SII-SWORD/CoKE huggingface dataset:
Pfam PF16593: Bridge helix of CRISPR-associated endonuclease Cas9 (family)
Cas9-BH is the bridge helix between the NUC and the REC lobes of Cas9 - the CRISPR-associated endonuclease Cas9. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive.
Pfam PF23257: Domain of unknown function (DUF7071) (domain)
This domain is found C-terminal in a group of uncharacterised proteins mainly from fungi. It is predicted to adopt a globular structure consisting of two alpha-helical repeats.
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 PF17526: Family of unknown function (DUF5448) (family)
This is a family of unknown function found in Gammaproteobacteria.
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 PF19904: Domain of unknown function (DUF6377) (repeat)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 250 amino acids in length. This domain is likely to be present in transcriptional regulators.
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 PF15948: Domain of unknown function (DUF4756) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 160 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 PF19164: Family of unknown function (DUF5846) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF13231: Dolichyl-phosphate-mannose-protein mannosyltransferase (family)
This family contains members that are not captured by [pfam:PF02366].
Pfam PF02321: Outer membrane efflux protein (family)
The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria.        Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm.
Wikipedia: The outer membrane efflux protein is a protein family member that forms trimeric (three-piece) channels allowing the export of a variety of substrates in gram-negative bacteria. Each efflux protein is composed of two repeats. The trimeric channel is composed of a 12-stranded beta-barrel that spans the outer membrane, and a long tail helical barrel that spans the periplasm.
Pfam PF05579: Equine arteritis virus serine endopeptidase S32 (family)
Serine peptidases involved in processing nidovirus polyprotein.
Pfam PF19365: Family of unknown function (DUF5941) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in actinobacteria.  The family is found in association with [pfam:PF01066]. This entry contains several transmembrane helices.
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 PF09445: RNA cap guanine-N2 methyltransferase (family)
RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyse methylation of the exocyclic N2 amine of 7-methylguanosine.
Pfam PF00898: Orbivirus outer capsid protein VP2 (family)
VP2 acts as an anchor for VP1 and VP3. VP2 contains a non-specific  DNA and RNA binding domain in the N-terminus.
Pfam PF05002: SGS domain (domain)
This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins.
Pfam PF09821: C-terminal AAA-associated domain (domain)
This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family, [pfam:PF00005].
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF13140: Domain of unknown function (DUF3980) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 90 amino acids in length.
Pfam PF03328: HpcH/HpaI aldolase/citrate lyase (domain)
This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase.
Pfam PF20394: DUF6688 N-terminal domain (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 360 and 412 amino acids in length.  This entry corresponds to the N-terminal integral membrane domain.
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 PF23459: RRP5 S1 domain (domain)
This entry represents several divergent S1 domains found in RRP5 proteins. The RRP5 protein family is essential for ribosomal RNA (rRNA) biogenesis, playing a critical role in the formation of mature 18S and 5.8S rRNA components of the ribosome. Members of the RRP5 family are necessary for specific cleavage events at sites A0, 1, and 2 within the 47S precursor rRNA. They are also known to directly interact with U3 small nucleolar RNA (snoRNA), which is involved in the early steps of rRNA processing. The RRP5 family's function is conserved across eukaryotes, as evidenced by its involvement in rRNA processing in organisms ranging from yeast to humans. In plants, the RRP5 protein is additionally required for normal development of female gametophytes, indicating a broader role in cellular growth and development.
Pfam PF05332: Vesivirus VP2 protein (family)
This family consists of several Calicivirus VP2 proteins. VP2 is a minor capsid protein encoded by all caliciviruses. forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface.
Pfam PF10262: Rdx family (family)
This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium.
