SII-SWORD/CoKE huggingface dataset:
Pfam PF05991: YacP-like NYN domain (domain)
This family consists of bacterial proteins related to YacP. This family is uncharacterised functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind.  Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.
Pfam PF17486: Cystine knot toxins (family)
This family is found in Araneaea (spiders) and family members are venomus peptides with 4 disulfide bonds. Cystine knot toxins (CKTs) are small, compact molecules cross-linked by three to five disulfide bonds and are often the key contributors to the activity and potency of the venom. While these disulfide-rich peptides can adopt a number of different structural motifs, three of the most observed structural scaffold motifs are the inhibitor cystine knot (ICK) and the disulfide-directed beta-hairpin (DDH) and Kunitz motif. These venomus peptides mainly act on membrane proteins in electro-excitable cell membranes by modulating voltage-activated sodium (NaV), calcium (CaV), and potassium (KV) channels, acid-sensing ion channels (ASICs), transient receptor potential (TRP) channels, and mechanosensitive channels (MSCs).
Pfam PF10757: Biofilm formation regulator YbaJ (family)
YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm
Pfam PF05786: Condensin complex subunit 2 (family)
This family consists of several Barren protein homologues from several eukaryotic organisms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologues in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons.  Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localises to chromatin throughout mitosis. Colocalisation and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase. This family forms one of the three non-structural maintenance of chromosomes (SMC) subunits of the mitotic condensation complex along with Cnd1 and Cnd3.
Pfam PF21296: Apoptotic protease-activating factor 1-like, winged-helix domain (domain)
This domain is found in Apoptotic protease-activating factor 1 from Mus musculus (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD).
Pfam PF02955: Prokaryotic glutathione synthetase, ATP-grasp domain (domain)
Prokaryotic glutathione synthetase 6.3.2.3 (glutathione synthase) catalyses the conversion of gamma-L-glutamyl-L-cysteine and glycine to orthophosphate and glutathione in the presence of ATP. This is the second step in glutathione biosynthesis. The enzyme is inhibited by 7,8-dihydrofolate, methotrexate and trimethoprim. This is the ATP-binding domain of the enzyme.
Wikipedia: Glutathione synthetase (GSS) is the second enzyme in the glutathione (GSH) biosynthesis pathway. It catalyses the condensation of gamma-glutamylcysteine and glycine, to form glutathione. Glutathione synthetase is also a potent antioxidant. It is found in many species including bacteria, yeast, mammals, and plants.
Pfam PF08299: Bacterial dnaA protein helix-turn-helix (domain)
This entry represents the C-terminal domain of bacterial DnaA proteins  that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC).

DnaA is a protein of about 50kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) .
Wikipedia: DnaA is a protein that activates initiation of DNA replication in bacteria. Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. It is a replication initiation factor which promotes the unwinding of DNA at oriC. The DnaA proteins found in all bacteria engage with the DnaA boxes to start chromosomal replication. The onset of the initiation phase of DNA replication is determined by the concentration of DnaA. DnaA accumulates during growth and then triggers the initiation of replication. Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to loop in preparation for melting open by the helicase DnaB.
Pfam PF08571: Yos1-like (family)
In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes.
Pfam PF17260: Family of unknown function (DUF5326) (family)
This is a family of unknown function mostly found in Actinobacteria. Many of the family members are predicted to contain two trans-membrane domains.
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 PF17148: Domain of unknown function (DUF5117) (family)
This domain may fall upstream of a met-zincin domain.
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 PF20405: Family of unknown function (DUF6695) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 329 and 354 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 PF01375: Heat-labile enterotoxin alpha chain (domain)
Escherichia coli heat-labile enterotoxin is a bacterial protein toxin with an AB5 multimer structure, in which the B pentamer (IPR001835) has a membrane-binding function and the A chain is needed for enzymatic activity . The B subunits are arranged as a donut-shaped pentamer, each subunit participating in ~30 hydrogen bonds and 6 salt bridges with its two neighbours .

The A subunit has a less well-defined secondary structure. It predominantly interacts with the pentamer via the C-terminal A2 fragment, which runs through the charged central pore of the B subunits. A putative catalytic residue in the A1 fragment (Glu112) lies close to a hydrophobic region, which packs two loops together. It is thought that this region might be important for catalysis and membrane translocation .
