SII-SWORD/CoKE huggingface dataset:
Pfam PF04706: Dickkopf N-terminal cysteine-rich region (domain)
Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This family represents the N-terminal one. The C-terminal region has been found to share significant sequence similarity to the colipase fold, [pfam:PF01114], [pfam:PF02740].
Pfam PF06483: Chitinase C (family)
This ~170 aa region is found at the C-terminus of [pfam:PF00704].
Pfam PF15911: WDR19 second beta-propeller (repeat)
This entry represents the second beta-propeller of human WDR19 (also known as IFT144) and its orthologue from C.elegans, DYF2. WDR19 is a component of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. Proteins in this entry are part of the core of the complex which is important for TULP3 localization to the cilia. The core of the complex is formed by the beta-propeller domains of its components (WDR19, IFT140 and IFT122).
Wikipedia: The WD40 repeat is a short structural motif of approximately 40 amino acids, often terminating in a tryptophan-aspartic acid (W-D) dipeptide. Tandem copies of these repeats typically fold together to form a type of circular solenoid protein domain called the WD40 domain.
Pfam PF08004: Protein of unknown function (DUF1699) (family)
This family contains many archaeal proteins which have very conserved sequences.
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 PF21888: Ferredoxin-like NFLD domain (domain)
This entry represents the NFLD domain, a domain found fused to the N-terminus of certain RNA methyltransferases (MTases), particularly in the TrmN/Trm14 family. The NFLD domain, which consists of a beta-sheet and two alpha-helices, was initially proposed to be an ancient RNA binding domain based on bioinformatics analyses. The NFLD domain is often fused to the minimal core of the THUMP domain, and together, they contribute to tRNA recognition and catalysis.
Pfam PF02654: Cobalamin-5-phosphate synthase (family)
This is family of Colbalmin-5-phosphate synthases, CobS, from bacteria. The CobS enzyme catalyses the synthesis of AdoCbl-5'-p from AdoCbi-GDP  and alpha-ribazole-5'-P.  This enzyme is involved in the cobalamin (vitamin B12) biosynthesis pathway in particular the nucleotide loop  assembly stage in conjunction with CobC, CobU and CobT.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF13836: Domain of unknown function (DUF4195) (domain)
This family is found at the N-terminus of metazoan proteins that carry PHD-like zinc-finger domains. 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 PF13851: Growth-arrest specific micro-tubule binding (coiled_coil)
This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localisation of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localised to regions of dynein regulation in mammalian cells.
Pfam PF23129: DotZ (family)
This entry represent the type 4 apparatus protein DotZ from Legionella pneumophila and related proteins found mainly in Gammaproteobacteria. DotZ is a component of Type 4B secretion (T4BS) system that translocates over 300 effectors into the host cell during infection. This protein is part of a subcomplex which recruits effector proteins and delivers them to the core transmembrane subcomplex. In the membrane-embedded T4 coupling complex (T4CC), DotZ makes extensive contacts with DotY and also interacts with the other components DotL, DotM and DotN. The DotLMNYZ components form a hetero-pentameric core of the T4CC complex from which the flexible IcmSW module protrudes. These hetero-pentameric complexes assemble and form an inner membrane channel for effectors to pass through. DotY and DotZ play a role in effector translocation and optimise secretion by modulating the delivery trajectory of the IcmSW module.
Pfam PF21376: Torsin-1A, C-terminal domain (domain)
This domain is found at the C-terminal end of Torsin-1A from humans (TOR1A), an AAA+ ATPase that resides in the endoplasmic reticulum and the contiguous perinuclear space primarily in nerve cells. TOR1A needs the AAA+-like proteins Lamina-associated protein 1 (LAP1) or Luminal domain like LAP1 (LULL1) to catalyze ATP hydrolysis. A single  amino acid deletion in the domain represented in this entry is known to be at the root of primary dystonia, probably by weakening these interactions. This small domain forms a three-helix bundle.
Pfam PF21877: PH domain-like (domain)
This entry represents the NF1 PH domain, a pleckstrin homology (PH)-like domain of potentially novel function discovered within the neurofibromin protein. Neurofibromin is a Ras-specific GTPase-activating protein (RasGAP) encoded by the NF1 gene, mutations in which cause neurofibromatosis type 1 (NF1). The NF1 PH domain forms a bipartite module with the Sec14p homologous segment, which together exhibit phospholipid binding activity. The domain interface architecture suggests a model of how the NF1 PH domain may regulate binding of a ligand by the Sec14 module.
Pfam PF24696: UGSC family (domain)
This entry represents a family of bacterial proteins of unknown function. Some proteins in this family are selenoprotein which are characterised by a UGSC motif where U is a selenocysteine residue. However, this residue is recoded from a stop codon and most matches are split into two distinct gene predictions. The family also includes non-selenoproteins which have a CGSC motif and these appear as full length matches in the alignments.
Pfam PF23670: PIGBOS1-like (family)
This protein family includes human Protein PIGBOS1 and similar sequences from eukaryotes. PIGBOS1 plays a role in the regulation of the unfolded protein response triggered by the endoplasmic reticulum (ER) stress resulting from the presence of unfolded proteins in the ER lumen.
