SII-SWORD/CoKE huggingface dataset:
Pfam PF08626: Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit (family)
This region is found at the N terminal of Saccharomyces cerevisiae Trs120 protein ([swissprot:Q04183]).  Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic. Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way. It is likely that there is a complex function for TRAPP II in multiple pathways.
Pfam PF04438: HIT zinc finger (domain)
This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein [swissprot:P46973]. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) [swissprot:Q15649] that specifically interact with the ligand binding domain of the thyroid receptor.
Pfam PF13012: Maintenance of mitochondrial structure and function (family)
This is C-terminal to the Mov24 region of the yeast proteasomal subunit Rpn11 and seems likely to regulate the mitochondrial fission and tubulation processes, ie the outer mitochondrial membrane proteins. This function appears to be unrelated to the proteasome activity of the N-terminal region.
Pfam PF06112: Gammaherpesvirus capsid protein (family)
This family consists of several Gammaherpesvirus capsid proteins. The exact function of this family is unknown.
Pfam PF10271: Putative transmembrane protein (family)
This is a family of conserved proteins found from worms to humans. They are putative transmembrane proteins but the function is unknown.
Pfam PF09744: RILP homology 1 domain (domain)
This is the RILP homology 1 (RH1) protein-protein interaction domain found at the N-terminal of Rab36-binding proteins including Rab interacting lysosomal proteins (RILP), RILP1/2 NK-interacting protein 3 (JIP3) and NK-interacting protein 4 (JIP4). This domain binds to the myosin Va globular tail domain (MyoVa-GTD).
Pfam PF04502: Saf4/Yju2 protein (family)
This is a family of eukaryotic proteins that includes CCDC130 and CCDC94 from humans, Saf4 from fission yeasts and Yju2 from budding yeasts. Saf4 (also known as cwc16) is involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. Yju2 is a splicing factor that is associated with the Prp 19-associated complex and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing.
Pfam PF17346: Family of unknown function (DUF5376) (family)
This is a family of unknown function found in Bacteria.
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 PF00850: Histone deacetylase domain (domain)
Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism.  Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins.
Wikipedia: Histone deacetylases (EC 3.5.1.98, HDAC) are a class of enzymes that remove acetyl groups (O=C-CH3) from an ε-N-acetyl lysine amino acid on both histone and non-histone proteins. HDACs allow histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. HDAC's action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins. In general, they suppress gene expression.
Pfam PF10870: Protein of unknown function (DUF2729) (family)
This viral family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11976: Ubiquitin-2 like Rad60 SUMO-like (family)
The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localisation, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).
Pfam PF17249: Family of unknown function (DUF5318) (family)
This family of unknown function is mostly found in Actinobacteria. Its fold was identified as part of the zinc-ribbon superfamily.
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 PF18484: Cadmium carbonic anhydrase repeat (repeat)
This domain is the cadmium carbonic anhydrase repeat unit of the beta-carbonic anhydrase of a marine diatom, that uses both zinc and cadmium for catalysis of the reversible hydration of carbon dioxide for use in inorganic carbon acquisition for photosynthesis (thus being a cambialistic enzyme). Compared with alpha- and gamma-carbonic anhydrases that use three histidines to coordinate the zinc-atom, this beta-carbonic anhydrase has two cysteines and one histidine, and rapidly binds cadmium.
Pfam PF18229: N-acetyl-beta-D-glucosaminidase N-terminal domain (domain)
This is the N-terminal domain found in N-acetyl-beta-D-glucosaminidase (GcnA) present in Streptococcus gordonii. GcnA is a family 20 glycosidase that cleaves N-acetyl-beta-D-glucosamine and N-acetyl-beta-D-galactosamine from 4-methylumbelliferylated substrates. Similar N-terminal domains have been observed in all family 20 glycosidases although the number of beta-sheet strands may vary from five.
Wikipedia: In molecular biology, glycoside hydrolase family 20 is a family of glycoside hydrolases.
Pfam PF00679: Elongation factor G C-terminus (domain)
This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a  ferredoxin-like fold.
