SII-SWORD/CoKE huggingface dataset:
Pfam PF18100: Phosphodiesterase 4 upstream conserved regions (UCR) (domain)
This is the upstream conserved region (UCR) found in Phosphodiesterase 4 (PDE4) enzymes. PDE4 is a contributor to intracellular signalling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain [pfam:PF00233] . Due to alternative promoters/start sites and variable mRNA splicing, transcription from the four PDE4 genes results in the expression of more than 25 different isoforms of PDE4. Each isoform has a unique N-terminal region that determines its specific subcellular localization by mediating interactions with scaffolding proteins. The isoforms are further classified into long, short, and supershort forms based on the presence or absence of two upstream conserved regions (UCRs, known as UCR1 and UCR2).  Long splice variants contain both UCR1 and UCR2, short variants lack UCR1, and the supershort forms of PDE4 additionally lack part of UCR2. The extent to which UCRs are present determines critical functional differences between the isoforms. Phosphorylation by protein kinase A (PKA) at a conserved site on UCR1 activates all long PDE4 isoforms. Mutation and deletion studies have shown that long forms of PDE4 are dimeric, with key dimerization interactions mediated by UCR1 and UCR2, and that the C-terminal half of UCR2 could play a negative regulatory role.
Pfam PF02050: Flagellar FliJ protein (coiled_coil)
The bacterial flagellum consists of three major parts: the basal body (including the rod), the hook, and the filament. Outer components of the flagellum are transported to the assembly site by a specialised type III export apparatus, which is related to the type III secretion system (T3SS). FliJ is a soluble regulatory component of the flagellar export apparatus . The function of FliJ is not clear.
Pfam PF06316: Enterobacterial Ail/Lom protein (family)
This family consists of several bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain.  The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis.
Wikipedia: Virulence-related outer membrane proteins, or outer surface proteins (Osp) in some contexts, are expressed in the outer membrane of gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion.
Pfam PF06294: CH-like domain in sperm protein (domain)
Spef is a region of sperm flagellar proteins. It probably exerts a role in spermatogenesis in that the protein is expressed predominantly in adult tissue. It is present in the tails of developing and epididymal sperm internal to the fibrous sheath and around the dense outer fibres of the sperm flagellum. The amino-terminal domain (residues 1-110) shows a possible calponin homology (CH) domain; however Spef does not bind actin directly under in vitro conditions, so the function of the amino-terminal calponin-like domain is unclear. Transcription aberrations leading to a truncated protein result in immotile sperm.
Pfam PF06682: SOCE-associated regulatory factor of calcium homoeostasis (family)
SARAF is as family of eukaryotic proteins embedded in the ER. SARAF is SOCE-associated regulatory factor, where SOCE is store operated calcium entry. ie a mechanism governing calcium homoeostasis in the cell and the mitochondria. SOCE involves the enabling of Ca2+ release-activated Ca2+ (CRAC) channels. SARAF is a single pass ER membrane protein whose systolic-facing domain is responsible for activity and whose luminary-facing domain carries out a regulatory function in conjunction with another membrane protein STIM, an ER single pass membrane protein that detects changes in ER Ca2+ levels through its EF-hand, conserved Ca2+ binding domain.  STIM is the major target for SARAF regulation, and thus SARAF negatively regulates the SOCE entry of calcium into cells protecting them from overfilling.
Pfam PF15330: SHP2-interacting transmembrane adaptor protein, SIT (family)
SIT, or SHP2-interacting transmembrane adaptor protein, is a disulfide-linked dimer that regulates human T Cell activation.
Pfam PF01010: NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus (domain)
This entry represents a carboxyl terminal extension of [pfam:PF00361]. It includes subunit 5 from chloroplasts, and bacterial subunit L.  This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. This family is largely a few TM regions of the F subunit of NADH-Ubiquinone oxidoreductase from plants. The TMs form part of the anti-porter subunit.
Wikipedia: NADH dehydrogenase is an enzyme that converts nicotinamide adenine dinucleotide (NAD) from its reduced form (NADH) to its oxidized form (NAD+). Members of the NADH dehydrogenase family and analogues are commonly systematically named using the format NADH:acceptor oxidoreductase. The chemical reaction these enzymes catalyze is generally represented with the following equation:NADH + H+ + acceptor ⇌ NAD+ + reduced acceptor
Pfam PF01220: Dehydroquinase class II (domain)
3-dehydroquinate dehydratase (4.2.1.10), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17kDa. They are found in some bacteria such as actinomycetales  and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.
