SII-SWORD/CoKE huggingface dataset:
Pfam PF09974: Uncharacterized protein conserved in archaea (DUF2209) (family)
This domain, found in various hypothetical archaeal 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 PF14912: Testicular haploid expressed repeat (repeat)
This repeat is the only conserved part of the THEG proteins from vertebrate spermatids. Both human and mouse THEG are specifically expressed in the nucleus of haploid male germ cells and are involved in the regulation of nuclear functions. Although the differential gene expression of THEG in spermatid-Sertoli cell co-culture supports the relevance of germ cell-Sertoli cell interaction for gene regulation during spermatogenesis, THEG was not found to be essential for spermatogenesis in mice.
Pfam PF24071: Phage FDXHR zinc binding domain (domain)
This entry represents a small family of uncharacterised phage proteins. According to structure predictions this domain contains two zinc binding clusters. This domain contains a highly conserved sequence motif FDXHR where X can be any amino acid.
Pfam PF03438: Pneumovirus NS1 protein (family)
This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication.
Pfam PF15230: Serine/arginine repetitive matrix protein C-terminus (family)
This domain is found near to the C-terminus of Serine/arginine repetitive matrix proteins 3 and 4.
Pfam PF12664: Protein of unknown function (DUF3789) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (V and 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 PF06516: Purine nucleoside permease (NUP) (family)
This family consists of several purine nucleoside permease from both bacteria and fungi.
Pfam PF11112: Pyocin activator protein PrtN (family)
PrtN is a transcriptional activator for pyocin synthesis genes. It activates the expression of various pyocin genes by interaction with the DNA sequences conserved in the 5' noncoding regions of the pyocin genes.
Pfam PF09321: Domain of unknown function (DUF1978) (family)
Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified.
Pfam PF21426: Tip pilin GBS104-like, Ig-like domain (domain)
This domain is found in Streptococcus agalactiae tip pilin GBS104 and similar proteins. It is usually associated with von Willebrand factor type A domain (e.g. [pfam:PF00092]), which inserts into the domain core composed of two sequentially segregated fragments. Members of this entry are likely to contain an intramolecular isopeptide bond. The domain represented by this entry does not include the two N-terminal strands that precede the inserted von Willebrand factor type A domain.
Pfam PF24393: Pepco (domain)
This entry represents a small domain co-occurring with peptidases like Trypsin, Caspase, and MPTase. The domain is homologous to Trypco1 and Trypco2 from MoxR-vWA-based ternary systems typically seen in multicellular bacteria. Peptidase cleavage of Pepco superfamily domains may trigger assembly into multimeric complexes, leading to cell suicide akin to processes seen in metazoan apoptosis.
Pfam PF20686: Carboxysome Shell Carbonic Anhydrase, catalytic domain (domain)
Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localised in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain. This entry represents the catalytic domain, consisting of a central five-stranded mixed beta-sheet with two helices flanking one side of the sheet and one helix flanking the other side.
Pfam PF09894: Uncharacterized protein conserved in archaea (DUF2121) (family)
This domain, found in various hypothetical archaeal 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 PF12255: Insecticide toxin TcdB middle/C-terminal region (family)
This domain family is found in bacteria, and is approximately 150 amino acids in length. The family is found in association with [pfam:PF03534]. This family is the C-terminal-sided middle region of the bacterial insecticide toxin TcdB.
Pfam PF19865: Family of unknown function (DUF6338) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001593) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the ficellomycin biosynthetic gene cluster from  Streptomyces ficellus.
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 PF17764: 3'DNA-binding domain (3'BD) (domain)
This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.
Pfam PF25029: MOM1-like domain (domain)
This domain is found in Helicase protein MOM1 from Arabidopsis thaliana (MOM1) and similar plant proteins. MOM1 is involved in the regulation of transcriptional gene silencing (TGS) independently of changes in DNA methylation. This domain is predicted to have an all-alpha helical configuration.
Pfam PF08603: Adenylate cyclase associated (CAP) C terminal (family)
Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, 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 (slim mold), 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 (CAP1 and CAP2) that share 64% amino acid identity.
This entry represents the C-terminal domain of CAP proteins, which is responsible for G-actin-binding. This domain has a superhelical structure, where the superhelix turns are made of two Î²-strands each .
