SII-SWORD/CoKE huggingface dataset:
Pfam PF04419: Small EDRK-rich factor 1/2-like, N-terminal (disordered)
Members of this entry are short proteins that are rich in aspartate, glutamate, lysine and arginine that are found to be ubiquitously expressed. This entry represents the N-terminal region of small EDRK-rich factors (SERFs), including SERF1 (UniProt:O75920), SERF2 from human, and similar proteins. This region appears to be found at the N-terminus of some longer proteins. Many proteins contain a C-terminal zinc finger domain [pfam:PF12907]. SERF1/2 are positive regulators of amyloid protein aggregation and proteotoxicity; they induce conformational changes in amyloid proteins, driving them into compact formations preceding the formation of aggregates.
Pfam PF07904: Chromatin modification-related protein EAF7 (family)
The S. cerevisiae member of this family [swissprot:P53911] is part of NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae involved in global histone acetylation.
Pfam PF19516: Family of unknown function (DUF6049) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in Actinobacteria. Proteins in this family are typically between 695 and 823 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 PF00484: Carbonic anhydrase (domain)
This family includes carbonic anhydrases as well as a family of non-functional homologues related to YbcF.
Pfam PF17169: MIT domain of nuclear receptor-binding factor 2 (domain)
This MIT domain is the microtubule interaction and trafficking of nuclear receptor-binding factor 2 - NRBF2 - in higher eukaryotes. It is a coiled-coil region at the N-terminus of [pfam:PF08961]. NRBF2 plays an essential role in autophagy, the cellular pathway that degrades long-lived proteins and other cytoplasmic contents through lysosomes.  NRBF2 binds Atg14L - a Beclin-binding protein - directly via the MIT domain and enhances Atg14L-linked Vps34 kinase (a class III phosphatidylinositol-3 kinase) activity and autophagy induction.
Pfam PF09420: Ribosome biogenesis protein Nop16 (family)
Nop16 is a protein involved in ribosome biogenesis.
Pfam PF06783: Uncharacterised protein family (UPF0239) (family)
This is a group of transmembrane proteins of unknown function.
Pfam PF14854: Leucine rich adaptor protein (family)
This family of proteins activate the canonical NF-kappa-B pathway, promote proinflammatory cytokine production and promote the antigen presenting and priming functions of dendritic cells.
Pfam PF09322: Domain of unknown function (DUF1979) (family)
Members of this family of functionally uncharacterised domains are found in various Oryza sativa mutator-like transposases.
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 PF07473: Spasmodic peptide gm9a; conotoxin from Conus species (family)
This family consists of several spasmodic peptide gm9a sequences. Conotoxin gm9a is a putative 27-residue polypeptide encoded by Conus gloriamaris and is known to be a homologue of the 'spasmodic peptide', tx9a, isolated from the venom of the mollusc-hunting cone shell Conus textile. Upon injection of this venom component, normal mice are converted into behavioural phenocopies of a well-known mutant, the spasmodic mouse.
Pfam PF01706: FliG C-terminal domain (domain)
FliG is a component of the flageller rotor, present in about 25 copies per flagellum.  This domain functions specifically in motor rotation.
Wikipedia: In molecular biology, the flagellar motor switch protein (Flig) is one of three proteins in certain bacteria coded for by the gene fliG. The other two proteins are FliN coded for by fliN, and FliM coded for by fliM. The protein complex regulates the direction of flagellar rotation and hence controls swimming behaviour. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce a switch in the flagellar motor direction of rotation.
Pfam PF09042: Titin Z (domain)
The titin Z domain, that recognises and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34. This interaction is essential for sarcomere assembly.
Pfam PF18856: Bacterial archaeo-eukaryotic release factor family 12 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pfam PF05741: Nanos RNA binding domain (family)
This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded  very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development.
Pfam PF00662: NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus (domain)
This entry represents an amino terminal extension of [pfam:PF00361]. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. 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.
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 PF04174: A circularly permuted ATPgrasp (family)
An ATP-grasp family that is present both as catalytically active and inactive versions. Contextual analysis suggests that  it functions in a distinct peptide synthesis/modification system that additionally contains a transglutaminase, an NTN-hydrolase, the Alpha-E domain, and a transglutaminase fused N-terminal to a  circularly permuted COOH-NH2 ligase. The inactive forms are often  fused N-terminal to the Alpha-E domain.
Pfam PF08465: Thymidine kinase from Herpesvirus C-terminal (family)
This domain is found towards the C terminus in Herpesvirus Thymidine kinases.