Wikipedia: The enzyme 3-dehydroquinate dehydratase (EC 4.2.1.10) catalyzes the chemical reaction3-dehydroquinate  3-dehydroshikimate + H2O
Pfam PF05858: Bovine immunodeficiency virus surface protein (SU) (family)
The bovine lentivirus also known as the bovine immunodeficiency-like virus (BIV) has conserved and hypervariable regions in the surface envelope gene. This family corresponds to the SU surface protein.
Pfam PF15332: Lck-interacting transmembrane adapter 1 (family)
LIME1 is a family of eukaryotic transmembrane adaptors. It plays an important role in linking BCR stimulation to B-cell activation and is expressed in primary B cells. LIME localises to lipid rafts in T cells in response to TCR stimulation, and is phosphorylated by Lck and recruits signalling molecules such as Lck, PI3K, Grb2, Gads, and SHP-2. LIME acts as the transmembrane adaptor linking BCR-induced membrane-proximal signalling to B-cell activation.
Pfam PF22266: Family of unknown function (DUF6953) (family)
This is a family of uncharacterised bacterial proteins. They share significant sequence similarity to HTH winged helix domains, in particular to the N-terminal domain of transcriptional regulator BrxR and RNA polymerase III subunit RPC82.
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 PF04016: Putative heavy-metal chelation (domain)
This domain of unknown function has a PLP-dependent transferase-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the C-terminus of proteins containing DUF4213, [pfam:PF13938]. The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the protein has an enolase N-terminal-like fold and this Rossmann-like C-terminal domain.  Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation.
Pfam PF19424: Protein UNC80 central region (repeat)
This family represents the protein UNC80 found in eukaryotes, a component of the NALCN sodium channel complex. NALC is a cation voltage-independent channel activated by substance P, neurotensin, acetylcholine and noradrenaline that controls neuronal excitability. UNC80 forms a complex with UNC79 and both are key regulators of the channel and required for the proper expression and axonal localisation of NALCN. UNC80 is required for NALCN control by GPCRs and essential for its sensitivity to extracellular calcium. This protein acts as a scaffold for Src family of tyrosine kinases (SFK) and UNC-79 to mediate interaction with NALCN.
Pfam PF23975: Family of unknown function (DUF7301) (family)
This entry represents a small family of uncharacterised phage proteins. These proteins contain a highly conserved RDR/KVL sequence motif that is likely 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 PF16492: Cadherin cytoplasmic C-terminal (family)
Cadherin_C_2 is the cytoplasmic C-terminal domain of some proto-cadherins. It is this region of the cadherins that allows cell-adhesion and the essential feature of metazoan multicellularity. Cadherins are cell-surface receptors that function in cell adhesion, cell polarity, and tissue morphogenesis.
Pfam PF06382: Protamine and protamine like (family)
This family consists of several insect proteins including protamine A (ProtA), protamine B (ProtB) and protamine-like protein 99C (Prtl99C) from Drosophila melanogaster. They contain a HMG-box and are involved in chromatin compaction during spermiogenesis. Prtl99C is a sperm chromatin-associated protein that is essential for male fertility.
Pfam PF03792: PBC domain (family)
The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.
Pfam PF24014: Family of unknown function (DUF7328) (family)
This entry represents a small family of phage proteins. Structure prediction suggests that these proteins form a single long alpha helix.
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 PF16448: LapD/MoxY periplasmic domain (domain)
This domain is the N-terminal periplasmic domain of the LapD and MoxY receptor proteins.
Pfam PF02540: NAD synthase (domain)
NAD synthase ([ec:6.3.5.1]) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation.
Pfam PF06554: Olfactory marker protein (family)
This family consists of several olfactory marker proteins. Expression of the olfactory marker protein (OMP) is highly restricted to mature olfactory receptor neurons in virtually all vertebrate species from fish to man.
Wikipedia: In molecular biology, olfactory marker protein is a protein involved in signal transduction.
It is a highly expressed, cytoplasmic protein found in mature olfactory sensory receptor neurons of all vertebrates. OMP is a modulator of the olfactory signal transduction cascade. The crystal structure of OMP reveals a beta sandwich consisting of eight strands in two sheets with a jelly-roll topology. Three highly conserved regions have been identified as possible protein–protein interaction sites in OMP, indicating a possible role for OMP in modulating such interactions, thereby acting as a molecular switch.
Pfam PF01817: Chorismate mutase type II (domain)
Chorismate mutase [ec:5.4.99.5] catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine.
Wikipedia: In enzymology, chorismate mutase is an enzyme that catalyzes the chemical reaction for the conversion of chorismate to prephenate in the pathway to the production of phenylalanine and tyrosine, also known as the shikimate pathway.
