SII-SWORD/CoKE huggingface dataset:
Pfam PF06226: Protein of unknown function (DUF1007) (family)
Family of conserved bacterial 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 PF19213: Coronavirus replicase NSP6 (family)
This entry represents proteins found in Coronaviruses and includes the Non-structural Protein 6 (NSP6). Coronaviruses encode large replicase polyproteins which are proteolytically processed by viral proteases to generate mature Nonstructural Proteins (NSPs). NSP6 is a membrane protein containing 6 transmembrane domains with a large C-terminal tail. NSP6 from  the avian coronavirus, infectious bronchitis  virus (IBV) and the mouse hepatitis virus (MHV) have been shown  to localise to the ER and to generate autophagosomes.  Coronavirus NSP6 proteins have also been shown to limit  autophagosome expansion. This may favour coronavirus infection  by reducing the ability of autophagosomes to deliver viral  components to lysosomes for degradation. NSP6 from IBV, MHV  and severe acute respiratory syndrome coronavirus (SARS-CoV)  have also been found to activate autophagy.
Pfam PF02778: tRNA intron endonuclease, N-terminal domain (domain)
Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron [ec:3.1.27.9].
Pfam PF13019: Yeast Splicing regulator sde2, N-terminal ubiquitin domain (domain)
Sde2 (Splicing regulator sde2, also known as silencing defective 2) is a splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. It is translated as an inactive precursor protein that harbours the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N terminus (this entry), which must be cleaved by the ubiquitin -specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2 gets incorporated into the spliceosome.
Pfam PF22261: GPR128 GAIN subdomain B (domain)
GRP128, also known as Adhesion G-protein coupled receptor G7 (AGRG7), is an orphan receptor of the adhesion family (subclass B2) that belongs to class B GPCRs. Expression of GPR128 was detected in the mouse intestinal mucosa and is thought to be involved in energy balance. It consists of an N-terminal HormR-like domain ([pfam:PF22257]), followed by the GAIN domain which consists of a stalk (consisting of subdomains A ([pfam:PF22259]) and B) and a GPS motif ([pfam:PF01825]), followed by a C-terminal transmembrane region ([pfam:PF00002]). This entry represents subdomain B of the stalk from GPR128 GAIN domain.
Pfam PF06605: Prophage endopeptidase tail (family)
This family is of prophage tail proteins that are probably acting as endopeptidases.
Pfam PF13388: Protein of unknown function (DUF4106) (family)
This family of proteins are found in large numbers in the Trichomonas vaginalis proteome.  The function of this protein is unknown.
Pfam PF01048: Phosphorylase superfamily (domain)
Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)
Pfam PF16533: STIM1 Orai1-activating region (domain)
SOAR is the Orai1-activating region of STIM1, where STIM1 are calcium sensors in the endoplasmic reticulum. As the store of calcium is depleted the calcium sensor in the ER activates Orai1, a Ca2+-release-activated Ca2+ (CRAC) channel, in the plasma membrane. The SOAR region, which runs from residues 340-443 on UniProtKB:Q13586, forms a dimer, and is essential for oligomerisation of the whole of STIM1.
Pfam PF04891: NifQ (family)
NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co), which is an integral part of the active site of dinitrogenase.  The conserved C-terminal cysteine residues may be  involved in metal binding.
Pfam PF24318: Domain of unknown function (DUF7490) (domain)
This domain is found in uncharacterised archaeal proteins. Members of this family have a PGF-CTERM motif [pfam:PF18204] at the C-termini.
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 PF00875: DNA photolyase (domain)
This domain binds a light harvesting cofactor.
Pfam PF02927: Cellulase N-terminal ig-like domain (domain)
Cellulases (Endoglucanases) 3.2.1.4 catalyse the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. This is the N-terminal ig-like domain of cellulase, enzymes containing this domain belong to family 9 of the glycoside hydrolases (GH9).
Pfam PF19864: Radical SAM proteins, N-terminal (domain)
This domain is found at the N-terminal of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyse diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation. The function of this domain is unknown.
Pfam PF02936: Cytochrome c oxidase subunit IV (family)
Cytochrome c oxidase, a 13 sub-unit complex, [ec:1.9.3.1] is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium member of this family is called COX VI [swissprot:P26310]. The yeast protein [swissprot:P53077] appears to be the yeast COX IV subunit.
Pfam PF18852: Large polyvalent protein associated domain 34 (domain)
This is a predicted enzymatic alpha and beta fold domain with a large, prominent helix with conserved glutamate residue and several additional conserved residues including the motifs HTxN and SN. The domain is associated with polyvalent proteins of firmicute conjugative elements.