Pfam PF23643: Trafficking protein particle complex subunit 13, C-terminal (domain)
Trafficking protein particle complex subunit 13 (TRAPPC13) is involved in regulating autophagy and survival in response to small molecule compound-induced Golgi stress. It is the orthologue of Trs65 from yeast. This entry represents the C-terminal domain of TRAPPC13 which may adopt a Ig-like fold.
Pfam PF03004: Plant transposase (Ptta/En/Spm family) (family)
Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families.
Pfam PF06100: MCRA family (family)
The MCRA (myosin-cross-reactive antigen) family of proteins were thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis. More recent work shows that these proteins act as hydratase enzymes that convert linoleic acid and oleic acid to their respective 10-hydroxy derivatives.  It has been suggested that MCRA proteins catalyse the first step in conjugated linoleic acid production. Proteins in this family act in an FAD dependent manner. The structure of a fatty acid double-bond hydratase from Lactobacillus acidophilus has been recently solved showing four structural domains.
Pfam PF18361: Single stranded DNA-binding protein ss DNA binding domain (domain)
This domain is found in the N-terminal of ThermoDBP, a single stranded DNA binding protein found in Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. This domain is responsible for ssDNA binding. Conserved motif 'LIYWIRSDR' is located at the C-terminal end of the domain and is thought to participate in ssDNA binding.
Pfam PF02545: Maf-like protein (domain)
Maf is a putative inhibitor of septum formation in eukaryotes,  bacteria, and archaea.
Pfam PF10788: Protein of unknown function (DUF2603) (family)
This family is conserved in Epsilon-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 PF22463: Ctf19, first RWD domain (domain)
This entry represents the first occurrence of the RWD domain within the Ctf19 subunit of the inner kinetochore in Kluyveromyces lactis. Ctf19 is a component of the constitutive centromere associated network (CCAN), which forms the structural basis of the kinetochore. The CCAN governs the timing of kinetochore assembly, establishes its position through interaction with a specialised nucleosome containing the histone H3 variant Cse4/CENP-A, and determines the arrangement of the microtubule attachment machinery. In this way, eukaryotic kinetochores establish a connection between spindle microtubules and chromosomal centromeres.
Pfam PF12234: RAVE protein 1 C terminal (family)
This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits.
Pfam PF07753: Protein of unknown function (DUF1609) (family)
This region is found in a number of hypothetical proteins thought to be expressed by the eukaryote Encephalitozoon cuniculi, an obligate intracellular  microsporidial parasite. It is approximately 200  residues long.
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 PF04924: Poxvirus A6 protein (family)
This entry represents Protein A6 from Vaccinia virus, also known as Virion morphogenesis protein OPG132, and similar proteins from poxvirus. A6 is a lipid-bound viral membrane assembly protein that plays an essential role in immature virion (IV) to mature virion (MV) transition . It functions in both crescent-shaped viral membranes formation and its enclosure to form immature virions . It also participates in targeting mature virion proteins to sites of virion assembly to ensure their correct localisation .
Pfam PF14065: Pvc16 N-terminal domain (domain)
This protein forms part of a contractile injection system. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. This entry include Pvc16.  This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 320 amino acids in length. This domain alone in Pvc16 is able to produce PVC particles with normal length but without the outer sheath, indicating the main function of this N-terminal domain in terminating the tube growth.
Pfam PF05387: Chorion family 3 (family)
This family consists of several Drosophila chorion proteins S36 and S38. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary.
Pfam PF22718: Short NACHT-associated C-Terminal domain, family 13 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF24649: Domain of unknown function (DUF7642) (domain)
This domain is found in uncharacterised sequences from plants.
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 PF09232: Caenorhabditis elegans Her-1 (domain)
Her-1 adopts an all-helical structure with two subdomains: residues 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst residues 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen Cys are conserved in all known HER-1 sequences and form seven disulfide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signaling during C. elegans sex determination. It also inhibits the function of tra-2a.
Wikipedia: In molecular biology the nematode Her-1 protein is a protein which adopts an all-helical structure with two subdomains: amino acids 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst amino acids 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen cysteines are conserved in all known HER-1 sequences and form seven disulphide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signalling during C. elegans sex determination. It also inhibits the function of tra-2a.
Pfam PF08664: YcbB domain (domain)
YcbB is a DNA-binding domain.