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 PF18378: Nuclear pore protein NUP188 C-terminal domain (repeat)
This is C-terminal domain of Nup188.  It is a right-handed arc-shaped superhelical structure built from 19 helices that form 6 helical repeats, which are stacked in regular order. The first helical pair (alpha1 and alpha2) forms a HEAT repeat followed by 5 ARM repeats.
Pfam PF09740: Uncharacterized conserved protein (DUF2043) (family)
This is a 100 residue conserved region of a family of proteins found from fungi to humans.  This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}.
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 PF05938: Plant self-incompatibility protein S1 (family)
This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties.
Pfam PF24338: Domain of unknown function (DUF7506) (domain)
This domain is found in a group of uncharacterised proteins from parasitic secernentean nematodes. It is predicted to adopt an OB-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 PF02919: Eukaryotic DNA topoisomerase I, DNA binding fragment (family)
Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain.
Pfam PF09998: Uncharacterized protein conserved in bacteria (DUF2239) (family)
This domain, found in various hypothetical bacterial 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 PF16679: DNA replication factor Cdt1 C-terminal domain (domain)
This is the C-terminal domain of DNA replication factor Cdt1. This domain binds the MCM complex.
Wikipedia: CDT1 is a protein that in humans is encoded by the CDT1 gene. It is a licensing factor that functions to limit DNA from replicating more than once per cell cycle.
Pfam PF23680: YecU-like (family)
This protein family includes Protein YecU from Escherichia coli, a 58-residues long protein encoded by a small open reading frame (smORF).
Pfam PF07007: Lysozyme inhibitor LprI (domain)
This family consists of several bacterial proteins of around 120 residues in length. Members of this family contain four highly conserved cysteine residues. Family members include lipoprotein LprI from Mycobacterium, which binds to and inhibits macrophage lysozyme, which may aid bacterial survival.
Pfam PF22914: Fibulin C-terminal Ig-like domain (domain)
This entry represents a C-terminal Ig-like domain found in fibulin proteins. This Ig-like domain seems most closely related to the cadherin domain [pfam:PF00028]. Fibulins are a family of ECM glycoproteins characterized by a fibulin-type C-terminal domain preceded by tandem calcium-binding epidermal growth factor (EGF)-like modules. They are involved in protein-protein interaction with the components of basement membrane and extracellular matrix proteins.
Pfam PF11865: Serine/threonine-protein kinase mTOR domain (repeat)
This entry represents a domain found in human serine/threonine-protein kinase mTOR and its homologues, a central regulator of cellular metabolism, growth and survival in response to hormones, growth factors, nutrients, energy and stress signals. In Saccharomyces cerevisiae, the TOR proteins, TOR1 and TOR2, regulate growth in a rapamycin-sensitive manner. This domain consists of HEAT repeats.
Pfam PF14475: Sec1-binding region of Mso1 (domain)
Mso1p is a component of the secretory vesicle docking complex whose function is closely associated with that of Sec1p. It is a small hydrophilic protein that is enriched in the microsomal membrane fraction, and this binding domain is towards the N-terminus of Mso1. The yeast Sec1p protein functions in the docking of secretory transport vesicles to the plasma membrane.  Mso1p and Sec1p interact at sites of exocytosis and the Mso1p-Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. The C-terminal region of Mso1 (not built) assists in targetting Sec1 to the sites of polarised membrane transport.
Pfam PF12650: Domain of unknown function (DUF3784) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 96 and 110 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 PF20232: C-terminal domain of Type VI secretion system FHA protein (domain)
This presumed domain is found at the C-terminus of a group of proteins thought to be expressed in a Type VI secretion system locus. These proteins contain an N-terminal FHA domain. The function of this domain is unknown.
Pfam PF16833: Erythroid krueppel-like transcription factor, transactivation 2 (domain)
This family is the second part of the minimal transactivation domain of erythroid-specific transcription factor EKFL in craniates. EKLF plays an important role in red blood cell development; it is post-translationally modified by ubiquitin on several lysine residues, and its turnover in the cell is regulated by ubiquitin-mediated degradation. In the first 90 residues at the N-terminus EKLF carries a minimal transactivation or TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains EKLF_TAD1 (residues 1-40), [pfam:PF16832], and EKLF_TAD2 (residues 51-90) that are both capable of independently activating transcription. Both TAD1 and TAD2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development.