Wikipedia: In molecular biology, the heat-labile enterotoxin family includes Escherichia coli heat-labile enterotoxin and cholera toxin (Ctx) secreted by Vibrio cholerae.
Pfam PF05273: Poxvirus RNA polymerase 22 kDa subunit (family)
This family consists of several poxvirus DNA-dependent RNA polymerase 22 kDa subunits.
Pfam PF09684: Phage tail protein (Tail_P2_I) (family)
These sequences represent the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria.
Pfam PF17536: Matrix and Matrix long proteins N-terminal (family)
This entry represents the N-terminal fragment of family members such as the Matrix (Mx) and Matrix protein long (ML) proteins. They are found in Thogoto virus (THOV), a tick-transmitted orthomyxovirus with a genome consisting of six single-stranded RNA segments that encode seven structural proteins. Matrix proteins of the family Orthomyxoviridae are major structural components of the viral capsid, located below the viral lipid membrane and provide protection for viral ribonucleoproteins (vRNPs). They serve as a major participant during the processes of virus invasion and budding. Furthermore, they play specific roles throughout the viral life cycle, usually by interacting with other viral components or host cellular proteins. ML protein, an extended version of the viral M protein, is a viral IFN antagonist. ML is essential for virus growth and pathogenesis in an IFN-competent host. In the presence of ML the activation and/or action of the interferon regulatory factor-3 (IRF-3) is severely affected. This effect depends on direct interaction of ML with the transcription factor IIB (TFIIB). ML suppresses IRF-7 in a similar manner as it suppresses IRF-3. Studies have revealed that ML associates with IRF-7 and prevents IRF-7 dimerization and interaction with TRAF6. Structural analysis revealed that N-terminal fragment of M protein (MN) undergoes conformational changes that result in specific, pH-dependent inter-molecular interactions. Comparison of THOV MN and influenza A virus (IAV) MN region, showed low sequence identity. However, superimposition of the two structures in neutral condition, showed that both matrix proteins contain nine helices connected with same topology. Since the matrix layer of IAV disassembles in acidic endosome at the beginning of infection and repacks in the neutral cytoplasm, a change of pH might be a key regulator for the capsid assembly/disassembly transition during these processes. Hence, pH-dependent conformational transition model was studied in THOV MN, where interactions such as hydrogen bonds and hydrophobic interactions are suggested to be involved in THOV matrix assembly.
Pfam PF08378: Nuclease-related domain (family)
The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins.  It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.
Pfam PF03175: DNA polymerase type B, organellar and viral (family)
Like [pfam:PF00136], members of this family are also DNA polymerase type B proteins. Those included here are found in plant and fungal mitochondria, and in viruses.
Wikipedia: A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.
These enzymes catalyze the chemical reactiondeoxynucleoside triphosphate + DNAn ⇌ pyrophosphate + DNAn+1.
Pfam PF01592: NifU-like N terminal domain (family)
This domain is found in NifU in combination with [pfam:PF01106]. This domain is found on isolated in several bacterial species such as [swissprot:O53156]. The nif genes are responsible for nitrogen fixation.  However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.
Pfam PF08530: X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain (domain)
This domain contains a beta sandwich domain.
Pfam PF23480: YGL204C (family)
This protein family includes the uncharacterised protein YGL204C from Saccharomyces cerevisiae, a micropeptide encoded by a small open reading frame (smORF).
Pfam PF01584: CheW-like domain (domain)
CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis.  The CheW-like regulatory domain in CheA binds to CheW, suggesting that these domains can interact with each other.
Pfam PF01298: C-lobe and N-lobe beta barrels of Tf-binding protein B (domain)
Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a "handle" domain made up of four (N lobe) or eight (C lobe) beta strands. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core.
Pfam PF15482: Coiled-coil domain-containing glutamate-rich protein family 1 (coiled_coil)
This is a family of coiled-coil family proteins found in eukaryotes. Proteins in this family are typically between 160 and 397 amino acids in length.
Pfam PF07852: Protein of unknown function (DUF1642) (family)
The sequences making up this family are derived from various hypothetical phage and prophage proteins. The region in question is approximately 140 amino acids long.