Pfam PF12090: Spt20, SEP domain (domain)
This is the SEP domain found in Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large complex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains. Spt20 is indispensable under endoplasmic reticulum (ER) stress conditions, being involved in the regulation of stress-responsive genes transcription. This domain interacts with LisH motif helices of Taf5.
Pfam PF05686: Glycosyl transferase family 90 (family)
This family of glycosyl transferases are specifically (mannosyl) glucuronoxylomannan/galactoxylomannan -beta 1,2-xylosyltransferases, [ec:2.4.2.-].
Pfam PF19823: Domain of unknown function (DUF6305) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 183 and 215 amino acids in length. This family may be distantly related to [pfam:PF09370] suggesting these proteins may function as an enzyme of unknown activity.
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 PF14308: X-domain of DnaJ-containing (domain)
IN certain plant and yeast proteins, the DnaJ-1 proteins have a three-domain structure.  The x-domain lies between the N-terminal DnaJ and the C-terminal Z domains. The exact function is not known.
Pfam PF07648: Kazal-type serine protease inhibitor domain (domain)
Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides.
Wikipedia: The Kazal domain  is an evolutionary conserved protein domain usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors.
Pfam PF05313: Poxvirus P21 membrane protein (family)
The P21 membrane protein of vaccinia virus, encoded by the A17L (or A18L) gene, has been reported to localise on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that P21 acts as a membrane anchor for the externally located fusion protein P14 (A27L gene).
Pfam PF05306: Protein of unknown function (DUF733) (family)
This family consists of several uncharacterised Drosophila melanogaster 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 PF03054: tRNA methyl transferase HUP domain (domain)
This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs.
Pfam PF11218: Protein of unknown function (DUF3011) (family)
This bacterial family of proteins has no known function. Most members belong to Proteobacteria.
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 PF23177: Iron-related transcription factor 3 bHLH domain (domain)
The founding member of this family is the bHLH domain of Iron-related transcription factor 3 from Oryza sativa. This transcription factor acts as negative regulator of the iron deficiency response and plays an important role for iron homeostasis in rice.
Pfam PF18773: Importin 13 repeat (repeat)
Importin 13 has a spiralic structure containing repeats structurally similar to HEAT repeats. It serves as receptor for nuclear  localization signals (NLS) in cargo substrates, mediating docking  of the importin/substrate complex to the nuclear pore complex (NPC).  It contains several repeats structurally similar to the HEAT repeat. This Pfam entry represents a single repeat unit.
Pfam PF05870: Phenolic acid decarboxylase (PAD) (domain)
This family consists of several bacterial phenolic acid decarboxylase proteins. Phenolic acids, also called substituted cinnamic acids, are important lignin-related aromatic acids and natural constituents of plant cell walls. These acids (particularly ferulic, p-coumaric, and caffeic acids) bind the complex lignin polymer to the hemicellulose and cellulose in plants. The Phenolic acid decarboxylase (PAD) gene (pad) is transcriptionally regulated by p-coumaric, ferulic, or caffeic acid; these three acids are the three substrates of PAD.
Pfam PF22862: Halocin 8-like N-terminal domain (domain)
This is a presumed domain found at the N-terminal of halocin 8 and similar sequences from archaea.
Pfam PF19036: First Longin domain of FUZ, MON1 and HPS1 (domain)
This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia.
Pfam PF10749: Protein of unknown function (DUF2534) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
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 PF14751: Domain of unknown function (DUF4474) (domain)
Domain found on N-termina of few families of uncharacterized Clostridia proteins. Typically followed by a proline-rich domain or other kinds of repeats
Pfam PF05236: Transcription initiation factor TFIID component TAF4 family (family)
This region of similarity is found in Transcription initiation factor TFIID component TAF4.
Wikipedia: Transcription initiation factor TFIID subunit 4 is a protein that in humans is encoded by the TAF4 gene.
Pfam PF21967: Mannosylglycerate synthase C-terminal domain (domain)
Mannosylglycerate synthase catalyses the formation of the stress protectant 2-O-alpha-D-mannosyl glycerate. It consists of a GT-like domain at the N-terminal and a C-terminal helical domain, represented in this entry, that is apparently involved in protein oligomerization.