SII-SWORD/CoKE huggingface dataset:
Pfam PF15460: Something about silencing, SAS, complex subunit 4 (family)
SAS4 is a family of largely fungal silencing regulators. This silencing is mediated by chromatin. SAS4 specifically silences the yeast mating-type genes HML and HMR. SAS4 is found to be one subunit of a complex, the SAS complex, that interacts with chromatin assembly factor Asf1p, and asf1 mutants show silencing defects similar to mutants in the SAS complex. Thus, ASF1-dependent chromatin-assembly may mediate the role of the SAS complex in silencing. Co-expression of Sas2, SAS4, and Sas5 in Escherichia coli leads to formation of a stable SAS complex that acetylates histones. SAS4 is essential for the acetyltransferase activity of Sas2, and Sas5 is also important.
Pfam PF22607: FAD binding domain-like (domain)
This domain is found in a number of FAD-binding enzymes.
Pfam PF02254: TrkA-N domain (domain)
This domain is found in a wide variety of proteins. These protein include potassium channels [swissprot:P31069], phosphoesterases [swissprot:Q59027], and various other transporters. This domain binds to NAD.
Pfam PF07767: Nop53 (60S ribosomal biogenesis) (family)
This nucleolar family of proteins are involved in 60S ribosomal biogenesis.  They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins.
Pfam PF10722: Putative bacterial sensory transduction regulator (domain)
YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabiliser for some other unstable proteins. This family was expanded to subsume other related families: DUF1790, DUF1821 and DUF2596.
Pfam PF05059: Orbivirus VP4 core protein (family)
Orbiviruses are double stranded RNA retroviruses of which the bluetongue virus is a member. The core of bluetongue virus (BTV) is a multienzyme complex composed of two major proteins (VP7 and VP3) and three minor proteins (VP1, VP4 and VP6) in addition to the viral genome. VP4 has been shown to perform all RNA capping activities and has both methyltransferase type 1 and type 2 activities associated with it.
Pfam PF10073: GapR-like, DNA-binding domain (domain)
GapR is a nucleoid-associated protein (NAP) critical for cellular function in Caulobacter crescentus (also known as Caulobacter vibrioides). Loss of GapR causes severe defects in growth, cell division, DNA replication, and chromosome segregation. This is a DNA-binding protein which has mainly an alpha-helical secondary structure. In the absence of DNA, GapR is a dimer, with each monomer folded into two extended alpha-helices, while in the presence of DNA, GapR forms a tetramer, with the C-terminal alpha-helix of each monomer reorganised into two shorter helices, which allows GapR to encircle the DNA. This is the DNA-binding domain of GapR from Caulobacter crescentus and related sequences. This domain is not only highly conserved in Alphaproteobacteria, it is also present in cyanobacteria, firmicutes, planctomycetes, actinobacteria, and even archaea and eukaryotes, possibly through horizontal gene transfer. This domain is also found in phages, in which it is associated to DNA-related processes.
Pfam PF17752: Burkholderia lethal factor 1 (family)
This family includes members such as BLF1 (Burkholderia lethal factor 1) also known as BPSL1549. BLF1 is a potent toxin from Burkholderia pseudomallei causing melioidosis. BLF1 interacts with the human translation factor eIF4A causing deamidation of Gln339 to Glu. Thereby, reducing endogenous host cell protein synthesis and triggering increased stress granule formation, which is associated with translational blocks. Structural analysis of BLF1 revealed an alpha/beta fold comprising a sandwich of two mixed beta-sheets surrounded by loops and alpha-helices, where the beta-sheet core of the catalytic pocket is structurally similar to that of the deamidase domain of CNF1 [pfam:PF05785].
Pfam PF17897: Vanadium chloroperoxidase N-terminal domain (domain)
This is the N-terminal domain found in Vanadium chloroperoxidase proteins found in fungi.
Pfam PF19936: Family of unknown function (DUF6399) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000967) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the calyculin A biosynthetic gene cluster from uncultured Candidatus Entotheonella sp.. This family  appears to be predominantly found in proteobacteria and  cyanobacteria.
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 PF04658: TAFII55 protein conserved region (family)
The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex.   TAFII55 binds to TAFII250 and inhibits it acetyltransferase activity. The exact role of TAFII55 is currently unknown.  The conserved region is situated towards the N-terminus of the protein.
Wikipedia: Transcription initiation factor TFIID subunit 7 also known as TAFII55 is a protein that in humans is encoded by the TAF7 gene.
Pfam PF06806: Putative excisionase (DUF1233) (family)
This family consists of several putative phage excisionase proteins of around 80 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 PF14614: Domain of unknown function (DUF4450) (family)
This is a family of bacterial 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 PF24429: CSLinker motif (conserved_site)
The CSLinker motif is found in the pyrenoid linker protein from Chlorella sorokiniana. It binds to the large subunit of Rubisco (RbcL) and is involved in phase separation of Rubisco in the pyrenoid, a sub-compartment of the chloroplast that is part of the CO2-concentrating mechanism in algae.  The motif consists of an alpha-helical region of approximately 10 residues that interacts with the N-terminal region of RbcL via two salt bridges and hydrophobic interactions. The key residues involved in binding are highly conserved.  CSLinker is able to phase separate Rubisco from various species across the green lineage, including some plants, demonstrating its potential for engineering pyrenoids in crop plants to enhance CO2 fixation.
