SII-SWORD/CoKE huggingface dataset:
Pfam PF06279: Protein of unknown function (DUF1033) (family)
This family consists of several hypothetical bacterial proteins. Many of the sequences in this family are annotated as putative DNA binding proteins but 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 PF25055: Domain of unknown function (DUF7792) (domain)
This domain is found N-terminal in uncharacterised eukaryotic proteins. It has detectable similarity to domains members of the MLKL N-terminal domain superfamily and 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 PF19275: HflX C-terminal domain (domain)
This entry represents the C-terminal domain of the HflX protein. HflX binds to the intersubunit face of the 50S subunit. Its C-terminal domain (CTD) predominantly interacts with the NTD of uL11 at the bL12 stalk base.  Truncation of the CTD rendered HflX inactive in 70S splitting.
Pfam PF04463: 2-thiouracil desulfurase (family)
This family of proteins, predominantly found in Bacteria, are involved in the desulfuration of 2-thiouracil into uracil in the 2-thiouridine degradation pathway. It has been demonstrated that these proteins contain a Fe-S cluster required for their activity.
Pfam PF17327: Acyl homoserine lactone synthase (family)
Members of this family are involved in quorum sensing processes. In gram negative bacteria, N-acylhomoserine lactones (AHLs) act as signals. As the bacterial density increases, AHLs accumulate, and once they reach a critical level (quorum), they interact with cognate receptor proteins, which then affect target gene expression. Some AHLs are synthesized by LuxM (AHL synthase) and homologs (VanM and opaM). LuxM enzymes use S-adenosyl-methionine (SAM) as one of its two substrates and are capable of using either acyl-acyl-carrier-protein (acyl-ACP) or acyl-coenzyme A (acyl-CoA) as the other substrate. VanM, the LuxM homolog, produces two auto-inducers C6HSL and 3OC6HSL. Both autoinducers are detected by the VanN receptor. The autoinducers HAI-1, is synthesized by the cytoplasmic enzymes LuxM.
Wikipedia: Acyl-homoserine-lactone synthase is an enzyme with systematic name acyl-(acyl-carrier protein):S-adenosyl-L-methionine acyltranserase . This enzyme catalyses the following chemical reactionacyl-[acyl-carrier protein] + S-adenosyl-L-methionine  [acyl-carrier protein] + S-methyl-5'-thioadenosine + N-acyl-L-homoserine lactone
Pfam PF03105: SPX domain (domain)
We have named this region the SPX domain after SYG1, Pho81 and XPR1. This 180 residue long domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 [swissprot:P17442] from Saccharomyces cerevisiae and NUC-2 [swissprot:Q01317] from Neurospora crassa, are also members of this family.  The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats [pfam:PF00023]. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine xenotropic and polytropic leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signalling and result in cell toxicity and death.  The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae, and many other diverse organisms. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor.
Pfam PF10883: Protein of unknown function (DUF2681) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 117 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 PF00173: Cytochrome b5-like Heme/Steroid binding domain (domain)
This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors such as [swissprot:O00264]. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases.  There is no known ligand for this domain in the chitin synthases.
Wikipedia: Cytochromes b5 are ubiquitous electron transport hemoproteins found in animals, plants, fungi and purple phototrophic bacteria. The microsomal and mitochondrial variants are membrane-bound, while bacterial and those from erythrocytes and other animal tissues are water-soluble. The family of cytochrome b5-like proteins includes hemoprotein domains covalently associated with other redox domains in flavocytochrome cytochrome b2, sulfite oxidase, plant and fungal nitrate reductases, and plant and fungal cytochrome b5/acyl lipid desaturase fusion proteins.
Pfam PF20472: PD-(D/E)XK nuclease superfamily domain (domain)
This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily.
Pfam PF14383: DUF761-associated sequence motif (domain)
This family is found frequently at the N-terminus of family DUF3741, [pfam:PF12552].
Pfam PF05567: PilY1 beta-propeller domain (repeat)
This domain is found in homologues of Type IV pilus biogenesis factor PilY1. PilY1 is involved in pilus assembly, twitching motility and adhesion to host cells. It regulates surface-activated virulence possibly by acting as a surface-attachment mechanosensor. This domain has been shown to adopt a beta--propeller structure.
