avian lenses); and delta-crystallin is found exclusively in reptiles and birds .

Alpha-crystallin occurs as large aggregates, comprising two types of related subunits or chains (A and B) that are highly similar to the small (15-30kDa) heat shock proteins (HSPs), particularly in their C-terminal halves. The relationship between these families is one of classic gene duplication and divergence, from the small HSP family, allowing adaptation to novel functions. Divergence probably occurred prior to evolution of the eye lens, alpha-crystallin being found in small amounts in tissues outside the lens .

Alpha-crystallin has chaperone-like properties including the ability to prevent the precipitation of denatured proteins and to increase cellular tolerance to stress . It has been suggested that these functions are important for the maintenance of lens transparency and the prevention of cataracts. This is supported by the observation that alpha-crystallin mutations show an association with cataract formation.
This entry represents the N-terminal domain of alpha-crystallin. It is not necessary for dimerisation or chaperone activity, but appears to be required for the formation of higher order aggregates .
Wikipedia: In anatomy, a crystallin is a water-soluble structural protein found in the lens and the cornea of the eye accounting for the transparency of the structure. It has also been identified in other places such as the heart, and in aggressive breast cancer tumors.
The physical origins of eye lens transparency and its relationship to cataract are an active area of research. Since it has been shown that lens injury may promote nerve regeneration,
crystallin has been an area of neural research. So far, it has been demonstrated that crystallin β b2 (crybb2) may be a neurite-promoting factor.
Pfam PF00119: ATP synthase A chain (domain)
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (7.1.2.2) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the Î±(3)Î²(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.
This entry represents subunit A (or subunit 6) found in the F0 complex of F-ATPases. This subunit is a key component of the proton channel, and may play a direct role in the translocation of protons across the membrane. Catalysis in the F1 complex depends upon the rotation of the central stalk and F0 c-ring, which in turn is driven by the flux of protons through the membrane via the interface between the F0 c-ring and subunit A. The peripheral stalk links subunit A to the external surface of the F1 domain, and is thought to act as a stator to counter the tendency of subunit A and the F1 Î±(3)Î²(3) catalytic portion to rotate with the central rotary element .
Wikipedia: MT-ATP6 is a mitochondrial gene with the full name 'mitochondrially encoded ATP synthase membrane subunit 6' that encodes the ATP synthase Fo subunit 6. This subunit belongs to the Fo complex of the large, transmembrane F-type ATP synthase. This enzyme, which is also known as complex V, is responsible for the final step of oxidative phosphorylation in the electron transport chain. Specifically, one segment of ATP synthase allows positively charged ions, called protons, to flow across a specialized membrane inside mitochondria. Another segment of the enzyme uses the energy created by this proton flow to convert a molecule called adenosine diphosphate (ADP) to ATP. Mutations in the MT-ATP6 gene have been found in approximately 10 to 20 percent of people with Leigh syndrome.
Pfam PF24407: HTH_upstream_double_PIN (domain)
This is an HTH domain found upstream to the double PIN in the permuted GreA/B-C conflict system.
Pfam PF19463: Family of unknown function (DUF6000) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000026) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes  a protein from the avilamycin A biosynthetic gene cluster from  Streptomyces viridochromogenes Tue57 and appears to be predominantly found in bacteria.
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 PF19201: Family of unknown function (DUF5873) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Phyconaviridae.
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 PF22749: Arb2 domain (domain)
This entry represents Arb2 domain that was first described in Argonaute-binding protein 2 from S. pombe, from which it gets the name. Arb2 protein is the orthologue of FAM172 from animals, including FAM12A from human, a protein associated with CHARGE syndrome, a severe multi-organ developmental disorder mainly affecting derivatives of cranial and cardiac neural crest cells (NCCs). A general pathological mechanism for CHARGE syndrome has been suggested to be a spliceosomopathy, the perturbation of chromatin-mediated alternative splicing. FAM172A and its homologues contain a large ARB2 domain split into two halves by a classical bipartite NLS that helps to stabilize the chromatin-spliceosome interface as part of a complex that includes CHD7 and AGO2. It has been suggested that FAM172A can connect the alternative splicing machinery to specific transcribed chromatin regions. Arb2 from S.pombe is a member of the argonaute siRNA chaperone (ARC) complex which is required for histone H3K9 methylation, heterochromatin assembly and siRNA generation. This domain has clear homology to alpha/beta-hydrolases but it lacks the catalytic triad of these enzymes.