Pfam PF06016: Reovirus core-spike protein lambda-2 (L2), C-terminal (domain)
Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the C-terminal (eighth) domain which, together with the sixth and seventh domains, forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA. This domain has a Ig-like, resembling a truncated V region of an antibody light chain.
Pfam PF22009: Yaba-Like Disease Virus IL18BP (domain)
YLDV-IL18BP is unique among the diverse family of mammalian and poxvirus IL18BPs in that it uses a bivalent binding mode and a unique set of interacting residues for binding IL18. YLDV-IL18BP binds to the same surface of IL18 used by other IL18BPs, suggesting that all IL18BPs use a conserved inhibitory mechanism by blocking a putative receptor-binding site on IL18. This domain adopts a typical Ig-like fold.
Pfam PF13570: PQQ-like domain (repeat)
Pyrrolo-quinoline quinone (PQQ) is a redox coenzyme, which serves as a cofactor for a number of enzymes (quinoproteins) and particularly for some bacterial dehydrogenases . A number of bacterial quinoproteins belong to this family.

Enzymes in this group have repeats of a Î² propeller.
Pfam PF24839: Domain of unknown function (DUF7718) (domain)
This domain is found in uncharacterised prokaryotic proteins. It is predicted to adopt alpha/beta structure consisting of a meander beta-sheet and a kinked alpha-helix. It contains several conserved aspartate and histidine residues that are predicted to come close in space and may constitute a metal binding site.
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 PF17429: Gene product 70 (family)
This family of unknown function is found in Mycobcterium phage and Actinobacteria.
Pfam PF18075: FtsX extracellular domain (domain)
This is the extracellular domain (ECD) found in FtsX enzyme, a homolog of the transmembrane PG-hydrolase regulator. The FtsX extracellular domain binds the PG peptidase Rv2190c/RipC N-terminal segment, causing a conformational change that activates the enzyme ileading to PG hydrolysis in Mycobacterium tuberculosis. Structural analysis of FtsX ECD reveals fold containing two lobes connected by a flexible hinge. Mutations in the hydrophobic cleft between the lobes showed reduction in RipC binding in vitro and inhibition of FtsX function in Mycobacterium smegmatis.
Pfam PF00029: Connexin (domain)
Connexin proteins form gap-junctions between cells. They carry four transmembrane regions, hence why this family now includes Connexin_CCC, which represented the second pair of TMs.
Wikipedia: Connexins (Cx), or gap junction proteins, are structurally related transmembrane proteins that assemble to form vertebrate gap junctions. An entirely different family of proteins, the innexins, forms gap junctions in invertebrates. Each gap junction is composed of two hemichannels, or connexons, which consist of homo- or heterohexameric arrays of connexins, and the connexon in one plasma membrane docks end-to-end with a connexon in the membrane of a closely opposed cell. The hemichannel is made of six connexin subunits, each of which consist of four transmembrane segments. Gap junctions are essential for many physiological processes, such as the coordinated depolarization of cardiac muscle, proper embryonic development, and the conducted response in microvasculature. Connexins also have non-channel dependant functions relating to cytoskeleton and cell migration. For these reasons, mutations in connexin-encoding genes can lead to functional and developmental abnormalities.
Pfam PF04671: Erythrocyte membrane-associated giant protein antigen 332 (repeat)
To date many different Plasmodium antigens recognised by the hyperimmune system human sera have been cloned, sequenced and characterised.  The majority contain tandemly repeated amino acid sequences which make up a considerable portion of the protein sequence. It has been suggested that these repeat-containing antigens may provide an immunological 'smokescreen' to the parasite in order to evade the human immune system. This repeat is found exclusively in the Plasmodium falciparum Ag332 protein and occupies most of its length.
Pfam PF02013: Cellulose or protein binding domain (domain)
This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria.
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF18265: Nas2 N_terminal domain (domain)
Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5.
Pfam PF01700: Orbivirus VP3 (T2) protein (family)
The orbivirus VP3 protein is part of the virus core and makes a 'subcore' shell made up of 120 copies of the 100K protein. VP3 particles can also bind RNA and are fundamental in the early stages of viral core formation. Also found in the family is structural core protein VP2 from   broadhaven virus which is similar to VP3 in bluetongue  virus. Orbivirus are part of the larger reoviridae which have a  dsRNA genome of 10-12 linear segments; orbivirus found in this family include bluetongue virus and epizootic hemorrhagic  disease virus.