Pfam PF04572: Alpha 1,4-glycosyltransferase conserved region (family)
The glycosphingolipids (GSL) form part of eukaryotic cell membranes. They consist of a hydrophilic carbohydrate moiety linked to a hydrophobic ceramide tail embedded within the lipid bilayer of the membrane. Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common synthetic precursor to the majority of GSL found in vertebrates. Alpha 1.4-glycosyltransferases utilise UDP donors and transfer the sugar to a beta-linked acceptor. This region appears to be confined to higher eukaryotes. No function has been yet assigned to this region.
Pfam PF06199: Phage tail tube protein (family)
Characterised members are major tail tube proteins from various phages, including lactococcal temperate bacteriophage TP901-1.
Pfam PF23482: YLR146W-A (family)
This protein family includes the uncharacterised protein YLR146W-A from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF). This protein is predicted to adopt an alpha-helical structure.
Pfam PF04385: Domain of unknown function, DUF529 (family)
This family represents a repeated region found in several Theileria parva proteins. The repeat is normally about 70 residues long and contains a conserved aromatic  residue in the middle.
Pfam PF01401: Angiotensin-converting enzyme (family)
Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes.
Pfam PF24361: Domain of unknown function (DUF7517) (domain)
This domain is found in a group of uncharacterised metazoan proteins. It is predicted to adopt a structure typical for HTH winged helix domains. This domain is usually found associated with [pfam:PF24359] and [pfam:PF24360].
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 PF21101: YqgU-like 6-bladed beta propeller domain (repeat)
This entry represents a beta propeller domain found in the B. subtilis YqgU protein. The proteins in this family contain an N-terminal lipid attachment motif suggesting they are lipoproteins.
Pfam PF22464: Spike protein P1, first jelly-roll domain (domain)
This entry represents the first jelly-roll domain of Spike protein P1 from Pseudoalteromonas phage PM2.
Pfam PF08122: NADH-ubiquinone oxidoreductase B12 subunit family (family)
This family consists of the NADH-ubiquinone  oxidoreductase B12 subunit proteins. NADH is the  central source of electrons in the mitochondrial  and bacterial respiration. NADH-ubiquinone oxidoreductase is involved in the transfer of  electrons from NADH to the electron transport  chain. This oxidation of NADH is coupled to  proton transfer across the membrane, generating  a proton motive force that is utilised for the  synthesis of ATP. The function of this subunit is unclear.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF11534: Hexameric tyrosine-coordinated heme protein (HTHP) (family)
HTHP is from the marine bacterium Silicibacter pomeroyi and has peroxidase and catalase activity. HTHP consists of six monomers which each binds a solvent accessible heme group and is stabilised by the interaction of three neighbouring monomers. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand.
Pfam PF10154: Ferry endosomal RAB5 effector complex subunit 3 (family)
This entry represents a human Ferry endosomal RAB5 effector complex subunit 3 (Fy-3) and similar sequences from animals and some fungal species. Fy-3 is a component of the FERRY complex (Five-subunit Endosomal Rab5 and RNA/ribosome intermediary), which is involved in the localisation and the distribution of specific mRNAs most likely by mediating their endosomal transport. The complex recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction.
Pfam PF15478: Family of unknown function with LKAAEAR motif (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 119 and 235 amino acids in length. There is a conserved LKAAEAR sequence motif.
Pfam PF00941: FAD binding domain in molybdopterin dehydrogenase (domain)
Oxidoreductases, that also bind molybdopterin, have essentially no similarity outside this common domain. They include aldehyde oxidase (1.2.3.1), that converts an aldehyde and water to an acid and hydrogen peroxide, and xanthine dehydrogenase (1.1.1.204), that converts xanthine to urate. These enzymes require molybdopterin and FAD as cofactors and have and two 2FE-2S clusters. Another enzyme that contains this domain is the Pseudomonas thermocarboxydovorans carbon monoxide oxygenase and nicotine dehydrogenase involved in the degradation of nicotine.
Pfam PF18870: HEPN/RES N-terminal domain 1 (domain)
Mostly alpha helical. Fused to HEPN (MAE_28990 superfamily), RES domain, a potential RNase found in various toxin systems.
Pfam PF22887: Family of unknown function (DUF7022) (family)
This uncharacterised protein is found in the T5 bacteriophage. The function of this protein 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 PF19800: Family of unknown function (DUF6283) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001735) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular  the pentostatine biosynthetic gene cluster from Streptomyces  antibioticus. 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 PF09248: Domain of unknown function (DUF1965) (domain)
Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined.
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 PF23987: Bacteriophage holin Pam3 gp28 family (family)
This family includes Pam3 gp28 which is annotated as a phage holin. These proteins contain two predicted transmembrane helices.