Pfam PF01128: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (family)
Members of this family are enzymes which catalyse the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from cytidine triphosphate and 2-C-methyl-D-erythritol 4-phosphate (MEP).
Wikipedia: In enzymology, a 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase is an enzyme that catalyzes the chemical reaction:2-C-methyl-D-erythritol 4-phosphate + CTP  diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
Pfam PF01371: Trp repressor protein (domain)
This protein binds to tryptophan and represses transcription of the Trp operon.
Wikipedia: Tryptophan repressor is a transcription factor involved in controlling amino acid metabolism. It has been best studied in Escherichia coli, where it is a dimeric protein that regulates transcription of the 5 genes in the tryptophan operon. When the amino acid tryptophan is plentiful in the cell, it binds to the protein, which causes a conformational change in the protein. The repressor complex then binds to its operator sequence in the genes it regulates, shutting off the genes.
Pfam PF05230: MASE2 domain (domain)
Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins.
Pfam PF08457: Sfi1 spindle body protein (family)
This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organising centres.
Pfam PF01078: Magnesium chelatase, subunit ChlI (domain)
Magnesium-chelatase is a three-component enzyme that  catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of  (bacterio)chlorophyll.  Due to this, it is thought that  Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
Wikipedia: Magnesium-chelatase is a three-component enzyme (EC 6.6.1.1) that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of chlorophyll and bacteriochlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth:
Pfam PF14847: Ras-binding domain of Byr2 (domain)
This domain is the binding/interacting region of several protein kinases, such as the Schizosaccharomyces pombe Byr2. Byr2 is a Ser/Thr-specific protein kinase acting as mediator of signals for sexual differentiation in S. pombe by initiating a MAPK module, which is a highly conserved element in eukaryotes. Byr2 is activated by interacting with Ras, which then translocates the molecule to the plasma membrane. Ras proteins are key elements in intracellular signaling and are involved in a variety of vital processes such as DNA transcription, growth control, and differentiation. They function like molecular switches cycling between GTP-bound 'on' and GDP-bound 'off' states.
Pfam PF18262: Phe-tRNA synthetase beta subunit B1 domain (domain)
This is the N-terminal domain found in human cytosolic phenylalanyl tRNA synthetase beta subunit.
Pfam PF13507: CobB/CobQ-like glutamine amidotransferase domain (domain)
This family captures members that are not found in [pfam:PF00310], [pfam:PF07685] and [pfam:PF13230].
Pfam PF10392: Conserved oligomeric Golgi complex subunit 5, N-terminal (repeat)
The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7. This domain is found at the N-terminal of COG5 and includes the LLR motif which is important to interact with COG7. Disruption of COG5-COG7 interface does not impair lobe B but causes aberrant cell surface glycosylation with major deficits in the trafficking of Golgi glycosyltransferases.
Pfam PF07044: Protein of unknown function (DUF1329) (domain)
This family consists of several hypothetical bacterial proteins of around 475 residues in length. The majority of family members are from Pseudomonas species but the family also contains sequences from Shewanella oneidensis and Thauera aromatica.
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 PF02511: Thymidylate synthase complementing protein (family)
Thymidylate synthase complementing protein (Thy1) complements the thymidine growth requirement of the organisms in which it is found, but shows no homology to thymidylate synthase. The bacterial members of this family at least are flavin-dependent thymidylate synthases.
Wikipedia: Thymidylate synthase (TS) is an enzyme that catalyzes the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP). Thymidine is one of the nucleotides in DNA. With inhibition of TS, an imbalance of deoxynucleotides and increased levels of dUMP arise. Both cause DNA damage.
Pfam PF15014: Ceroid-lipofuscinosis neuronal protein 5 (family)
This protein family consists of Bis(monoacylglycero)phosphate synthase CLN5 and CLN5-like proteins. CLN5, in the secreted form, catalyses the synthesis of bis(monoacylglycero)phosphate (BMP) via transacylation of 2 molecules of lysophosphatidylglycerol (LPG) . BMP (also known as lysobisphosphatidic acid) plays a key role in the formation of intraluminal vesicles and in maintaining intracellular cholesterol homeostasis . CLN5 can use only LPG as the exclusive lysophospholipid acyl donor for base exchange and displays BMP synthase activity towards various LPGs (LPG 14:0, LPG 16:0, LPG 18:0, LPG 18:1) with a higher preference for longer chain lengths . Defects in CLN5 are the cause of neuronal ceroid lipofuscinosis type 5 (CLN5), also known as Finnish variant late-infantile neuronal ceroid lipofuscinosis (vLINCL). Neuronal ceroid lipofuscinoses are progressive neurodegenerative, lysosomal storage diseases characterised by intracellular accumulation of autofluorescent liposomal material .

