SII-SWORD/CoKE huggingface dataset:
Pfam PF22791: Domain of unknown function (DUF7011) (domain)
This domain of unknown function is found in a group of proteins predominantly from proteobacteria. It has a LxHDGK/RRL motif and a highly conserved W residue.
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 PF11845: Tll0287 (domain)
This entry includes Tll0287 protein from Thermosynechococcus vestitus ([swissprot:Q8DM36]) and similar bacterial proteins. Tll0287 is a c-type heme protein that shows a beta-sheet with four antiparallel beta-strands surrounded by five alpha-helices. This structure is similar to some kinases and sensor proteins, but its specific function is unknown.
Pfam PF09266: Viral DNA topoisomerase I, N-terminal (domain)
Members of this family are predominantly found in viral DNA topoisomerase, and assume a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3.
Pfam PF19263: Family of unknown function (DUF5906) (family)
This is a family of proteins of unknown function found in viruses. This family is a P-loop member whose proteins are thought to be SF3 helicases, which are involved in replication initiation.
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 PF11476: Toxoplasma gondii micronemal protein 1 TgMIC1 (domain)
TgMIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex which consists of TgMIC4-MIC1-MIC6 participates in host cell attachment and penetration and is critical in invasion. This is the C terminal domain of TgMIC1 which has a Galectin-like fold which interacts with and stabilises TgMIC6 providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes.
Pfam PF08792: A2L zinc ribbon domain (domain)
This zinc ribbon domain is found associated with some viral A2L transcription factors.
Pfam PF17612: Family of unknown function (DUF5507) (family)
This is a family of unknown function found in Escherichia.
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 PF22873: Out at first, C-terminal (domain)
This entry represents the putative C-terminal cysteine-rich mature peptide found in OAF proteins.
Pfam PF05456: Eukaryotic translation initiation factor 4E binding protein (EIF4EBP) (family)
This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1 ,2 and 3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognised by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F.
Pfam PF15436: Plasminogen-binding protein pgbA N-terminal (family)
PGBA_N is an N-terminal family of bacterial proteins that bind plasminogen. This activity was identified in In Helicobacter pylori where it is thought to contribute to the virulence of this bacterium. Both PgbA and PgbB are surface-exposed proteins that mediate binding to plasminogen such that it can be converted into plasmin in the presence of a Pg activator.
Pfam PF14446: Prokaryotic RING finger family 1 (family)
RING finger family found sporadically in bacteria and archaea, and  associated in gene neighborhoods with other components of the  ubiquitin-based signaling and degradation system, including ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase.  The bacterial versions contain transmembrane helices.
Pfam PF23632: RNF34/RFFL SAP domain (domain)
This entry represents the SAP domains found in the RNF34/RFFL protein family.  The RNF34/RFFL protein family consists of E3 ubiquitin-protein ligases that play a crucial role in various biological processes by mediating the ubiquitin-mediated proteasomal degradation of target proteins. Members of this family are involved in the regulation of apoptosis by ubiquitinating and promoting the degradation of caspases CASP8 and CASP10. They also participate in the regulation of the tumor necrosis factor-mediated signaling pathway, mainly through the 'Lys-48'-linked polyubiquitination and degradation of RIPK1. Additionally, they have a role in the negative regulation of p53/TP53, either directly through ubiquitination or indirectly via the degradation of SFN. Some family members are implicated in metabolic regulation by targeting PPARGC1A for degradation, influencing brown fat cell metabolism, and in innate immunity by the ubiquitination of NOD1. Furthermore, the RFFL subset of proteins is involved in endocytic recycling, highlighting the diversity of functions within the family.
Pfam PF21385: Acetyl-CoA carboxylase, BT domain (domain)
This is the BC-CT interaction domain (BT) which is between the BC (biotin carboxylase, which catalyses the MgATP-dependent carboxylation of N1' atom of biotin) and BCCP (biotin carboxyl carrier protein) domains of Acetyl-CoA carboxylase. This domain helps to mediate interactions between the BC and CT (carboxyltransferase) domains.
Pfam PF05864: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7) (family)
This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA.
Pfam PF03713: Domain of unknown function (DUF305) (domain)
Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1.  This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important.  This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha 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 PF24241: Putative cytidine deaminase, C-terminal domain (domain)
This domain is found at the C-terminal end of a group of sequences from proteobacteria. Foldseek predicts high structure similarity of this domain with Cytidine deaminases.