Pfam PF04555: Restriction endonuclease XhoI (family)
This family consists of type II restriction enzymes ([ec:3.1.21.4]) that recognise the double-stranded sequence CTCGAG and cleave after C-1.
Wikipedia: In molecular biology, XhoI is a type II restriction enzyme EC that recognise the double-stranded DNA sequence CTCGAG and cleaves after C-1. Type II restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
Pfam PF02723: Coronavirus small envelope protein E (family)
This family includes E proteins, well conserved among Coronavirus strains. They are small, integral membrane proteins involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. They act as a viroporin by oligomerizing after insertion in host membranes to create a hydrophilic pore that allows ion transport. SARS-CoV E protein forms a Ca2+ permeable channel in the endoplasmic reticulum Golgi apparatus intermediate compartment (ERGIC)/Golgi membranes. The E protein ion channel activity alters Ca2+ homeostasis within cells boosting the activation of the NLRP3 inflammasome, leading to the overproduction of IL-beta. SARS-CoV overstimulates the NF-kappaB inflammatory pathway, triggering p38 MARK activation. CoV E proteins have a short hydrophilic N terminus, followed by a large hydrophobic transmembrane (TM) domain, and end with a long, hydrophilic C-terminal which comprises the majority of the protein. The hydrophobic region of the TM domain contains at least one predicted amphipathic alpha-helix that pentamerizes to form an ion-conductive pore in membranes. CoV E proteins are involved in the secretory pathway, altering lumenal environments and rearranging secretory organelles and leading to efficient trafficking of virions, and they may also play a role protein-protein interactions and targeting, among other roles.
Pfam PF08837: Protein of unknown function (DUF1810) (family)
This is a family of uncharacterised proteins.  The structure of one of the members in this family has been solved and it adopts a mainly alpha helical 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 PF19677: Family of unknown function (DUF6179) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001520) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from  the aurantinin B biosynthetic gene cluster from Bacillus subtilis. This family appears to be predominantly found in firmicutes.
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 PF10045: Uncharacterized conserved protein (DUF2280) (family)
Members of this family of hypothetical bacterial proteins have 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 PF19407: Domain of unknown function (DUF5979) (domain)
This domain is found as tandem repeats in bacterial cell surface proteins, associated with TED adhesive domains. This domain contains a conserved lysine, glutamic acid and asparagine diagnostic of an intradomain isopeptide bond.
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 PF05926: Phage head completion protein (GPL) (family)
This family consists of several phage head completion protein (GPL) as well as related bacterial sequences. Members of this family allow the completion of filled heads by rendering newly packaged DNA in the heads resistant to DNase. The protein is thought to bind to DNA filled capsids.
Pfam PF18233: Cdc13 OB4 dimerization domain (domain)
This domain is found in Cdc13 proteins in several Candida species. The Cdc13-Stn1-Ten1 complex is crucial for telomere protection. This domain is the C-terminal OB4 domain and is responsible for dimerization. Dimerization of Cdc13 is important for high-affinity DNA binding.
Pfam PF23864: Domain of unknown function (DUF7222) (domain)
This entry represents a family of uncharacterised proteins found in various cyanophages, bacteriophages and bacteria species. The domain is approximately 100-160 amino acids in length. Structure prediction shows this domain is alpha helical.
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 PF23773: Domain of unknown function (DUF7169) (domain)
This domain family consists of a group of uncharacterized proteins, typically between 99 to 116 amino acids in length, found in bacteriophages that infect Microbacterium and Arthrobacter bacterial hosts. These proteins are encoded in the genomes of phages belonging to the Caudoviricetes class, primarily within the families Azeevirinae, Dismasvirus, Yangvirus, Manhattanvirus, Liebevirus, Zetavirus, and Armstrongvirus. An AlphaFold prediction shows these proteins are composed of two alpha helices. AlphaFold also predicts that these proteins likely form homodimers.
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 PF07744: SPOC domain (domain)
The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling.
Pfam PF18772: APOBEC2 (family)
APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most vertebrates including cartilaginous fishes. APOBEC2 is poorly understood in terms of their molecular functions and substrate specificity.
Pfam PF04071: Cysteine-rich small domain (family)
Probable metal-binding domain.
Pfam PF07961: MBA1-like protein (domain)
Mba1 is an inner membrane protein that is part of the mitochondrial protein export machinery.  It binds to the large subunit of mitochondrial ribosomes and cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C-terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70.  It is proposed that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane.