Pfam PF04020: Mycobacterial 4 TMS phage holin, superfamily IV (family)
These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organisms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyse export of nucleases.
Pfam PF04326: Schlafen, AlbA_2 (domain)
This is the AlbA_2 domain from the Schlafen (SLFN) family of proteins which are important in cell differentiation and defense against viruses. This domain is present at the N-terminal of all SLFN proteins and includes the SLFN box, a sequence unique to these proteins that may form a dimer interface. The AlbA_2 domain is RNA-binding and RNase region as it contains the highly conserved catalytic glutamic acid residues.
Pfam PF05965: F/Y rich C-terminus (family)
This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.
Pfam PF05906: Herpesvirus-7 repeat of unknown function (DUF865) (repeat)
This family consists of a series of 12 repeats of 35 amino acids in length which are found exclusively in Herpesvirus-7. The function of this family is unknown.
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 PF09846: Origin-associated protein OapB (family)
This entry includes archaeal proteins whose function is unclear. Some members of this entry have been described as OapB/Arvb, encoded by oapB gene which is part of the three-gene cluster oapABC, involved in generation of extracellular vesicles (arv, archaeal vesiculating GTAse). It has been suggested that OapB/ArvB could be a guanine nucleotide exchange factor (GEF), however, further experimental research is required to confirm this.
Pfam PF00176: SNF2-related domain (domain)
This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Wikipedia: In molecular biology, SWI/SNF, is a subfamily of ATP-dependent chromatin remodeling complexes, which is found in eukaryotes. In other words, it is a group of proteins that associate to remodel the way DNA is packaged. This complex is composed of several proteins – products of the SWI and SNF genes, as well as other polypeptides. It possesses a DNA-stimulated ATPase activity that can destabilize histone-DNA interactions in reconstituted nucleosomes in an ATP-dependent manner, though the exact nature of this structural change is unknown. The SWI/SNF subfamily provides crucial nucleosome rearrangement, which is seen as ejection and/or sliding. The movement of nucleosomes provides easier access to the chromatin, enabling binding of specific transcription factors, and allowing genes to be activated or repressed.
Pfam PF13092: Centromere protein L (family)
CENP-L is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta1 is the equivalent component of the fission yeast Sim4 complex. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-L forms a channel with CENP-N through which a DNA duplex threads.
Pfam PF08453: Peptidase family M9 N-terminal (repeat)
This domain is found in microbial collagenase metalloproteases to the N-terminus of [pfam:PF01752].
Pfam PF11199: Protein of unknown function (DUF2891) (family)
This is a bacterial family of uncharacterised proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24362: Family of unknown function (DUF7518) (family)
This family includes a group of short from archaea. Members are predicted to adopt an alpha-helical structure in the N-terminal and show a disordered C-terminal region.
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 PF23790: Kyanoviridae Gp96 protein (domain)
This family represents the Gp96 protein from Synechococcus phages.  Sequences in the family are typically around 110 residues in length. Gp96 homologues are found in a variety of different Synechococcus phages belonging to the Kyanoviridae family of viruses. The function of Gp96 is currently unknown.
Pfam PF24816: Cilia- and flagella-associated protein 65-like, Ig-like domain (domain)
This domain is found in human Cilia- and flagella-associated protein 65 (CFAP65) and similar animal sequences. CFAP65 plays a role in flagellar formation and sperm motility. This protein is predicted to have several tandem Ig-like domains, including the one represented in this entry. This domain is also found in Hydrocephalus-inducing protein which is required for ciliary motility.
Pfam PF02394: Interleukin-1 propeptide (family)
The Interleukin-1 cytokines are translated as precursor proteins.  The N terminal approx. 115 amino acids form a propeptide that is cleaved off to release the active interleukin-1.
Pfam PF02617: ATP-dependent Clp protease adaptor protein ClpS (family)
In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins.
Wikipedia: ClpS is an N-recognin in the N-end rule pathway. ClpS interacts with protein substrates that have a bulky hydrophobic residue at the N-terminus. The protein substrate is then degraded by the ClpAP protease.
Pfam PF14038: YqzE-like protein (family)
The YqzE-like protein family includes the B. subtilis YqzE protein [swissprot:O32020], which is functionally uncharacterised. It is a part of the ComG operon, which is regulated by the competence transcription factor ComK.  This family of proteins is found in bacteria. Proteins in this family are typically between 49 and 66 amino acids in length.
Pfam PF13154: Protein of unknown function (DUF3991) (family)
This family of proteins is often associated with family Toprim, [pfam:PF01751].