Pfam PF23414: Echinoderm microtubule-associated protein second beta-propeller (repeat)
This entry represents beta-propeller domains of echinoderm microtubule-associated protein (EMAP)-like (EML) proteins, a family of proteins that contribute to formation of the mitotic spindle and interphase microtubule network. In these proteins, the beta-propellers are intimately associated as a pair which was defined as tandem atypical propeller in EMLs (TAPE) domain. There is a hydrophobic core between the propellers which corresponds the HELP motif ([pfam:PF03451]) that contributes blades 1 and 14 buried at the interface and joints them. This model completes the second beta-propeller of the TAPE pair in EMLs. In some members, such as EML5 and EML6, there are three TAPE pairs. The first beta-propeller of  the pair is represented in [pfam:PF23409].
Pfam PF17530: Non-structural protein NS3 (family)
This is a family of proteins found in Densoviruses. Members of this family such as NS3 found in Junonia coenia have been shown to be involved in viral DNA replication. Generation of deletion mutants and replicative cycle analysis show that NS3 is required for viral DNA replication. Bioinformatics analysis of Bombyx mori densovirus protein NS3, show that it has two putative zinc-finger motifs, 6 putative N glycosylation sites, and 4 putative phosphorylation sites.
Pfam PF24152: Family of unknown function (DUF7405) (family)
This entry represents a family or archaeal proteins whose function is unknown. They may adopt a dimeric alpha/beta barrel 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 PF11526: Pcf11, Clp1-interaction domain (domain)
Pcf11 is a subunit and an essential component of the cleavage and polyadenylation factor CFIA from yeast and the orthologue from human CFII which is involved in pre-mRNA 3' end processing and in transcription termination. Pcf11-mediated termination is essential for vertebrate development. Pcf11 binds to Clp1, another subunit of CFIA/CFII, whose interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery. This entry represents the Clp1-interaction region (Clp1 ID) of Pcf11 from yeast and vertebrates.
Pfam PF24194: Family of unknown function (DUF7419) (family)
This entry represents a family of uncharacterised mycobacteria phage proteins that adopt a zinc binding domain composed of 5 potential ligand residues. The zinc binding motif is composed of a CXXC and a CXXHH motif.
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 PF18395: Cas3 C-terminal domain (domain)
This is the C-temrinal domain of Cas3 proteins.  The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase.  Deletion of the CTD (aa 819-924) reduced CRISPR interference.  It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter.
Pfam PF23930: Family of unknown function (DUF7268) (family)
This entry represents uncharacterised proteins found mainly in Halobacteria. They are predicted to contain three transmembrane helices and likely associate with the membrane.
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 PF19475: Family of unknown function (DUF6012) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000128) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein encoded by the pyoluteorin biosynthetic gene cluster from  Pseudomonas sp. M18
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 PF17242: Disordered region of unknown function (DUF5315) (family)
This is a family of unknown function found mostly in Saccharomycetales.
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 PF11846: Virulence factor membrane-bound polymerase, C-terminal (repeat)
Wzy is a membrane-bound polymerase of 12 TMs, found in Gram-positive bacteria such as Streptococcus pnuemoniae. It forms part of the EPS or exopolysaccharide system. This family is the 6xTMs at the C-terminal end of the molecule. Wzy functions in polymerizing the oligosaccharide repeat subunits to form high-molecular-weight capsular polysaccharides. A contiguous emebrane-bound flippase, Wzx, [pfam:PF01943], transports the repeat units to the external surface of the membrane.  These polysaccharides form the capsule and their differing compositions contribute to the multidudinous pneumococcal capsular serotypes, all being structurally and antigenically different.
Pfam PF02238: Cytochrome c oxidase subunit VII (family)
Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family also contains both heart and liver isoforms of cytochrome c oxidase subunit VIIa.
Pfam PF17640: Uncharacterized UL17 (family)
This is a family of unknown function found in beta-herpesviruses such as Human cytomegalovirus (HCMV).
Pfam PF14266: YceG domain (domain)
YceG is a family of proteins found in bacteria. Proteins in this family are approximately 540 amino acids in length. YceG is an additional gene-product encoded in the Ter operon and might thus be part of a 'biosynthetic module' encoding certain enzymes. Members of this family contain 2-3 copies of this domain.
