SII-SWORD/CoKE huggingface dataset:
Pfam PF06581: Mad1 and Cdc20-bound-Mad2 binding (family)
This family is involved in the cell-cycle surveillance mechanism called the spindle checkpoint. This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, and Mad2 exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerisation and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex.
Pfam PF19541: Family of unknown function (DUF6065) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001418) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the myxochromide D  biosynthetic gene cluster from Hyalangium minutum.
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 PF01243: Pyridoxamine 5'-phosphate oxidase (domain)
This entry includes pyridoxamine 5'-phosphate oxidases, FMN flavoproteins that catalyse the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. The binding sites for FMN and for substrate have been highly conserved throughout evolution. In some species, the coenzyme F420 may perform the FMN role. This entry represents the N-terminal segment of these proteins, which is involved in FMN binding when they form the dimer. In human PNPO, it has been shown that this region contains some of the residues that constitute the PLP allosteric site which regulates its activity. The C-terminal region of these proteins ([pfam:PF10590]) is involved in dimerisation and also contributes some residues to the PLP allosteric site.   Some of the members included in this entry are involved in phenazine biosynthesis.
Pfam PF12755: Vacuolar 14 Fab1-binding region (repeat)
Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. This domain appears to be the one responsible for binding to Fab1. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system.
Pfam PF06173: Protein of unknown function (DUF986) (family)
This family consists of several bacterial putative membrane proteins of 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 PF22131: CRISPR-associated endonuclease CjCas9 PI-CTD domain (domain)
In the type II CRISPR-Cas system, the Cas9 effector nuclease associates with dual guide RNAs (crRNA and trans-activating crRNA (tracrRNA)) and cleaves double-stranded DNA targets complementary to the crRNA guide. Cas9 is composed of multiple domains. This entry represents the C-terminal lobe of the so-called PAM-interacting domain (PI-CTD) that is found in Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologues. The PI domain is involved in the recognition of PAM-containing duplex formed by the target and non-target DNA strands. This domain facilitates the target DNA unwinding and the heteroduplex formation. The CjCas9 PI-CTD domain adopts a partly open six-stranded beta-barrel with a SH3-like topology.
Pfam PF23970: Family of unknown function (DUF7297) (family)
This entry represents a family of uncharacterised phage proteins. The family includes [swissprot:M9MUF4] which is annotated as a baseplate I protein. Proteins in this family are about 450 residues 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 PF03251: Tymovirus 45/70Kd protein (family)
Tymoviruses are single stranded RNA viruses.  This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase.
Pfam PF05103: DivIVA protein (family)
The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate mini-cells. Inactivation of divIVA produces a mini-cell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype. These proteins appear to contain coiled-coils.
Pfam PF08856: Protein of unknown function (DUF1826) (domain)
These proteins are functionally uncharacterised.
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 PF17712: Family of unknown function (DUF5557) (family)
This is a family of unknown function found in primates.
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 PF12597: Cytochrome c oxidase assembly protein COX20 (family)
Complex IV (CIV) is a copper-heme oxidase that couples electron transfer from cytochrome c to oxygen with proton extrusion across the inner membrane to contribute to the proton gradient required for ATP generation. This entry includes fungal mitochondrial complex IV assembly factor Cox20 and its homologues (also known as FAM36A in metazoa. Human CIV is formed by three catalytic core subunits (COX1/2/3). COX20 has been found to form a complex with SCO1, SCO2, and newly synthesized COX2. It may act as a chaperone in the early steps of COX2 maturation.
Pfam PF10463: Peptidase U49 (family)
This family contains Lit peptidase from Escherichia coli. Lit protease functions in bacterial cell death in response to infection by bacteriophage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Pfam PF20146: Nose resistant-to-fluoxetine protein, N-terminal domain (domain)
This is the N-terminal domain of Caenorhabditis elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4) proteins; the domain is also present in several other worm and fly proteins. NRF-6 and NDG-4 are multipass transmembrane proteins which may act together in a complex to function to transport fluoxetine across the hypodermal barrier to the inside of the animal, where it can then act on neuromuscular targets to induce muscle contraction.The complex may more generally play a role in regulation of membrane transport in C. elegans .