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 PF22163: Salmonella Invasion protein A, C-terminal actin binding domain (domain)
This domain is found at the C-terminal end of Cell invasion protein SipA (Salmonella Invasion protein A) from Salmonella typhimurium. SipA actin-binding protein that interferes with host cell actin cytoskeleton, and reduce the critical concentration for the formation of F-actin, contributing to bacterial invasion. This domain adopts a a compact, heart-shaped fold dominated by a helical secondary structure. It is responsible for the actin-binding and polymerisation activities of the protein.
Pfam PF10873: Cysteine and tyrosine-rich protein 1 (family)
Members in this family of proteins are annotated as  Cysteine and tyrosine-rich protein 1, however currently  no function is known.
Pfam PF09515: Thiamine transporter protein (Thia_YuaJ) (family)
Members of this protein family have been assigned as thiamine transporters by a phylogenetic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Streptococcus mutans and Streptococcus pyogenes), yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicates thiamine uptake is coupled to proton translocation.
Wikipedia: Members of this protein family have been assigned as thiamine transporters by a phylogenomic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species, yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicates thiamine uptake is coupled to proton translocation.
Pfam PF03711: Orn/Lys/Arg decarboxylase, C-terminal domain (domain)
Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates . One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group. Ornithine decarboxylase is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. Arginine decarboxylase catalyzes the decarboxylation of arginine and lysine decarboxylase catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life .
Wikipedia: In molecular biology, group III pyridoxal-dependent decarboxylases are a family of bacterial enzymes comprising ornithine decarboxylase EC 4.1.1.17, lysine decarboxylase EC 4.1.1.18 and arginine decarboxylase EC 4.1.1.19.
Pfam PF07163: Pex26 protein (family)
This family consists of Pex26 and related mammalian proteins. Pex26 is a type II peroxisomal membrane protein which recruits Pex6-Pex1 complexes to peroxisomes. Mutations in Pex26 can lead to human disorders.
Pfam PF18535: Gal11 activator-binding domain (ABD1) (domain)
This is activator-binding domain (ABD1) found in Gal11/med15 proteins. Structural analysis indicate that it binds to the central activator domain (cAD) of Gcn4. Mutations in Gal11-ABD1 W196 residue abolishes the binding to Gcn4 cAD.
Pfam PF22778: VCPO second helical-bundle domain (domain)
This domain is found in homologues of Vanadium-dependent haloperoxidases, NapH1 and  NapH3, that catalyze stereospecific chlorofunctionalization reactions on naphthoquinone-based meroterpeneoids. These enzymes contain two similar helical domains composed of five alpha-helices. This domain harbours the catalytic residues.
Pfam PF01474: Class-II DAHP synthetase family (domain)
Members of this family are aldolase enzymes that catalyse the first step of the shikimate pathway.
Wikipedia: 3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.
Pfam PF09108: Switch protein XOL-1, N-terminal (domain)
Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and six antiparallel beta sheets, in a beta-alpha-beta-beta-beta-alpha-beta-alpha-alpha-alpha-beta arrangement. The fold of this family is similar to that found in ribosomal protein S5 domain 2-like.
Wikipedia: In molecular biology, Xol-1 is a protein domain, also named the Switch protein, is essentially a sex-determining protein. This entry focuses on the N-terminal domain of Xol-1.
Xol-1, the master switch gene controlling sex-determination system and dosage
compensation. This protein is normally expressed in males, where it promotes male development and prevents dosage compensation.
Pfam PF06183: DinI-like family (family)
This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known.
Wikipedia: In molecular biology, the DinI-like protein family is a family of short proteins. The family includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co-protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known.
Pfam PF04066: Multiple resistance and pH regulation protein F (MrpF / PhaF) (family)
Members of the PhaF / MrpF family are predicted to be an integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation.                          It is also involved in symbiosis in Rhizobium meliloti.  MrpF is part of a Na+/H+ antiporter complex, also involved in pH homeostasis.    MrpF is thought to be an efflux system for Na+ and cholate. The Mrp system in Bacilli may also have primary energisation capacities.
Pfam PF06957: Coatomer (COPI) alpha subunit C-terminus (repeat)
This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the [pfam:PF04053] domain.
Wikipedia: COPI is a coatomer, a protein complex that coats vesicles transporting proteins from the cis end of the Golgi complex back to the rough endoplasmic reticulum (ER), where they were originally synthesized, and between Golgi compartments. This type of transport is retrograde transport, in contrast to the anterograde transport associated with the COPII protein. The name "COPI" refers to the specific coat protein complex that initiates the budding process on the cis-Golgi membrane. The coat consists of large protein subcomplexes that are made of seven different protein subunits, namely α, β, β', γ, δ, ε and ζ.