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 PF16626: Linking region between Kunitz_BPTI and I-set on papilin (disordered)
Papilin_u7 is a conserved region of natively unstructured residues on proteoglycan-like sulfated glycoprotein - papilin 0 in higher eukaryotes.  It links the Kunitz_BPTI, [pfam:PF00014], and I-set domains [pfam:PF07679].  The function is not known.
Pfam PF17834: Beta-sandwich domain in beta galactosidase (domain)
This entry corresponds to a beta sandwich like domain found in glycosyl hydrolase family 35 beta galactosidase enzymes.
Pfam PF17255: EbsA-like protein (domain)
This is a family of unknown function which contains the EbsA protein [swissprot:P36920] from Enterococcus faecalis. The uncharacterized family is mainly found in lactobacilli and consists of two N-terminal transmembrane helices followed by a bacterial PH domain.
Pfam PF07064: RIC1 (family)
RIC1 has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network.  It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor.
Pfam PF01080: Presenilin (family)
Mutations in presenilin-1 are a major cause of early onset Alzheimer's disease.  It has been found that presenilin-1 ([swissprot:P49768]) binds to beta-catenin in-vivo. This family also contains SPE proteins from C.elegans.
Wikipedia: Presenilins are a family of related multi-pass transmembrane proteins which constitute the catalytic subunits of the gamma-secretase intramembrane protease protein complex. They were first identified in screens for mutations causing early onset forms of familial Alzheimer's disease by Peter St George-Hyslop. Vertebrates have two presenilin genes, called PSEN1 that codes for presenilin 1 (PS-1) and PSEN2 that codes for presenilin 2 (PS-2). Both genes show conservation between species, with little difference between rat and human presenilins. The nematode worm C. elegans has two genes that resemble the presenilins and appear to be functionally similar, sel-12 and hop-1.
Pfam PF00837: Iodothyronine deiodinase (family)
Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3).
Pfam PF05978: Ion channel regulatory protein UNC-93 (family)
The proteins in this family are represented by UNC-93 from Caenorhabditis elegans and also includes protein unc-93 homologue A (UNC93A), protein unc-93 homologue B1 (UNC93B1), and UNC93-like protein MFSD11 (also called major facilitator superfamily domain- containing protein 11 or protein ET). UNC-93 colocalizes with SUP-10 and SUP-9 within muscle cells. UNC-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans. UNC93B1 controls intracellular trafficking and transport of a subset of Toll-like receptors (TLRs), including TLR3, TLR7 and TLR9, from the endoplasmic reticulum to endolysosomes where they can engage pathogen nucleotides and activate signaling cascades. MFSD11 is ubiquitously expressed in the periphery and the central nervous system of mice, where it is expressed in excitatory and inhibitory mouse brain neurons.
Pfam PF01234: NNMT/PNMT/TEMT family (family)
Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented.

Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5-methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order . Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI ), shared by other AdoMet-Mtases , is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments , although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases . The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences .
Several cytoplasmic vertebrate methyltransferases are evolutionary related , including nicotinamide N-methyltransferase (2.1.1.1) (NNMT); phenylethanolamine N-methyltransferase (2.1.1.28) (PNMT); and thioether S-methyltransferase (2.1.1.96) (TEMT). NNMT catalyses the N-methylation of nicotinamide and other pyridines to form pyridinium ions. This activity is important for the biotransformation of many drugs and xenobiotic compounds. PNMT catalyses the last step in catecholamine biosynthesis, the conversion of noradrenalin to adrenalin; and TEMT catalyses the methylation of dimethyl sulphide into trimethylsulphonium. These three enzymes use S-adenosyl-L-methionine as the methyl donor. They are proteins of 30 to 32kDa.
Pfam PF09969: Uncharacterized conserved protein (DUF2203) (family)
This domain, found in various hypothetical bacterial 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 PF24446: Family of unknown function (DUF7565) (family)
This entry represents a small family of uncharacterised proteins found in archaea and eukaryotes. These proteins contain two pairs of conserved cysteines and two pairs of conserved histidines that are probably involved in zinc coordination. These proteins likely resemble two classical C2H2 zinc fingers that pack on each other and form a compact globular 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 PF07667: Protein of unknown function (DUF1600) (family)
These proteins appear to be specific to Mycoplasma species.
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.