Pfam PF20559: Family of unknown function (DUF6770) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 514 and 521 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 PF06533: Protein of unknown function (DUF1110) (family)
This family consists of hypothetical proteins specific to Oryza sativa. One sequence ([swissprot:Q943P1]) appears to be tandemly repeated.
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 PF20164: GspA/SrpA SigLec-like domain (domain)
This domain is an adhesive domain that binds to sialoglycan. A Thr-Arg motif conserved across homologous carbohydrate-binding adhesins that may orient the sialic acid moiety of carbohydrate ligands.
Pfam PF00457: Glycosyl hydrolases family 11 (domain)
The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (3.2.1.4), cellobiohydrolases (3.2.1.91) (exoglucanases), or xylanases (3.2.1.8) . Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family G  or as the glycosyl hydrolases family 11 (GH11) .

The GH11 domain folds into a jelly-roll shape likened to a partially closed right hand. Several anti-parallel Î²-strands bend almost 90deg to produce a substrate-binding groove characteristic of the GH11 domain active sites. Two catalytic Glu residues face each other from opposite sides of the groove. The hydrolysis reaction is believed to follow a double- displacement mechanism, with one Glu residue acting as a general acid/base catalyst and the other as a nucleophile.
Wikipedia: In molecular biology, Glycoside hydrolase family 11 is a family of glycoside hydrolases.
Pfam PF18206: Porphyranase beta-sandwich domain 1 (domain)
This domain is found in porphyranase protein present in Bacteroides plebeius. Porphyranase breaks down porphyran during digestion of red seaweed glycans. It is worth noting that red seaweed glycans contain sulfate esters that are absent in terrestrial plants. This domain follows the catalytic domain of the porphyranase protein and folds into beta-sandwich.
Pfam PF20753: Phage tail C-terminal domain (domain)
This family includes uncharacterised proteins from Firmicutes and phages, some members are phage tail-related proteins. Included in this entry is the prophage-derived protein YomH from Bacillus subtilis (swiss:O31977).
Pfam PF21807: PfEMP1 protein, CIDRalpha1 domain (domain)
This domain is found in the surface protein PfEMP1 from Plasmodium falciparum. PfEMP1 is essential for the virulence of this organism. This protein interacts with the endothelial protein C receptor (EPCR) through its cysteine-rich interdomain region (CIDRalpha1, this entry). This domain show binding surfaces that are conserved in shape and bonding potential, despite dramatic sequence diversity. The domain is built around a long three-helical core bundle, with a four-stranded beta-sheet on one side and two alpha-helices on the opposite side.
Pfam PF10664: Cyanobacterial and plastid NDH-1 subunit M (family)
The proton-pumping NADH:ubiquinone oxidoreductase catalyses the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organisms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides.  Homologues of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 sub-complexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit. The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organisms. The three subunits of NDH-1, NdhM, NdhN and NdhO are essential for effecting cyclic electron flow around photosystem I, by supplying extra-ATP for photosynthesis in both plastids and cyanobacteria.
Pfam PF21587: AP-5 complex subunit beta-1, N-terminal (repeat)
AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport. This entry represents the N-terminal domain which adopts an alpha-solenoid structure.
Pfam PF14288: 1,3-beta-glucan synthase subunit FKS1, domain-1 (family)
The FKS1_dom1 domain is likely to be the 'Class I' region just N-terminal to the first set of transmembrane helices that is involved in 1,3-beta-glucan synthesis itself. This family is found on proteins with family Glucan_synthase, [pfam:PF02364].
Pfam PF08864: UPF0302 domain (domain)
This family is known as UPF0302. It is currently uncharacterised.
Pfam PF16237: Domain of unknown function (DUF4896) (family)
A small family of uncharacterized proteins around 50 or 570 residues in length and found in various Thermotoga species. The function of this family is unknown.