Pfam PF03434: DUF276 (family)
This family is specific to Borrelia burgdorferi.  The protein is encoded on extra-chromosomal DNA.                  This domain 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 PF10119: Predicted methyltransferase regulatory domain (family)
Members of this family of domains are found in various prokaryotic methyltransferases, where they regulate the activity of the methyltransferase domain.
Pfam PF02591: C4-type zinc ribbon domain (domain)
Zn-ribbon_9 is a Zn-ribbon domain rich in aromatic and positively charged amino acid residues. This C-terminal Zn-ribbon domain consists of two beta-strands acting as a scaffold for the two Zn knuckles. Both pairs of cysteines making up the two Zn knuckles are situated at highly conserved sharp beta-turns, an arrangement that facilitates the tetrahedral coordination of the divalent Zn ion. The two Zn-knuckle cysteine motifs are separated by 20 residues, 9 of which form an alpha-helix (helix 4).Structural modelling suggests this domain may bind nucleic acids. The domain appears to bind flaA-mRNA, thus contributing to flagellum formation and motility.
Pfam PF22033: Inner capsid protein lambda-1/VP3 (domain)
The reovirus inner capsid protein lambda-1 displays nucleoside triphosphate phosphohydrolase (NTPase),RNA-5'-triphosphatase (RTPase), and RNA helicase activity and may play a role in the transcription of the virus genome, the unwinding or reannealing of double-stranded RNA during RNA synthesis. Lambda1 is an Orthoreovirus core protein, VP3 is the homologous core protein in Aquareoviruses.
Pfam PF21598: Restriction endonuclease PvuRts1 I-like, N-terminal (domain)
This domain is found at the N-terminal end of Restriction endonuclease PvuRts1 I from Proteus vulgaris and similar bacterial sequences. PvuRts1I a modification-dependent endonuclease with high selectivity for 5-hydroxymethylcytosine, an epigenetic marker that is crucial for multiple biological processes, over 5-methylcytosine and cytosine. This protein is organised into a nuclease domain (this entry) and a C-terminal SRA domain ([pfam:PF18491]). This domain adopts a typical three- layered alpha-beta-alpha sandwich configuration, with a central five-stranded beta-sheet surrounded by three alpha-helices on one side and one alpha-helix on the other side.
Pfam PF04712: Radial spokehead-like protein (family)
This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologues, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene.
Pfam PF10910: Phage gene 29 protein family (family)
This entry represents a family of phage proteins related to gene 29 protein from Mycobacterium phage D29 and L5. The function of the proteins in this family is unknown. AlphaFold multimer shows that the proteins in the family adopt a confident dimeric structure. The individual proteins are not compact in isolated structure predictions.
Pfam PF06430: Lactococcus lactis RepB C-terminus (family)
This family consists of the C-terminal region of RepB proteins from Lactococcus lactis (See [pfam:PF01051]).
Pfam PF06467: MYM-type Zinc finger with FCS sequence motif (domain)
MYM-type zinc fingers were identified in MYM family proteins. Human protein [swissprot:Q14202] is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1. [swissprot:Q9UBW7] is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1; in atypical myeloproliferative disorders it is rearranged. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons.
Pfam PF04205: FMN-binding domain (domain)
This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins. This domain is post-translationally flavinylated that may facilitate electron transfer, and thus, resembles multiheme cytochromes.
Pfam PF10708: Protein of unknown function (DUF2510) (family)
This is family of proteins conserved in Actinobacteria. Many members are annotated as putative membrane proteins but this could not be confirmed.
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 PF13126: Protein of unknown function (DUF3975) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length.
Pfam PF10241: Uncharacterized conserved protein (domain)
This is a family of short proteins which are conserved over a region of 80 residues.  There is a characteristic KxDL motif towards the C-terminus.  The function is unknown.
Pfam PF24845: Domain of unknown function (DUF7721) (domain)
This domain is found in uncharacterised proteins from fungi. It is predicted to adopt globular structure consisting of array of helices.
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 PF19291: Trehalase-like, N-terminal (domain)
This presumed domain is found at the N-terminal region of bacterial and archaeal trehalases which catalyse the hydrolysis of alpha,alpha-trehalose into two molecules of D-glucose, followed by the glycoside hydrolase domain ([pfam:PF00723]). This domain is also found in the uncharacterised protein C4H3.03c from S. pombe. The function of this domain is not clear.
Pfam PF10985: Protein of unknown function (DUF2805) (family)
This is a bacterial family of proteins with unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.