SII-SWORD/CoKE huggingface dataset:
Pfam PF15350: Ewing's tumour-associated antigen 1 homologue (family)
This family of proteins is found in eukaryotes, where members are expressed at high levels in the brain, liver kidney and Ewing tumour cell lines. Proteins in this family are typically between 648 and 898 amino acids in length.
Pfam PF16114: ATP citrate lyase citrate-binding (domain)
This is the citrate-binding domain of ATP citrate lyase. This domain has a Rossmann fold.
Pfam PF06080: Protein of unknown function (DUF938) (family)
This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. 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 PF21562: G7C, Tail fiber protein, domain 3 (repeat)
This domain is found in Tail fiber protein from Escherichia virus G7C (Gp63) and similar proteins from tailed bacteriophages and bacterial prophages. Gp63 is a receptor-binding proteins (RBP) that emanate from the phage particle in the form of fibres for the virus to recognise and bind to their host. It deacetylates surface polysaccharides of E. coli leaving the backbone of the polysaccharide intact. This entry represents domain 3 of Ggp63, which shows structural similarity to a small domain that connects the sialidase domain with the N-terminal particle-binding domain in phage tailspikes with sialidase activity ([pfam:PF12218]). It shows two beta-helical rungs capped by an N-terminal alpha-helix oriented perpendicular to the rungs' axis.
Pfam PF22484: Domain of unknown function (DUF6986) (domain)
This entry represents a family of TIM barrel proteins that are most closely related to [pfam:PF03328]. This strongly suggests that these proteins are enzyme with a possibly related 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 PF10724: Protein of unknown function (DUF2516) (family)
This family is conserved in Actinobacteria. 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 PF04515: Plasma-membrane choline transporter (family)
This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals.
Pfam PF21279: YhfX-like, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of bacterial proteins, including Uncharacterized protein YhfX from Escherichia coli, which may be related to DNA recombination. The function of this domain is still unknown. It is often found associated to [pfam:PF01168].
Pfam PF23637: SH3BP4 C-terminal helical domain (domain)
This domain is found in SH3 domain-binding protein 4 (SH3BP4) and related proteins such as Metastasis-associated in colon cancer protein 1 (MACC1). SH3BP4 binds and negative regulates Rag GTPase complex. This binding abrogates the interaction of mTORC1 with Rag GTPase complex and the recruitment of mTORC1 to the lysosome, thus inhibiting amino acid-induced mTORC1 activation and cell growth and promoting autophagy. MACC1 acts as a transcription activator for MET and as a key regulator of HGF-MET signaling. It promotes cell motility, proliferation and tumor growth and metastasis in vivo. The domain represented by this entry is predicted to fold into a mainly helical structure with a DEATH domain-like topology.
Pfam PF21228: Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical (domain)
This domain is found in Ribulose bisphosphate carboxylase/oxygenase activase from Nicotiana tabacum (RuBisCO activase) and similar proteins from plants and cyanobacteria. This enzyme facilitates the removal of the sugar phosphate inhibitors of RuBisCO, the enzyme that catalyses the fixation of atmospheric CO2 in photosynthesis. This protein is organised into an N-terminal, followed by a AAA module and a 23-residue C-terminal extension. The AAA module has an alpha-beta and an alpha-helical subdomains. This entry covers part of the alpha-helical subdomain and the C-terminal extension.
Pfam PF01761: 3-dehydroquinate synthase N-terminal (domain)
The 3-dehydroquinate synthase [ec:4.6.1.3] domain is present in isolation in various bacterial 3-dehydroquinate  synthases and also present as a domain in the pentafunctional AROM polypeptide [swissprot:P07547]. 3-dehydroquinate (DHQ) synthase catalyses the formation of  dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate. This reaction is part of the shikimate pathway which is involved  in the biosynthesis of aromatic amino acids. This is the Rossmann fold domain found at the N-terminal of these proteins, which binds NAD+ in an inverted orientation to that observed in all other classic Rossmann fold proteins.
Wikipedia: The enzyme 3-dehydroquinate synthase catalyzes the chemical reaction[[3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate]]  3-dehydroquinate + phosphate
Pfam PF19627: Activity-dependent neuroprotector homeobox protein N-terminal (domain)
This entry represent the N-terminal domain of Activity-dependent neuroprotector homeobox protein (ADNP, also known as Activity- dependent neuroprotective protein), which contains zinc finger motifs. It is involved in transcriptional regulation and it is vital for mammalian brain formation. In humans, de novo mutations result in a syndromic form of autism-like spectrum disorder (ASD), including cognitive and motor deficits, the ADNP syndrome. This protein is also related to autophagy and the pathophysiology of schizophrenia.
Pfam PF03492: SAM dependent carboxyl methyltransferase (family)
This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesised through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N.  The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine.
Pfam PF17455: Late transcription unit B (family)
This is a family of unknown function. Family members include the Chlamydia late transcription unit B protein.
Pfam PF17686: Family of unknown function (DUF5534) (family)
This is a family of unknown function found in mammals. Family members have one or several predicted trans-membrane regions.