Pfam PF03975: CheD chemotactic sensory transduction (family)
This chemotaxis protein stimulates methylation of MCP proteins. The chemotaxis machinery of Bacillus subtilis is similar to that of the well characterised system of Escherichia coli. However, B. subtilis contains several chemotaxis genes not found in the E. coli genome, such as CheC and CheD, indicating that the B. subtilis chemotactic system is more complex. CheD plays an important role in chemotactic sensory transduction for many organisms. CheD deamidates other B. subtilis chemoreceptors including McpB and McpC. Deamidation by CheD is required for B. subtilis chemoreceptors to effectively transduce signals to the CheA kinase. The structure of a complex between the signal-terminating phosphatase, CheC, and the receptor-modifying deamidase, CheD, reveals how CheC mimics receptor substrates to inhibit CheD and how CheD stimulates CheC phosphatase activity. CheD resembles other cysteine deamidases from bacterial pathogens that inactivate host Rho-GTPases. Phospho-CheY, the intracellular signal and CheC target, stabilises the CheC-CheD complex and reduces availability of CheD. A model is proposed whereby CheC acts as a CheY-P-induced regulator of CheD; CheY-P would cause CheC to sequester CheD from the chemoreceptors, inducing adaptation of the chemotaxis system.
Pfam PF08602: Mgr1-like, i-AAA protease complex subunit (family)
The S. cerevisiae Mgr1 protein has been shown to be required for mitochondrial viability in yeast lacking mitochondrial DNA. It is a mitochondrial inner membrane protein, which interacts with Yme1 and is a new subunit of the i-AAA protease complex.
Pfam PF07509: Protein of unknown function (DUF1523) (family)
This entry is represented by Bacteriophage phiNM3, A0EWY4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Members of this family are mainly found in Proteobacteria. The function of these proteins 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 PF04318: Protein of unknown function (DUF468) (family)
These conserved ORFs probably are probably not translated into protein [Personal communication, Val Wood].
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 PF09345: SiaC family regulatory phosphoprotein (domain)
This entry represents the SiaC family regulatory phosphoprotein which undergoes a regulatory phosphorylation at Thr-68 of founder protein PA0170 from Pseudomonas aeruginosa, but in more distant homologs, T can be S. Also, it is part of motif NTSS, so may contain more than one phosphorylation site. Phosphorylation causes regulatory change to protein-protein interaction, in a pathway that seems broadly distributed, involves a diguanylate cyclase, and in the case of Pseudomonas aeruginosa affects aggregation and biofilm formation responses.
Pfam PF19631: Trypsin-co-occurring domain 2 (domain)
Trypsin-like peptidase effector in the classical NTP-dependent ternary system (vWA-MoxR-VMAP) frequently co-occurs with one of two proteins (Trypco1 or Trypco2) which are mostly mutually exclusively. This entry also includes a member of a biosynthetic gene cluster (BGC).  This BGC (BGC0000949) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the A-500359 A biosynthetic gene cluster from Streptomyces griseus and appears to be predominantly found in bacteria.
Pfam PF02078: Synapsin, N-terminal domain (domain)
This family is structurally related to the PreATP-grasp domain.
Wikipedia: The synapsins are a family of proteins that have long been implicated in the regulation of neurotransmitter release at synapses. Specifically, they are thought to be involved in regulating the number of synaptic vesicles available for release via exocytosis at any one time. Synapsins are present in invertebrates and vertebrates and are strongly conserved across all species. They are expressed in highest concentration in the nervous system, although they also express in other body systems such as the reproductive organs, including both eggs and spermatozoa. Synapsin function also increases as the organism matures, reaching its peak at sexual maturity.
Pfam PF05404: Translocon-associated protein, delta subunit precursor (TRAP-delta) (family)
This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown.
Pfam PF22012: Cytokine receptor-like factor 2, domain 1 (domain)
Cytokine receptor-like factor 2 also known as TSLPR is a receptor for thymic stromal lymphopoietin. It contains two ectodomains with Ig-like topology. This family represents the first of these domains. It also includes domains of interleukin-13 receptor subunit alpha-2 also known as IL-13RA2 that is known to bind with high affinity to interleukin-13.
Pfam PF03643: Vacuolar protein sorting-associated protein 26 (family)
Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking.  In particular, Vps26  assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps29 and Vps35. This family also contains Down syndrome critical region 3/A.
Pfam PF12491: Apolipoprotein B100 C terminal (family)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport.
Pfam PF07233: Protein of unknown function (DUF1425) (family)
This family consists of uncharacterised bacterial proteins mainly found in Proteobacteria, including YcfL from Escherichia coli and Putative lipoprotein from Campylobacter jejuni. This protein adopts a single domain configuration with two beta-sheets formed respectively by three and four beta-strands (beta-sandwich) and contains a Greek key motif, representing a singular variant of the Ig-like fold. Many proteins of this group have a lipid attachment site at the N-terminal of this domain, which together with the structure solved, suggests a role in bacterial lipoproteins.
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 PF00220: Neurohypophysial hormones, N-terminal Domain (family)
C-terminal is in hormone5
Wikipedia: The neurohypophysial hormones form a family of structurally and functionally related peptide hormones. Their representatives in humans are oxytocin and vasopressin. They are named after the location of their release into the blood, the neurohypophysis.
Pfam PF04749: PLAC8 family (family)
This family includes [swissprot:Q9NZF1], the Placenta-specific gene 8 protein.
Pfam PF12406: Surface protein (disordered)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 131 and 312 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.