Pfam PF24660: GPI inositol-deacylase beta-sandwich domain (domain)
This domain is found in the human GPI inositol-deacylase PGAP1 and related proteins. PGAP1 is involved in inositol deacylation of GPI-anchored proteins. This domain is predicted to fold into a beta-sandwich with a topology similar to galactose-binding domains.
Pfam PF21072: EFR3 protein (repeat)
This entry represents the HEAT-like repeat region from the EFR3 protein. Protein EFR3 homologue A (EFR3A) is a component of a phosphatidylinositol 4-kinase (PI4K) complex, composed of PI4KA, EFR3 (EFR3A or EFR3B), TTC7 (TTC7A or TTC7B) and FAM126 (FAM126A or FAM126B). This complex is required for the attachment of phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. EFR3A is palmitoylated at its N terminus, anchoring the protein to the plasma membrane, and probably acts as the membrane-anchoring component in the complex. In yeast, the Efr3p protein is a main regulator of the Stt4p phosphatidylinositol 4-kinase at contact sites between the endoplasmic reticulum and the plasma membrane.
Pfam PF10147: Growth arrest and DNA-damage-inducible proteins-interacting protein 1 (family)
Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity.
Pfam PF05378: Hydantoinase/oxoprolinase N-terminal region (family)
This family is found at the N-terminus of the [pfam:PF01968] family.
Pfam PF22074: Cep192 domain 5 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the fifth domain of the metazoan Cep192 homologs. This domain along with domain 4 constitutes the so-called Spd2 domain that is ubiquitously present in all SPD2/CEP192 homologues beyond Metazoa and represents the most conserved region amongst them.
Pfam PF14304: Transcription termination and cleavage factor C-terminal (domain)
The C-terminal section of CSTF proteins is a discreet structure is crucial for mRNA 3'-end processing. This domain interacts with Pcf11 and possibly PC4, thus linking CstF2 to transcription, transcriptional termination, and cell growth.
Pfam PF15085: Neuropeptide FF (family)
Neuropeptide FF (together with neuropeptides AF and SF, which are derived from the same precursor) belongs to a family of neuropeptides containing an RF-amide motif at their C-termini . Neuropeptide FF is found at high concentrations in the posterior pituitary, spinal cord, hypothalamus and medulla, and is believed to be involved in pain modulation, opioid tolerance, cardiovascular regulation, memory and neuroendocrine regulation.
Wikipedia: Neuropeptide FF is a mammalian amidated neuropeptide originally isolated from bovine brain and characterized as a pain-modulating peptide, with anti-opioid activity on morphine-induced analgesia.
Pfam PF11356: Type II secretion system protein C (family)
This is the greater N-terminal region of GspC-type proteins. GspC proteins form part of the sophisticated transport mechanism of Gram-negative pathogens for injecting divers proteins into their hosts, a type-II secretion system - T2SS. The region is made up of a short N-terminal cytoplasmic domain that is followed by the single transmembrane helix, a Pro-rich linker, and the so-called homology region domain in the periplasm. This inner membrane GspC interacts with the outer membrane secretin GspD via periplasmic domains, an interaction which is critical for the effectiveness of type II secretion.
Pfam PF06292: MUN domain (repeat)
This entry corresponds to the MUN domain found in Munc13 proteins. These constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. Structural studies have defined MHD1 and MHD2 to be part of the larger MUN domain which forms an elongated structure composed of any pairs of alpha helices.
Pfam PF23690: YqfI-like (family)
This protein family includes Protein YqfI from Escherichia coli, a 27-residues long sequence predicted to adopt an alpha -helical configuration.
Pfam PF13048: Protein of unknown function (DUF3908) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 140 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Pfam PF16574: Coiled-coil region of centrosome protein CE290 (coiled_coil)
CEP290 and similar centrosomal proteins carry a number of coiled-coil regions, and this is the fifth along the length of the protein. It is thought that the proteins are involved in cilia biosynthesis.
Pfam PF11015: Protein of unknown function (DUF2853) (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 PF12879: SICA C-terminal inner membrane domain (domain)
The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies.  The C-terminal domain is thought to remain in the erythrocyte, found juxtaposition to the single transmembrane domain.  To date, all full length proteins contain a single copy of this domain.
Pfam PF02663: FmdE, Molybdenum formylmethanofuran dehydrogenase operon (domain)
This entry represents the FmdE protein that is encode by the molybdenum formylmethanofuran dehydrogenase operon.  FmdE does not co-purify with the molybdenum isozyme that is formed by FmdC and FmdB.  The domain is typically found as a single copy, but is repeated in some sequence two to three times.  It is also common place to find this domain co-occurs with a zinc-beta ribbon domain, suggesting that is may bind nucleic acid and be involved in transcription regulation.