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 PF06970: Replication initiator protein A (RepA) N-terminus (family)
This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Pfam PF05711: Macrocin-O-methyltransferase (TylF) (domain)
This family consists of bacterial macrocin O-methyltransferase (TylF) proteins. TylF is responsible for the methylation of macrocin to produce tylosin. Tylosin is a macrolide antibiotic used in veterinary medicine to treat infections caused by Gram-positive bacteria and as an animal growth promoter in the swine industry. It is produced by several Streptomyces species. As with other macrolides, the antibiotic activity of tylosin is due to the inhibition of protein biosynthesis by a mechanism that involves the binding of tylosin to the ribosome, preventing the formation of the mRNA-aminoacyl-tRNA-ribosome complex. The structure of one representative sequence from this family, NovP, shows it to be an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyses the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic. It is likely that the key structural features of NovP are common to the rest of the family and include: a helical 'lid' region that gates access to the co-substrate binding pocket and an active centre that contains a 3-Asp putative metal binding site. A further conserved Asp probably acts as the general base that initiates the reaction by de-protonating the 4-OH group of the noviose unit.
Pfam PF09524: Conserved phage C-terminus (Phg_2220_C) (domain)
This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Pfam PF11012: Protein of unknown function (DUF2850) (family)
This family of proteins with unknown function appear to be restricted to Vibrionaceae.
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 PF03586: Herpesvirus UL36 tegument protein (family)
The UL36 open reading frame (ORF) encodes the largest herpes simplex virus type 1 (HSV-1) protein, a 270-kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells. This family only covers a small central part of this large protein.
Pfam PF13614: AAA domain (domain)
This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF03159: XRN 5'-3' exonuclease N-terminus (family)
This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity [ec:3.1.11.-]. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus.
Pfam PF01207: Dihydrouridine synthase (Dus) (domain)
Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA.  Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae.  Most dihydrouridines are found in the D loop of t-RNAs.  The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap.  Dus 1 ([swissprot:Q9HGN6]) from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 ([swissprot:P53720]) acts on pre-tRNA-Tyr and pre-tRNA-Leu.  Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD.  Some family members may be targeted to the mitochondria and even have a role in mitochondria.
Wikipedia: In molecular biology, tRNA-dihydrouridine synthase is a family of enzymes which catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.
Pfam PF10425: C-terminus of bacterial fibrinogen-binding adhesin (domain)
This is the C-terminal half of a bacterial fibrinogen-binding adhesin SdrG. SdrG is a Gram-positive cell-wall-anchored adhesin that allows attachment of the bacterium to host tissues via specific binding to the beta-chain of human fibrinogen (Fg). SdrG binds to its ligand with a dynamic "dock, lock, and latch" mechanism which represents a general mode of ligand-binding for structurally related cell wall-anchored proteins in most Gram-positive bacteria. The C-terminal part of SdrG(276-596) is integral to the folding of the immunoglobulin-like whole to create the docking grooves necessary for Fg binding. The domain is associated with families of Cna_B, [pfam:PF05738].
Wikipedia: In molecular biology, the protein domain SdrG C terminal refers to the C terminus domain of an adhesin found only on the cell walls of bacteria. More specifically, SdrG is only found in gram-positive bacteria. This particular domain binds to a glycoprotein named fibrinogen. SdrG stands for serine-aspartate dipeptide repeats, which as its name suggests, contains repeats of two amino acids, serine and aspartate.
Pfam PF13422: Domain of unknown function (DUF4110) (family)
This is a family that is found predominantly at the C-terminus of Kelch-containing proteins. However, the exact function of this region 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 PF00012: Hsp70 protein (family)
Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release.  Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.
Wikipedia: The 70 kilodalton heat shock proteins are a family of conserved ubiquitously expressed heat shock proteins. Proteins with similar structure exist in virtually all living organisms. Intracellularly localized Hsp70s are an important part of the cell's machinery for protein folding, performing chaperoning functions, and helping to protect cells from the adverse effects of physiological stresses. Additionally, membrane-bound Hsp70s have been identified as a potential target for cancer therapies and their extracellularly localized counterparts have been identified as having both membrane-bound and membrane-free structures.