Pfam PF10948: Protein of unknown function (DUF2635) (family)
This is a family of phage 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 PF09002: Card1-like, endonuclease domain (domain)
This is the endonuclease domain found in a set of bacterial proteins, including Card1 (cyclic-oligoadenylate-activated single-stranded ribonuclease and single-stranded deoxyribonuclease 1) from Treponema succinifaciens ([swissprot:F2NWD3]), a protein that is part of type III CRISPR-Cas immune response system. This protein consists of a CARF (CRISPR-associated Rossman fold) domain at the N-terminal, an helical hinge domain and a C-terminal endonuclease domain.
Pfam PF01709: TACO1/YebC second and third domain (family)
This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region. This entry represents the second and third domains in this protein, with one domain nested within the other.
Pfam PF24045: Domain of unknown function (DUF7354) (domain)
This domain of unknown function, which is found in a small group of bacterial proteins, shows a high structural similarity with the N-terminal domain of Magnetotaxis protein MtxA from Magnetospirillum gryphiswaldense ([swissprot:A4TUL6]).
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 PF12344: Ultra-violet resistance protein B (family)
This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00271], [pfam:PF02151], [pfam:PF04851]. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species.
Pfam PF05420: Cellulose synthase operon protein C C-terminus (BCSC_C) (family)
This family contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown.
Pfam PF23456: Cold shock domain-containing protein E1 CSD domain (domain)
This entry represents several divergent cold-shock domains found in the CSDE1 protein.  The CSDE1 family comprises RNA-binding proteins that play a crucial role in translationally coupled mRNA turnover. Members are involved in the cytoplasmic deadenylation, translation, and decay processes, particularly interacting with the mCRD domain of FOS mRNA. They are essential for the efficient formation of stress granules, cellular structures that form in response to environmental stress, aiding in the storage and management of untranslated mRNAs. Additionally, the human variant is implicated in the internal initiation of translation of human rhinovirus RNA, suggesting a role in microbial infection responses.
Pfam PF20562: Domain of unknown function (DUF6772) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 292 and 316 amino acids in length. An AlphaFold prediction show similarity to the concanavalin superfamily suggesting that this family may be involved in carbohydrate binding.
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 PF21272: E3 ubiquitin-protein ligase CARP1/2, FYVE/PHD zinc finger (domain)
This is the FYVE/PHD zinc finger form E3 ubiquitin-protein ligase RNF34 and RFFL, also known as Caspase regulator 1 and 2 (CARP1/2), respectively. CARP2, also termed E3 ubiquitin-protein ligase rififylin (RFFL) is a novel caspase regulator that regulates the p53 signaling pathway through degrading 14-3-3 sigma and stabilizing MDM2. CARP1 ubiquitinates the caspases CASP8 and CASP10, promoting their proteasomal degradation, to negatively regulate cell death downstream of death domain receptors in the extrinsic pathway of apoptosis. It negatively regulates p53/TP53 through its direct ubiquitination and targeting to proteasomal degradation.
Pfam PF17344: Family of unknown function (DUF5374) (family)
This is a family of unknown function found in Pasteurellaceae.
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 PF11174: Protein of unknown function (DUF2970) (family)
This short family is conserved in Proteobacteria. The function is not known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08888: HopJ type III effector protein (domain)
Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins in this family are called HopJ after the original member HopPmaJ.
Pfam PF02449: Beta-galactosidase (domain)
This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.
Wikipedia: In molecular biology, glycoside hydrolase family 42 is a family of glycoside hydrolases.
Pfam PF03663: Glycosyl hydrolase family 76 (repeat)
Family of alpha-1,6-mannanases.
Wikipedia: In molecular biology, glycoside hydrolase family 76 is a family of glycoside hydrolases.
Pfam PF22597: Dynein heavy chain, ATPase lid domain (domain)
Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head with six AAA-domains, a coiled-coil stalk with a microtubule binding domain (MTBD) and a linker  This entry represents the lid domain found at the C-terminal of the third AAA+ ATPase domain in dyneins.