Pfam PF22350: Internalin, EF-hand domain (domain)
This entry represents the N-terminal EF-hand domain present in the internalin family. Internalin is a virulence-associated surface protein of Listeria monocytogenes and related bacteria.
Pfam PF19758: Family of unknown function (DUF6245) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces  tenjimariensis.
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 PF12423: Kinesin protein 1B (family)
This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with [pfam:PF00225], [pfam:PF00498]. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells.
Pfam PF07599: Protein of unknown function (DUF1563) (family)
A small family of short hypothetical proteins in Leptospira interrogans.
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 PF00628: PHD-finger (domain)
PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains.  Several PHD fingers have been identified as binding modules of methylated histone H3.
Wikipedia: The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain proteins HAT3.1 in Arabidopsis and maize ZmHox1a. 
The PHD zinc finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.
Pfam PF16901: C-terminal domain of alpha-glycerophosphate oxidase (family)
DAO_C is the C-terminal region of alpha-glycerophosphate oxidase.
Pfam PF14107: Domain of unknown function (DUF4280) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 129 and 456 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12411: Choline sulfatase enzyme C terminal (family)
This domain family is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. The family is found in association with [pfam:PF00884]. There are two completely conserved residues (R and W) that may be functionally important. This family is the C terminal of choline sulfatase, the enzyme responsible for catalysing the conversion of choline-O-sulfate and, at a lower rate, phosphorylcholine, into choline.
Pfam PF09177: Syntaxin 6/10/61, N-terminal (domain)
Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Syntaxin 6 regulates chemotactic cell migration through integrin trafficking to the cell surface and is a common transcriptional target of p53 family members. Syntaxin 10 interacts with syntaxin 6 and 16, but its role in regulating trans-Golgi network protein traffic is unknown. Syntaxin 61 plays a role in the exocytic trafficking of cellulose synthases and the transport of cell wall components to the plasma membrane. Together with VTI12 it is required for membrane fusion. This entry also includes the yeast homologue, t-SNARE affecting a late Golgi compartment protein 1 (Tlg1). Tlg1 plays a role in endosome-TGN vesicle fusion and forms a SNAREpin complex with Tlg2 and Vti1.
Wikipedia: Syntaxin-6 is a protein that in humans is encoded by the STX6 gene.
Pfam PF16867: Dimethlysulfonioproprionate lyase (domain)
Breaks down into dimethylsulfoniopropionate (DMSP) into acrylate and dimethyl sulfide.
Pfam PF16682: CXC domain of E3 ubiquitin-protein ligase MSL2 (domain)
MSL2-CXC is an autonomously folded domain containing that binds three zinc ions. It lies on the E3 ubiquitin-protein ligase MSL2 in eukaryotes. The CXC domain critically contributes to the DNA-binding activity of MSL2. It carries 9 invariant cysteines within about a 50 residue region.
Pfam PF08061: P68HR (NUC004) repeat (repeat)
This short region is found in two copies in p68-like RNA helicases.
Pfam PF21084: Winged Helix-turn-helix domain (domain)
This domain is found at the N-terminus of the TruD protein a protein involved in cyanobactin heterocyclisation. It adopts a winged helix-turn-helix structure. It is also found in the related LynD protein.
Pfam PF02153: Prephenate dehydrogenase, nucleotide-binding domain (domain)
Members of this family are prephenate dehydrogenases (PDHs) [ec:1.3.1.12] involved in tyrosine biosynthesis. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended beta-sheet sandwiched by three helices on each face.
Pfam PF08468: Methyltransferase small domain N-terminal (family)
This domain is found to the N-terminus of the methyltransferase small domain ([pfam:PF05175]) in bacterial proteins.
Pfam PF16289: PIN domain (domain)
This domain is found on the N-terminal region of uncharacterized proteins. It shows homology to other PIN-like families and contains several acidic residues critical for chelating metal ions that are conserved in other PIN-like domains.
Wikipedia: In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length. PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence- or structure-dependent manner.