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 PF03411: Penicillin-insensitive murein endopeptidase (family)
This group of peptidases belong to MEROPS peptidase family M74 (murein endopeptidase family, clan MD). The type example is murein endopeptidase from Escherichia coli (MepA). The entry represents a family of penicillin-insensitive murein endopeptidases involved in the removal of murein from the sacculus by cleaving the peptide bonds between neighbouring strands in mature murein. The crystal structure of MepA has been determined revealing similarities to the D-Ala-D-Ala carboxypeptidases in MEROPS peptidase family M15 .
Pfam PF14486: Domain of unknown function (DUF4432) (family)
This family of proteins has not been characterised.
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 PF21154: 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix (domain)
RPN7/PSDM6 are regulatory subunits from the 26S proteasome. This entry represents the C-terminal helix.
Pfam PF07600: Protein of unknown function (DUF1564) (family)
A family of paralogous proteins in Leptospira interrogans. Several (e.g. [swissprot:Q8F4V2]) have been annotated as possible CopG-like transcriptional regulators (see [pfam:PF01402]).
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 PF03515: Colicin-like bacteriocin tRNase domain (family)
The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro. The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding.
Wikipedia: A colicin is a type of bacteriocin produced by and toxic to some strains of Escherichia coli. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis.
Pfam PF13114: RecO N terminal (domain)
This entry contains members that are not captured by [pfam:PF11967].
Pfam PF01669: Myelin basic protein (family)
The myelin sheath is a multi-layered membrane, unique to the nervous system, that functions as an insulator to greatly increase the velocity of axonal impulse conduction . Myelin basic protein (MBP)  is a hydrophilic protein that may function to maintain the correct structure of myelin, interacting with the lipids in the myelin membrane by electrostatic and hydrophobic interactions. In mammals various forms of MBP exist which are produced by the alternative splicing of a single gene; these forms differ by the presence or the absence of short (10 to 20 residues) peptides in various internal locations in the sequence. The major form of MBP is generally a protein of about 18.5 Kd (170 residues). MBP is the target of many post-translational modifications: it is N-terminally acetylated, methylated on an arginine residue, phosphorylated by various serine/threonine protein-kinases, and deamidated on some glutamine residues.
Wikipedia: Myelin basic protein (MBP) is a protein believed to be important in the process of myelination of nerves in the nervous system. The myelin sheath is a multi-layered membrane, unique to the nervous system, that functions as an insulator to greatly increase the velocity of axonal impulse conduction. MBP maintains the correct structure of myelin, interacting with the lipids in the myelin membrane.
Pfam PF23442: Family of unknown function (DUF7125) (family)
This family represents a group of proteins from halobacteria. Members are predicted to show an alpha-beta configuration with similarity to the KaiC domain ([pfam:PF06745]).
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 PF23090: MBTPS1, fourth GATase-like domain (domain)
This domain is found in the family of serine proteases such as MBTPS1 and SBT6.1 that are involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signaling and regulation. The MBTPS1 proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position. They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C. In plants, SBT6.1 participate in stress response signaling and cell wall remodeling by processing factors like BZIP17 and pectinesterases. The domain represented by this entry is predicted to fold into a globular structure with significant similarity to domains belonging to class I glutamine amidotransferase superfamily.
Pfam PF02440: Adenovirus E3 region protein CR1 (domain)
Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. This region called CR1 (conserved region 1) is found three times in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain (A. Bateman pers. observation).
Pfam PF14363: Domain associated at C-terminal with AAA (family)
This domain is found in association with the AAA family, [pfam:PF00004].
Pfam PF22340: Tubulin-like protein TubZ, C-terminal domain (domain)
This domain is found at the C-terminal end of Tubulin-like protein TubZ from Clostridium botulinum C phage and similar sequences found in tailed bacteriophages and prophages mainly from Clostridium bacteria. TubZ is a tubulin-like, filament forming GTPase. This protein adopts a tubulin/FtsZ protein family fold organised into two domains, a canonical N-terminal GTP-binding domain, and a C-terminal GTPase domain (this entry).
Pfam PF17989: Actin like proteins N terminal domain (domain)
This is the N-terminal domain found in archaeal actin homolog Ta0583 found in thermophilic archaeon Thermoplasma acidophilum. Structural analysis indicate that the fold of Ta0583 contains the core structure of actin indicating that it belongs to the actin/Hsp70 superfamily of ATPases. Furthermore,Ta0583 co-crystallised with ADP shows that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. It has been suggested that Ta0583 might function in the cellular organisation of T. acidophilum. Other family members include ParM another actin-like protein found in Staphylococcus aureus. Crystal structure co-ordinates revealed that this protein is most structurally related to the chromosomally encoded Actin-like proteins (Alp) Ta0583 from the archaea Thermoplasma acidophilum.  Furthermore, biophysical analyses have suggested that ParM filaments undergo a treadmilling-like mechanism of motion in vitro similar to that of F-actin. The recruitment of ParM to the segrosome complex, was shown to be required for the conversion of static ParM filaments to a dynamic form proficient for active segregation and facilitated by the C-terminus of ParR
Pfam PF20319: Family of unknown function (DUF6614) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 120 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 PF18312: Copper resistance protein ScsC N-terminal domain (domain)
This is the N-terminal domain found in Copper resistance protein ScsS present in Proteus mirabilis. ScsC is a powerful disulfide isomerase that is able to refold and reactivate the scrambled disulfide form of the model substrate RNase A. The protein has a thioredoxin 4 domain ([pfam:PF13462]) but, unlike other characterized proteins in this family, it is trimeric. The N-terminal domain is responsible for trimerization of ScsC which is needed for isomerase activity.