Hence, this enzyme has one substrate, chorismate, and one product, prephenate. Chorismate mutase is found at a branch point in the pathway. The enzyme channels the substrate, chorismate to the biosynthesis of tyrosine and phenylalanine and away from tryptophan. Its role in maintaining the balance of these aromatic amino acids in the cell is vital. This is the single known example of a naturally occurring enzyme catalyzing a pericyclic reaction. Chorismate mutase is only found in fungi, bacteria, and higher plants. Some varieties of this protein may use the morpheein model of allosteric regulation.
Pfam PF07556: Protein of unknown function (DUF1538) (family)
This family contains several conserved glycines and phenylalanines.
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 PF17091: Inovirus G7P protein (family)
Tail virion protein 7P is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane.
Pfam PF24348: Domain of unknown function (DUF7508) (domain)
This domain is found in uncharacterised prokaryotic proteins. Is has significant sequence similarity to GIY-YIG endonuclease domains and it is predicted to adopt similar structure.
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 PF09269: Domain of unknown function (DUF1967) (domain)
Members of this family contain a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. They are predominantly found in the bacterial GTP-binding protein Obg, and are still functionally uncharacterised.
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 PF08655: DASH complex subunit Ask1 (family)
The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro.  Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules.
Pfam PF12382: Retrotransposon peptidase (family)
This is a small family of fungal retroviral aspartyl peptidases.
Pfam PF22639: Tail sheath protein Gp18-like domain I (domain)
This entry represents domain I from bacteriophage tail sheath proteins such as Gp18, a protein that surrounds the central non-contractile tail tube of the tail sheath from bacteriophages, which contracts during infection. These proteins consist of three domains, domains I, II ([pfam:PF17481]) and III ([pfam:PF17482]). Domains I and II form the protease-resistant fragment.
Pfam PF09448: Methylmuconolactone methyl-isomerase (domain)
MmlI is a short, approx 115 residue, protein of two alpha helices and four beta strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species and tetrameric in others. The known structure shows two copies of the protein form a dimeric alpha beta barrel.
Pfam PF01527: Transposase (family)
Transposase proteins are necessary for efficient DNA transposition.  This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF11261: Interferon regulatory factor 2-binding protein zinc finger (domain)
IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger represented in this family and  C-terminal RING finger domains.
Pfam PF18466: Glutamate--tRNA ligase N-terminal domain (domain)
This is an N-terminal domain of Glutamate--tRNA ligase (GluRS, [ec:6.1.1.17]). The domain adopts a classical glutathione S-transferase (GST)-like fold and it interacts with tRNA-aminoacylation cofactor ARC1 (Arc1p) N-terminal domain for the formation of aminoacyl-tRNA synthetase (aaRS) complex in yeast.
Pfam PF06042: Nucleotidyltransferase (domain)
This family consists of several hypothetical bacterial proteins of unknown function. This family was recently identified as belonging to the nucleotidyltransferase superfamily.
Pfam PF19694: Family of unknown function (DUF6194) (domain)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001597) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the fluvirucin B2 biosynthetic gene cluster from Actinomadura fulva  subsp. indica. This family appears to be predominantly 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 PF00706: Anenome neurotoxin (domain)
Wikipedia: Sea anemone neurotoxin is the name given to neurotoxins produced by sea anemones with related structure and function.
Sea anemone neurotoxins can be divided in two functional groups that either specifically target the sodium channel or the potassium channel.
Pfam PF02995: Protein of unknown function (DUF229) (family)
Members of this family are uncharacterised.  They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
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 PF04787: Late protein H7 (family)
Family of poxvirus late H7 proteins.
Pfam PF16445: Domain of unknown function (DUF5042) (family)
This family consists of several uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species. 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 PF23331: VWC2L, C-terminal domain (domain)
This domain is found at the C-terminal end of human von Willebrand factor C domain-containing protein 2-like (VWC2L) and similar proteins predominantly found in vertebrates. VWC2L may play a role in neurogenesis, bone differentiation and matrix mineralisation. This domain is predicted to adopt an all-beta configuration.
Pfam PF15018: TRP-interacting helix (conserved_site)
This highly conserved motif is thought to be a transmembrane helix that binds to transient receptor potential (TRP) calcium channel. It is known that proline-rich proteins inactivate tannins found in food compounds, and it is putatively thought that PRR24 does too. This is important since tannins often inhibit the uptake of iron.  InaF is a protein required for TRP calcium channel function in Drosophila. TRP-related channels have been suggested to mediate store-operated calcium entry, important for Ca2+ homeostasis in a wide variety of cell types.  The amino acid sequence of PRR-24 contains two completely conserved Y residues that may be functionally important. This domain family is found in eukaryotes, and is approximately 40 amino acids in length.
Pfam PF03184: DDE superfamily endonuclease (family)
This family of proteins are related to [pfam:PF00665] and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localised to the centromere.