Pfam PF21277: Type VI secretion system spike protein VgrG3-like, C-terminal (domain)
This domain is found in a group of proteins from tailed bacteriophages and prophages mainly found in proteobacteria, including Type VI secretion system spike protein VgrG3 from Vibrio cholerae. VgrG3 degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region through its muramidase activity. This domain adopts a canonical phage- T4-lysozyme-like fold showing eight alpha-helices and two 3-10 helices, which pack against a three-stranded antiparallel beta-sheet.
Pfam PF02282: DNA polymerase processivity factor (UL42) (domain)
The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerisation and makes little contribution to the catalytic activity of the  polymerase.
Pfam PF23590: CCR4-NOT transcription complex subunit 1, NOT1_connector (repeat)
This entry represents a region of human CCR4-NOT transcription complex subunit 1 (CNOT1), an scaffolding component of the CCR4-NOT complex, which is one of the major cellular mRNA deadenylases. This region shows several repeats of the HEAT type.
Pfam PF16710: N-terminal N1 domain of Vibrio phage CTXphi pIII (domain)
CTXphi_pIII-N1 is the N-terminal domain, N1, of the pIII protein of the CTXphi bacteriophage of Vibrio cholerae. CTXphi is a ssDNA Inovirus. pIII is a minor coat protein. This domain interacts directly with the C-terminus of TolA, a periplasmic protein of Vibrio cholerae itself as part of the infection mechanism.
Pfam PF15761: Immortalisation up-regulated protein (disordered)
This family of proteins is found in eukaryotes. Proteins in this family are approximately 100 amino acids in length. There are two conserved sequence motifs: GDPK and KKPK.
Pfam PF00304: Gamma-thionin family (domain)
Wikipedia: Plant defensins are a family of primitive, highly stable, cysteine-rich defensins found in plants that function to defend them against pathogens and parasites. Defensins are integral components of the innate immune system and belong to the ancient superfamily of antimicrobial peptides (AMPs). AMPs are also known as host defense peptides (HDPs), and they are thought to have diverged about 1.4 billion years ago before the evolution of prokaryotes and eukaryotes. They are ubiquitous in almost all plant species, functionally diverse, and their primary structure varies significantly from one species to the next, except for a few cysteine residues, which stabilize the protein structure through disulfide bond formation. Plant defensins usually have a net positive charge due to the abundance of cationic amino acids and are generally divided into two classes. Those in the class II category contain a C-terminal pro-peptide domain of approximately 33 amino acids and are targeted to the vacuole, while the class I defensins lack this domain and mature in the cell wall. Unlike their class I counterparts, class II plant defensins are relatively smaller, and their acidic C-terminal prodomain is hypothesized to contribute to their vacuolar targeting. The first plant defensins were discovered in barley and wheat in 1990 and were initially designated as γ-thionins. In 1995, the name was changed to 'plant defensin' when it was identified that they are evolutionarily unrelated to other thionins and were more similar to defensins from insects and mammals.
Pfam PF23569: SMAX1 nucleotide binding domain (domain)
This domain is found in a number of SMAX1-like proteins and in the chaperone protein ClpB. SMAX1-like proteins are thought to be components of a transcriptional corepressor complex whereas ClpB is a part of a stress-induced multi-chaperone system and it is involved in the recovery of the cell from heat-induced damage. In ClpB from T. thermophilus, this domain is involved in ATP binding and contributes to the ATPase activity. It has significant sequence and structural similarity to other known AAA+ nucleotide binding domains.
Pfam PF02393: US22 like (family)
US22 proteins have been found across many animal DNA viruses and some vertebrates. The name sake of this family US22 [swissprot:P09722] is an early nuclear protein that is secreted from cells.  The US22 family may have a role in virus replication and pathogenesis. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is  homologous to several other families like SMI1 and SYD (commonly  called SUKH superfamily). Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins.
Pfam PF08812: YtxC-like family (family)
This family includes proteins similar to B. subtilis YtxC an uncharacterised protein.
Pfam PF25108: YMR265C C-terminal (domain)
This is the presumed C-terminal domain of the uncharacterised yeast protein YMR265C, which has a HAD domain at the N-terminal, found in Swiss Army Knife RNA repair proteins. The function of this domain is unknown.
