SII-SWORD/CoKE huggingface dataset:
Pfam PF21384: CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain (domain)
This domain is found at the N-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa and similar sequences predominantly found in proteobacteria. In the type I-F CRISPR-Cas system, Cas3 is fused with Cas2 at the N terminus. This entry represents the Cas2 domain of Cas3, which shows a four-stranded beta-sheet and two alpha-helices, in a structure that resembles that of Cas2 from the Escherichia coli. It appears N- terminal to the histidine-aspartate (HD)-type nuclease domain ([pfam:PF18019]).
Pfam PF14233: Domain of unknown function (DUF4335) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 204 and 480 amino acids in length. There are two completely conserved residues (G and D) that may be functionally important.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11293: Protein of unknown function (DUF3094) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF10844: Protein of unknown function (DUF2577) (family)
This family of proteins 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 PF17128: Domain of unknown function (DUF5107) (family)
This family is found in range of different bacterial species. In many proteins it lies N-terminal to a TPR-repeat region at the C-terminus.
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 PF03268: Caenorhabditis protein of unknown function, DUF267 (family)
This family of proteins, from Caenorhabditis species, have not been characterised though a number are annotated as 'serpentine receptor, class r' proteins.
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 PF07065: D123 (family)
This family contains a number of eukaryotic cell division cycle 123 (Cdc123, also known as D123) proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate. D123 proteins are regulators of eIF2, the central regulator of translational initiation. Family members include ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is found in eukaryotes as well as NCDLVs and diverse bacteria. In eukaryotes, the domain is found in both the CDC123 enzymes and a related clade of proteins found in amoeboid organisms, while in bacteria it is observed embedded in polymorphic toxin loci.
Pfam PF20250: Flagellar Assembly Protein A N-terminal region (family)
This entry represents an N-terminal region of the FapA protein and its homologues. This region is found in multiple copies in some proteins such as [swissprot:Q1NVZ6]. Members of this family include FapA (flagellar assembly protein A) [swissprot:Q7MBR0] found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility.  Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis.  The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction.
Pfam PF10842: Protein of unknown function (DUF2642) (family)
This family of proteins with unknown function appear to be restricted to Bacillus spp.
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 PF02465: Flagellar hook-associated protein 2 N-terminus (family)
The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the N-terminal region of this family of proteins.
Pfam PF21328: Sliding-clamp-loader large subunit, AAA+ ATPase lid domain (domain)
Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA+ superfamily of ATPases which form pentameric complexes that load sliding DNA clamps onto the DNA, key for processive chromosomal replication. This entry represents the AAA+ ATPase lid domain.
Pfam PF11742: Protein of unknown function (DUF3302) (family)
This family of unknown function is expressed by proteobacteria.
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 PF01652: Eukaryotic initiation factor 4E (domain)
Eukaryotic translation initiation factor 4E (eIF-4E)  is a protein that binds to the cap structure of eukaryotic cellular mRNAs. eIF-4E recognises and binds the 7-methylguanosine-containing (m7Gppp) cap during an early step in the initiation of protein synthesis and facilitates ribosome binding to a mRNA by inducing the unwinding of its secondary structures. A tryptophan in the central part of the sequence of human eIF-4E seems to be implicated in cap-binding .
Wikipedia: In molecular biology, the eukaryotic translation initiation factor 4E family (eIF-4E) is a family of proteins that bind to the cap structure of eukaryotic cellular mRNAs. Members of this family recognise and bind the 7-methyl-guanosine-containing (m7Gppp) cap during an early step in the initiation of protein synthesis and facilitate ribosome binding to an mRNA by inducing the unwinding of its secondary structures. A tryptophan in the central part of the sequence of human eIF-4E seems to be implicated in cap-binding.
Pfam PF22784: Swiss Army Knife protein, DSP-PTPase phosphatase domain (domain)
The Swiss Army Knife class of proteins features a diverse domain repertoire acting to repair RNA damaged in the wake of RNase attacks. PTP-SAK is one such domain, a phosphatase of the rhodanese-phosphatase superfamily. It is predicted to 'clean' RNA ends by removing phosphate groups, preparing them for ligation by their associating RNA ligases.
Pfam PF21219: Harmonin, N-terminal domain (domain)
This domain is found at the N-terminal end of Harmonin from humans (USH1C) and similar proteins from vertebrates. Harmonin is a master scaffold in the assembly of the Usher protein complexes present in the inner ear and the retina. Defects in these proteins are related to a hereditary hearing-vision loss disease, Usher syndrome I (USH1). The N-terminal domain of USH1C, which precedes the first PDZ protein- binding domain ([pfam:PF00595]), adopts a compact five-helix-bundle structure.
Pfam PF12367: Pyruvate ferredoxin oxidoreductase beta subunit C terminal (family)
This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF02775]. There are two completely conserved residues (A and G) that may be functionally important. PFO is involved in carbon dioxide fixation via a reductive TCA cycle. It forms a heterodimer (alpha/beta). The beta subunit has binding motifs for Fe-S clusters and thiamine pyrophosphate.
Pfam PF17172: Glutathione S-transferase N-terminal domain (domain)
This domain is homologous to [pfam:PF02798].
Wikipedia: Glutathione S-transferases (GSTs), previously known as ligandins, are a family of eukaryotic and prokaryotic phase II metabolic isozymes best known for their ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification. The GST family consists of three superfamilies: the cytosolic, mitochondrial, and microsomal—also known as MAPEG—proteins. Members of the GST superfamily are extremely diverse in amino acid sequence, and a large fraction of the sequences deposited in public databases are of unknown function. The Enzyme Function Initiative (EFI) is using GSTs as a model superfamily to identify new GST functions.