Pfam PF17258: Family of unknown function (DUF5324) (family)
This is a family of unknown function, mostly found in Actinobacteria. Most of the family members contain one trans-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 PF21054: Rubicon, PI3K-binding domain (domain)
This is the PI3K-binding domain (PIKBD) localised in the middle region of Rubicon, a potent negative regulator of autophagy through the interaction with Rab7-GTP. This domain is predicted to have disordered and helical regions. This domain is also found in Pacer.
Pfam PF03452: Anp1 (family)
The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localise within the cis Golgi, and that they are physically associated in two distinct  complexes.
Pfam PF00535: Glycosyl transferase family 2 (domain)
Diverse family, transferring sugar from UDP-glucose, UDP-N-acetyl- galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.
Pfam PF03892: Nitrate reductase cytochrome c-type subunit (NapB) (family)
The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase.
Wikipedia: Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.
Pfam PF05014: Nucleoside 2-deoxyribosyltransferase (domain)
Nucleoside 2-deoxyribosyltransferase [ec:2.4.2.6] catalyses the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides.
Wikipedia: In enzymology, a nucleoside deoxyribosyltransferase is an enzyme that catalyzes the chemical reaction2-deoxy-D-ribosyl-base1 + base2  2-deoxy-D-ribosyl-base2 + base1
Pfam PF19980: Family of unknown function (DUF6416) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001300) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the anthracimycin biosynthetic gene cluster from Streptomyces sp. CNH365.
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 PF13031: Protein of unknown function (DUF3892) (family)
DUF3892 is related to the truncated RNaseH fold-containing ribosome hibernation factors. Predicted to function as a possible conflict effector domain at the ribosome, based on comparable genome contextual associations with DUF2188, including repeated association with nucleotide-activated effector conflict systems.
Pfam PF00939: Sodium:sulfate symporter transmembrane region (family)
There are also some members in this family that do not match the Prosite motif, and belong to the subfamily  SODIT1.
Wikipedia: Sodium sulfate symporters are integral membrane proteins that mediate the intake of a wide variety of molecules with the concomitant uptake of sodium ions. These sodium symporters can be grouped, on the basis of sequence and functional similarities into a number of distinct families. One of these families, also known as SLC13 transporters, consists of the following proteins:Mammalian sodium/sulphate cotransporter.
Mammalian renal sodium/dicarboxylate cotransporter, which transports succinate and citrate.
Mammalian intestinal sodium/dicarboxylate cotransporter.
Chlamydomonas reinhardtii putative sulphur deprivation response regulator SAC1.
Pfam PF21010: Helicase associated domain (HA2), ratchet-like (domain)
The helicase associated domain (HA2) has an all alpha-helical fold and consists of a N-terminal winged-helix (WH) domain ([pfam:PF04408]) and a C-terminal degenerate helical-bundle domain, referred to as the ratchet-like domain. These domains collaborate with the RecA domains at the N-terminal in completing an RNA binding channel to allow the helicases to keep a stable grip on the RNA. This entry represents the ratchet-like domain, which may be important for RNA translocation.
Pfam PF02770: Acyl-CoA dehydrogenase, middle domain (domain)
Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.
Pfam PF15744: Uncharacterized protein family UPF0492 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 78 and 408 amino acids in length.
Pfam PF07969: Amidohydrolase family (domain)
Amidohydrolases are a diverse superfamily of enzymes which catalyse the hydrolysis of amide or amine bonds in a large number of different substrates including urea, cytosine, AMP, formylmethanofuran, etc . Also included in this superfamily are the phopshotriesterase enzymes, which hydrolyse P-O bonds. Members participate in a large number of processes including nucleotide metabolism, detoxification and neuronal development. They use a variety of divalent metal cofactors for catalysis: for example adenosine deaminase binds a single zinc ion, phopsphotriesterase binds two, while urease binds nickel. It has been postulated that since some of these proteins, such as those some of those involved in neuronal devlopment, appear to have lost their metal-binding centres, their function may simply be to bind, but not hydrolyse, their target molecules.

This entry represents a subset of amidohydrolase domains that participate in different functions including cytosine degradation, atrazine degradation and other metabolic processes. The structure of the domain from Escherichia coli has been studied, and like other amidohydrolases it forms a classical Î±-Î² TIM-barrel fold . The active site is located in the mouth of the enzyme barrel and contains a bound iron ion that coordinates a hydroxyl nucleophile. Substrate binding involves a significant conformational change that sequesters the reaction complex from solvent.