CLN5 also plays a role in influencing the retrograde trafficking of lysosomal sorting receptors SORT1 and IGF2R from the endosomes to the trans-Golgi network by controlling the recruitment of retromer complex to the endosomal membrane . CLN5 also exhibits palmitoyl protein thioesterase (S-depalmitoylation) activity in vitro and most likely plays a role in protein S-depalmitoylation .
Wikipedia: Ceroid-lipofuscinosis neuronal protein 5 is a protein that in humans is encoded by the CLN5 gene.
Pfam PF24889: WNK CCTL2 domain (domain)
This is the CCT-like domain 2 (CCTL2) from WNK proteins (WNK1-4), which are serine/threonine-protein kinase components of the WNK-SPAK/OSR1 kinase cascade, that plays an important role in the regulation of electrolyte homeostasis, cell signalling survival, and proliferation. The exact function of this domain is not clear, it has been suggested that it may play a regulatory function.
Pfam PF11868: Protein of unknown function (DUF3388) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 261 to 275 amino acids in length. This protein is found associated with [pfam:PF01842].
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 PF16801: Dimerisation domain of Male-specific-Lethal 1 (coiled_coil)
MSL1_dimer is the short coiled dimerisation domain of higher eukaryotic MSL1, part of the MSL or Male-Specific Lethal complex. This complex regulates the dosage compensation of the male X chromosome in Drosophila and other eukaryotes. The structure of the MSL1/MSL2 core shows that two MSL2 subunits bind to a dimer formed by two molecules of MSL1. MSL11 is a substrate for MSL2 E3 ubiquitin ligase activity.
Pfam PF21600: ZSWIM1/3, helical domain (domain)
This entry represents a helical domain found in ZSWIM1 and ZSWIM3, ZSWIM-type zinc finger domain containing proteins. The function of ZSWIM3 is not yet clear. ZSWIM1 is thought to play in the development or function of T helper cells. This domain seems to be similar to [pfam:PF20784].
Pfam PF12786: GB virus C genotype envelope (family)
This the envelope protein from the ssRNA GB virus genotype C.
Pfam PF08282: haloacid dehalogenase-like hydrolase (domain)
This family contains haloacid dehalogenase-like hydrolase enzymes.
Wikipedia: The haloacid dehydrogenase superfamily is a superfamily of enzymes that include phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, and are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification.
Pfam PF13318: 1-carboxybiuret hydrolase subunit AtzG-like (family)
AtzG is essential for the production of soluble, active AtzE, which is a 1-carboxybiuret hydrolase.
Pfam PF19681: Family of unknown function (DUF6183) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001726) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the pactamides biosynthetic  gene cluster from Streptomyces pactum. This family appears to be predominantly found in Actinobacteria.
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 PF09217: Restriction endonuclease EcoRII, N-terminal (domain)
The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not.
Wikipedia: Restriction endonuclease (REase) EcoRII is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.
Pfam PF20279: C-terminal domain 12 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF18763: ddrB-like ParB superfamily domain (family)
A member of the ParB/sulfiredoxin superfamily of proteins found in polyvalent proteins prototyped by the version in the phage P1 ddRB protein. These proteins are predicted to function as nucleases.
Pfam PF18345: Zinc finger domain (domain)
This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process.
Pfam PF15619: Ciliary protein causing Leber congenital amaurosis disease (coiled_coil)
Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localised at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis.
Pfam PF20669: Exocyst complex component Exo70 N-terminal (repeat)
The Exo70 protein is a subunit of the exocyst complex, first identified in yeast, which is evolutionarily conserved in eukaryotes. It mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion. It also plays a role in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis. It is a member of the the Complex Associated with Tethering Containing Helical Rods (CATCHRs) family which also includes Conserved Oligomeric Golgi complex (COG) and Golgi-Associated Retrograde Protein complex (GARP) and DSL1 complexes, all evolutionarily related and share structural features consisting of alpha-helical bundles at the C-terminus and coiled-coil region at the N-terminus. Exo70 interacts with the Rho3 GTPase and phospholipids. This entry represents the N-terminal coiled-coil region which participates in the central pair-wise interactions by forming an antiparallel 'zipper' with Exo84 subunit. Exo70-Exo84 'zipper' interacts with Sec10-Sec15 counterpart to form a four-helical bundle.
Pfam PF07818: HCNGP-like protein (family)
This family comprises sequences bearing significant  similarity to the mouse transcriptional regulator  protein HCNGP ([swissprot:Q02614]). This protein is localised to the nucleus and is thought to be involved in the  regulation of beta-2-microglobulin genes.
Pfam PF05773: RWD domain (domain)
This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices.
Pfam PF22324: Winged helix domain (domain)
This winged helix-turn-helix domain is often found in proteobacteria and is likely to be involved in DNA-binding.