Pfam PF20375: Family of unknown function (DUF6670) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 345 and 372 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 PF04641: Rtf2 RING-finger (family)
It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family.
Pfam PF03090: Replicase family (family)
This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family.  These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones.
Pfam PF03026: Influenza C virus M1 protein (family)
This family represents the matrix 1 protein of influenza C virus. The protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see [pfam:PF03021]).
Pfam PF09449: Domain of unknown function (DUF2020) (domain)
Protein of unknown function 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 PF10891: Protein of unknown function (DUF2719) (family)
This family of proteins with unknown function appears to be restricted to Nucleopolyhedrovirus.
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 PF06902: Divergent 4Fe-4S mono-cluster (domain)
Members of this family contain three highly conserved cysteine residues. This family includes proteins containing divergent domains which are most likely to bind to iron-sulfur clusters.
Pfam PF18629: Family of unknown function (DUF5629) (family)
This is a domain of unknown function found in hypothetical proteins from Pseudomonas aeruginosa.
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 PF24126: Family of unknown function (DUF7394) (family)
This entry represents a protein of unknown function, found primarily in phage proteins of about 60 to 75 amino acids in length.  It contains a single predicted transmembrane helix in many members. Most sequences also contain a region of predicted intrinsic disorder at the C-terminus rich in basic and acidic residues. Further experimental study is required to determine the function of these proteins. Some proteins are annotated as holins but the source of this annotation 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 PF22219: DUF3829-like, C-terminal domain (domain)
This domain is found at the C-terminal end of uncharacterised DUF3829-like proteins. It is often found associated to [pfam:PF20893]. Its function is unknown. It shows four 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 PF08103: Uperin family (family)
This family consists of the uperin family of antimicrobial peptides.  Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic alpha-helix with distinct hydrophilic and hydrophobic faces.
Pfam PF21697: Exopolyphosphatase, C-terminal (domain)
This domain is found at the C-terminal end of Exopolyphosphatase from Agrobacterium fabrum (Ppx) and similar proteins mainly found in alphaproteobacteria. This domain is usually found associated with [pfam:PF02541].
Pfam PF13336: Acetyl-CoA hydrolase/transferase C-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 PF02629: CoA binding domain (domain)
This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases.
Pfam PF15876: Domain of unknown function (DUF4732) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 201 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 PF18525: Cas9 C-terminal domain (domain)
This is the C-terminal domain of Cas9 enzymes found in actinobacteria.
Pfam PF04810: Sec23/Sec24 zinc finger (domain)
COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.
Pfam PF13657: HipA N-terminal domain (domain)
This domain is found to the N-terminus of HipA-like proteins. It is also found in isolation in some proteins.
Pfam PF21434: Phage G20C small terminase, N-terminal domain (domain)
This entry represents the N-terminal helix-turn-helix domain of the terminase small subunit (TerS) from Thermus phage G20c, which oligomerises into a nonamer that binds DNA, stimulates terminase large subunit (TerL) ATPase activity, and inhibits TerL nuclease activity.
Pfam PF01273: LBP / BPI / CETP family, N-terminal domain (family)
The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.
Wikipedia: In molecular biology, the lipid-binding serum glycoproteins family, also known as the BPI/LBP/Plunc family or LBP/BPI/CETP family represents a family which includes mammalian lipid-binding serum glycoproteins and/or proteins containing a structural motif known as the BPI fold. Members of this family include:Bactericidal permeability-increasing protein (BPI)
Lipopolysaccharide-binding protein (LBP)
Cholesteryl ester transfer protein (CETP)
Phospholipid transfer protein (PLTP)
Palate, lung and nasal epithelium carcinoma-associated protein (PLUNC)
Pfam PF22051: Protein GndA (family)
This family represents Protein GndA from Escherichia coli, a smORF-encoded heat shock protein with a predicted transmembrane helix.
Pfam PF00644: Poly(ADP-ribose) polymerase catalytic domain (domain)
Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active.
Pfam PF16348: Coronavirus replicase NSP4, C-terminal (domain)
This is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex (RTC) to modified endoplasmic reticulum membranes. This predominantly alpha-helical domain may be involved in protein-protein interactions. It has been shown that in Betacoronavirus, the coexpression of NSP3 and NSP4 results in a membrane rearrangement to induce double-membrane vesicles (DMVs) and convoluted membranes (CMs), playing a critical role in SARS-CoV replication. There are two well conserved amino acid residues (H120 and F121) in NSP4 among Betacoronavirus, essential for membrane rearrangements during interaction with NSP3.
Pfam PF13957: Toxin YafO, type II toxin-antitoxin system (family)
YafO is a toxin which inhibits protein synthesis. It acts as a ribosome-dependent mRNA interferase. It forms part of a type II toxin-antitoxin system, where the YafN protein acts as an antitoxin. This domain forms complexes with yafN antitoxins containing [pfam:PF02604].
Wikipedia: The SymE-SymR toxin-antitoxin system consists of a small symbiotic endonuclease toxin, SymE, and a non-coding RNA symbiotic RNA antitoxin, SymR, which inhibits SymE translation. SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems.
Pfam PF20343: Family of unknown function (DUF6638) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 412 and 454 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.