Pfam PF02550: Acetyl-CoA hydrolase/transferase N-terminal domain (domain)
This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase [ec:3.1.2.1] ([swissprot:P32316]) catalyses the formation of acetate from acetyl-CoA, CoA transferase (CAT1) [ec:2.8.3.-] ([swissprot:P38946]) produces succinyl-CoA, and acetate-CoA transferase [ec:2.8.3.8] ([swissprot:Q59323]) utilises acyl-CoA and acetate to form acetyl-CoA.
Pfam PF03706: Lysylphosphatidylglycerol synthase TM region (family)
LPG_synthase_TM is the N-terminal region of this family of bacterial phosphatidylglycerol lysyltransferases. The function of the family is to add lysyl groups to membrane lipids, and this region is the transmembrane domain of 7xTMs. In order to counteract attack by membrane-damaging external cationic antimicrobial molecules - from host immune systems, bacteriocins, defensins, etc - bacteria modify their anionic membrane phosphatidylglycerol with positively-charged L-lysine; this results in repulsion of the foreign cationic peptides.
Pfam PF24900: Zinc finger MYM-type protein 4-like, (domain)
This domain is found in human Zinc finger MYM-type protein 4 (ZMYM4), which plays a role in the regulation of cell morphology and cytoskeletal organisation.
Pfam PF04729: ASF1 like histone chaperone (family)
This family includes the yeast and human ASF1 protein.  These proteins have histone chaperone activity.  ASF1 participates in both the replication-dependent and replication-independent pathways.  The structure three-dimensional has been determined as a a compact immunoglobulin-like beta sandwich fold topped by three helical linkers.
Wikipedia: In molecular biology, the ASF1 like histone chaperone family of proteins includes the yeast and human ASF1 proteins. These proteins are of the chaperone protein group and in particular can be placed into the histone chaperone subgroup. ASF1 participates in both the replication-dependent and replication-independent pathways. The three-dimensional structure has been determined as a compact immunoglobulin-like beta sandwich fold topped by three helical linkers.
Pfam PF24245: INO80 complex subunit F (domain)
This entry represents the helical region from INO80 subunit F (also known as TCF3 fusion partner, TFTP or amida) from vertebrates. It plays an important role in p53-independent cellular apoptosis and it also plays a role in cell arrest and spermatogenesis. It is likely a regulatory component of the chromatin remodelling INO80 complex. This entry also includes the orthologues from S.pombe Hap2 (SwissProt:Q9P7Z9) and Ino80 complex HMG box subunit Nht1 (SwissProt:O42648).
Pfam PF01825: GPCR proteolysis site, GPS, motif (conserved_site)
The GPS motif is found in GPCRs, and is the site for auto-proteolysis, so is thus named, GPS. The GPS motif is a conserved sequence of ~40 amino acids containing canonical cysteine and tryptophan residues, and is the most highly conserved part of the domain. In most, if not all, cell-adhesion GPCRs these undergo autoproteolysis in the GPS between a conserved aliphatic residue (usually a leucine) and a threonine, serine, or cysteine residue. In higher eukaryotes this motif is found embedded in the C-terminal beta-stranded part of a GAIN domain - GPCR-Autoproteolysis INducing (GAIN). The GAIN-GPS domain adopts a fold in which the GPS motif, at the C-terminus, forms five beta-strands that are tightly integrated into the overall GAIN domain. The GPS motif, evolutionarily conserved from tetrahymena to mammals, is the only extracellular domain shared by all human cell-adhesion GPCRs and PKD proteins, and is the locus of multiple human disease mutations. The GAIN-GPS domain is both necessary and sufficient functionally for autoproteolysis, suggesting an autoproteolytic mechanism whereby the overall GAIN domain fine-tunes the chemical environment in the GPS to catalyse peptide bond hydrolysis. In the cell-adhesion GPCRs and PKD proteins, the GPS motif is always located at the end of their long N-terminal extracellular regions, immediately before the first transmembrane helix of the respective protein.
Pfam PF21773: ODAD1 central coiled coil region (domain)
This domain, previously know as DUF6872, is found in Outer dynein arm-docking complex subunit 1 (ODAD1, CCDC114) from humans and similar eukaryotic proteins. In mammals, CCDC114 forms a hetero-coiled coil with ODAD1/CCDC151 within the A07/A08 interprotofilament cleft, analogous to the DC1/2 coiled coil of the trimeric ODA-DC observed in C. reinhardtii axoneme. DC2 is a homolog of the human ODAD1/CCDC151 and in C.reinhardtii it is a part of the ODA-DC that consists of three proteins: DC1, DC2, and DC3. The N-terminal halves of DC1 and DC2 form a microtubule-bound heteromeric coiled-coil.
Pfam PF02653: Branched-chain amino acid transport system / permease component (family)
This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH [swissprot:P08340] and LivM  [swissprot:P22729] both of which are form the LIV-I transport system. Also found with in this family are proteins from the galactose transport system permease and a ribose transport system.
Pfam PF03656: Pam16 (family)
The Pam16 protein ([swissprot:P42949]) is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM).  In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane.  Pam16 has a degenerate J domain.  J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle.  Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel.  Pam18 stimulates the ATPase activity of mtHsp70.
Pfam PF03715: Noc2p family (family)
At least one member, Noc2p from yeast, is required for a late step in 60S subunit export from the nucleus. It has also been shown to co-precipitate with Nug1p, a nuclear GTPase also required for  ribosome nucleus export. This family was formerly known as UPF0120.
Pfam PF16681: Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain (domain)
Ig_5 is an immunoglobulin domain found on T-cell surface glycoprotein CD3 epsilon chain. It forms a first-order complex with T-cell surface glycoprotein CD3 delta chain as part of the T-cell receptor complex.
Wikipedia: The immunoglobulin domain, also known as the immunoglobulin fold, is a type of protein domain that consists of a 2-layer sandwich of 7-9 antiparallel β-strands arranged in two β-sheets with a Greek key topology, consisting of about 125 amino acids.
Pfam PF22084: Ufm1 specific protease UfSP N-terminal MPN domain (domain)
UfSP is a cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. UfSP from C. elegans consists of three domains: MPN domain, N-domain and a catalytic domain. This entry represents the MPN domain that forms an alpha/beta globular structure with a central mixed beta-sheet packed on both sides with helices and a pair of two strands and a helix. This domain modulates both substrate recognition and deufmylation activity.
Pfam PF11735: Cryptococcal mannosyltransferase 1 (family)
The capsule of pathogenic fungi is a complex polysaccharide whose formation is determined by a number of enzymes including, most importantly, alpha-1,3-mannosyltransferase 1, [ec:2.4.1.-].
Pfam PF21681: Type-I-A Cascade subunit Csa5 (family)
This group of archaeal proteins includes CRISPR type I-A cluster 1/Apern-associated protein Csa5-1 from Saccharolobus solfataricus (Csa5), the small subunit of the archaeal-specific Type-I-A Cascade complex for CRISPR-mediated antiviral immunity. This protein consists of two domains: an all alpha-helical arrangement and an insertion that shows a single helix and six beta-strands arranged as three anti-parallel two-stranded beta-sheets.
Pfam PF12286: Protein of unknown function (DUF3622) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
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 PF06584: DIRP (family)
DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of fruit fly and mustard weed. Studies of lin-9  and  aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway.
Pfam PF18219: SidC N-terminal domain (domain)
This is the N-terminal domain of SidC present in Legionella pneumophilia. SidC appears to be involved in modulating mammalian trafficking by promoting the communication between ER-derived vesicles and the Legionella containing vacuole. The N-terminal domain (SidC-N) has a novel fold with 4 potential subdomains. SidC-N does not show structural similarity to any known protein domain in the protein data bank.
Pfam PF12000: Glycosyl transferase family 4 group (family)
This domain is found associated with [pfam:PF00534].
Pfam PF24844: DNA polymerase II large subunit DP2, central domain (domain)
This entry represents the central domain of DNA polymerase II large subunit from Pyrococcus abyssi (PolC) and similar sequences mainly found in archaea. This domain, which is found C-terminal to [pfam:PF03833], shows an alpha-beta configuration.
Pfam PF19367: Domain of unknown function (DUF5943) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in proteobacteria and sporadically in archaea, and is approximately 100 amino acids in length. There are two conserved sequence motifs: NNH and RLS. This domain is often found to the N-terminus of [pfam:PF02830].
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 PF18301: pre ATP-grasp 3 domain (domain)
This domain is found just before the N-terminal of the ATP grasp 3 domain ([pfam:PF02655]). The domain is carried by species such as Azospirillum brasilense and Methylobacter tundripaludum.
Pfam PF08144: CPL (NUC119) domain (repeat)
This C-terminal domain is found in Penguin-like proteins associated  with Pumilio like repeats.