Pfam PF12338: Ribulose-1,5-bisphosphate carboxylase small subunit (family)
This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00101]. There is a conserved APF sequence motif. There are two completely conserved residues (L and P) that may be functionally important. This family is the small subunit of ribulose-1,5-bisphosphate.
Pfam PF15303: E3 ubiquitin-protein ligase Arkadia N-terminus (family)
This domain is found at the N-terminus of E3 ubiquitin-protein ligase Arkadia.
Wikipedia: E3 ubiquitin-protein ligase Arkadia is an enzyme that in humans is encoded by the RNF111 gene.
Pfam PF08401: N-terminal domain of anti-restriction factor ArdC (domain)
This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4  and the Tc-38 domain found in kinetoplastid minicircle binding proteins. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin. This domain is also found in the N-terminal region of the RP4 TraC1 primase, together with the Toprim domain (pfam:PF01751, pfam:PF13362 and pfam:PF13662).
Pfam PF09618: CRISPR-associated protein (Cas_Csy4) (family)
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4.
Pfam PF19086: Terpene synthase family 2, C-terminal metal binding (domain)
Wikipedia: In molecular biology, this protein domain belongs to the terpene synthase family (TPS). Its role is to synthesize terpenes, which are part of primary metabolism, such as sterols and
carotene, and also part of the secondary metabolism. This entry will focus on the C terminal domain of the TPS protein.
Pfam PF24762: IF140/IFT172 TPR domain (repeat)
IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) 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. The beta-propeller domains of IFT140 contact the beta-propeller domains of IFT121 from the adjacent complex. IFT172 is a component of the IFT-B complex which interacts with IFT-A complex. This entry represents the TPR region of IFT140/IFT172 and similar proteins. This domain of IFT140 forms an interface with IFT144.
Pfam PF06819: Archaeal Peptidase A24 C-terminal Domain (domain)
This region is of unknown function but is found in some archaeal [pfam:PF01478]. It is predicted to be of mixed alpha/beta secondary structure by JPred.
Pfam PF09198: Bacteriophage T4 beta-glucosyltransferase (domain)
Members of this family are DNA-modifying enzymes encoded by bacteriophage T4 that transfer glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA. It is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
Wikipedia: In enzymology, a DNA beta-glucosyltransferase is an enzyme that catalyzes the chemical reaction in which a beta-D-glucosyl residue is transferred from UDP-glucose to an hydroxymethylcytosine residue in DNA. It is analogous to the enzyme DNA alpha-glucosyltransferase.
Pfam PF08136: Ribosome hibernation factor SRA (family)
This family represents the stationary-phase-induced ribosome-associated protein SRA also known as protein D. This protein was originally thought to be a ribosomal protein. More recently it was shown that this is a ribosome hibernation factor that together with the factors Rmf, Hpf and RaiA is bound to the ribosomes during the onset and a few first days of the stationary phase when translation is strongly suppressed. In the prolonged stationary phase these factors dissociate from the ribosomes.
Pfam PF18628: Viral coat protein P2 N-terminal domain (domain)
P2 (30.2 kDa) is the major outer-coat protein of the marine lipid-containing bacteriophage PM2. Each sub-unit of P2 is composed of two beta barrel jelly rolls, disposed normal to the surface of the capsid, which lend pseudo-6-fold symmetry to the molecules, facilitating their close packing within the capsid. There is a Ca2+ ion located between the two beta barrels of P2 that helps PM2 molecular organizations stabilization. This entry represents the N-terminal jelly roll domain of P2.
Wikipedia: The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins. Taken together, the jelly roll and Greek key structures comprise around 30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database.
Pfam PF21142: Bacterial alpha-2 macroglobulin MG2 domain (domain)
Bacterial alpha-2 macroglobulin (A2M) are located in the periplasm and may protect the cell by trapping external proteases through a covalent interaction with an activated thioester. Macroglobulin (MG) beta sandwich domains appear to play a structural role. This entry represents bacterial MG2 (bMG2) domain which, with MG1, plays the role of a linker associating the main body of A2M to the bilayer.
Pfam PF19647: Family of unknown function (DUF6150) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 93 and 116 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 PF22167: PH0730-like, N-terminal domain (domain)
This domain is found at the N-terminal end of PH0730 from Pyrococcus horikoshii and similar archaeal proteins that contain the domain [pfam:PF14544] at the C-terminal. This domain adopts a winged helix fold.