Pfam PF04415: Protein of unknown function (DUF515) (family)
Family of hypothetical Archaeal 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 PF11814: Peptidase_C39 like family (domain)
This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Pfam PF00976: Corticotropin ACTH domain (family)
Pro-opiomelanocortin is present in high levels in the pituitary and is processed into 3 major peptide families: adrenocorticotrophin (ACTH); alpha-, beta- and gamma-melanocyte- stimulating hormones (MSH); and beta-endorphin . ACTH regulates the synthesis and release of glucocorticoids and, to some extent, aldosterone in the adrenal cortex. It is synthesised and released in response to corticotrophin-releasing factor at times of stress (i.e. heat, cold, infection, etc.), its release leading to increased metabolism. The action of MSH in man is poorly understood, but it may be involved in temperature regulation . Full activity of ACTH resides in the first 20 N-terminal amino acids, the first 13 of which are identical to alpha-MSH .

The function of this region is not known, though it is found near the centre of these proteins.
Pfam PF14360: PAP2 superfamily C-terminal (domain)
This family is closely related to the C-terminal a region of PAP2.
Pfam PF17263: Family of unknown function (DUF5329) (family)
This is a bacterial family of proteins with unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24066: Histidine N-acetyltransferase, C-terminal (domain)
This domain is found at the C-terminal end of Histidine N-acetyltransferase from the fish Oreochromis niloticus (Hisat) and similar animal sequences. Hisat is responsible for the N-acetyl-histidine (NAH) synthesis, which is a major constituent of brain and lens of ectothermic vertebrates.
Pfam PF15104: Cilia- and flagella-associated protein 141 (family)
This family includes Cilia- and flagella-associated protein 141 (CFAP141, also known as C1orf189 protein). Members of this family may be microtubule inner proteins (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.
Pfam PF25115: Agd3 deacetylase domain (domain)
This entry represents the carbohydrate esterase (CE) domain of the exopolysaccharide deacetylase Agd3 from Aspergillus fumigatus, a protein required for biofilm formation. This domain has structural similarity to members of the carbohydrate esterase family (CE4) but the amino acid sequences is too divergent and constitutes a founding member of a CE family.
Pfam PF19722: Sentrin-specific protease 3/5 N-terminal (domain)
Sentrin/SUMO-specific proteases (SENPs) reversibly regulate the covalent modification of proteins by SUMO. SENP3 and 5 share considerable sequence homology and exhibit similar substrate specificity, as they are active against SUMO-2 and SUMO-3 but less so for SUMO-1. They are more closely related than to SENP1/2. This entry covers the N-terminal domain of SENP5, which contains a conserved region directly preceding the catalytic domain, which is shared with SENP3. This domain is responsible for the subcellular localisation. SENP3 and 5 colocalise in the nucleolus and their depletion causes defects in ribosome biogenesis.
Pfam PF19329: BTB/POZ domain-containing protein KCTD11/21 C-terminus (family)
This family represents the C-terminal region of BTB/POZ domain-containing protein KCTD11 (known as REN: EGF-, NGF- and retinoic acid-responsive gene) and one homologue, a member of KCTD containing, Cullin3 adaptor, suppressor of Hedgehog (KCASH) family, KCASH2-KCTD21 protein. They share high similarity and a BTB domain responsible for oligomerization and formation of a Cullin3 ubiquitin ligase complex, specific expression in brain and cerebellum where they have a role in neuronal differentiation, and suppressor activity on acetylation-dependent Hedgehog/Gli signalling through ubiquitination and degradation of histone deacetylase 1. These proteins have been described as tumor suppressors that inhibit medulloblastoma growth by antagonizing Hedgehog signalling.
Pfam PF18137: Origin recognition complex winged helix C-terminal (domain)
This is the C-terminal winged-helix (WH) DNA-binding domain of the origin recognition complex present in Drosophila melanogaster. The WH domain is responsible for recognizing origin sequences.
Pfam PF03724: META domain (domain)
Small domain family found in proteins of of unknown function. Some are secreted (e.g. [swissprot:O25998]) and implicated in motility in bacteria. Also occurs in Leishmania spp. as an essential gene.  Over-expression in L.amazonensis increases virulence ([swissprot:O43987];). A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond.