SII-SWORD/CoKE huggingface dataset:
Pfam PF11860: N-acetylmuramidase (family)
Endolysins are bacteriophage encoded proteins synthesized at the end of the lytic infection cycle. They degrade the peptidoglycan (PG) of the host bacterium to allow viral progeny release. This domain family is found in bacteria and viruses. It is also found associated with [pfam:PF01471]. One of the family members is the modular Gp110 endolysin found in the Salmonella phage. This domain represents the catalytic region found in the C-terminal of Gp110. It has been demonstrated to have N-acetylmuramidase (lysozyme) activity cleaving the beta-(1,4) glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues in the sugar backbone of the PG. Furthermore, sequence alignments containing this domain show that the Gp110 E101 residue is conserved (suggesting that is is the catalytic residue), and followed by serine (a common feature in lysozymes). The structure of endolysins varies depending on their origin. In general, most of the endolysins from phages infecting Gram-positive bacteria have a modular structure consisting of one or two N-terminal enzymatic active domains (EADs) and a C-terminal cell wall binding domain (CBD) separated by a short linker. In silico analysis indicate that this endolysin has a modular structure harboring this EAD family at the C terminus and a PG_binding_1 CBD at the N terminus.
Pfam PF10330: Putative Sin3 binding protein (family)
This is a family of the conserved N-terminal end of a group of proteins conserved in fungi. It is likely to be a Sin3 binding protein. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 is a DNA-binding protein.
Pfam PF14252: Domain of unknown function (DUF4347) (family)
This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. There are two completely conserved residues (C and G) 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 PF04683: Proteasome complex subunit Rpn13, Pru domain (domain)
This family was thought originally to be involved in cell-adhesion, but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37.
Pfam PF19146: Family of unknown function (DUF5828) (family)
This is a family of proteins of unknown function predominantly found in Halobacteria.
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 PF18972: Cns1/TTC4 Wheel domain (domain)
The wheel domain is found at the C-terminus of yeast Cns1 and human TTC4 proteins. The structure of the domain shows an overall fold consisting of a twisted five-stranded beta sheet surrounded by several alpha helices. The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast. Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90.
Pfam PF09272: Hepsin, SRCR domain (domain)
Members of this family form an extracellular domain of the serine protease hepsin. They are formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate.
Wikipedia: Serine protease hepsin is an enzyme that in humans is encoded by the HPN gene.
Pfam PF01818: Bacteriophage translational regulator (domain)
The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs.
Pfam PF01666: DX module (family)
This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges.
Pfam PF12730: ABC-2 family transporter protein (family)
This family is related to the ABC-2 membrane transporter family [pfam:PF01061].
Wikipedia: The ABC transporters, ATP synthase (ATP)-binding cassette transporters are a transport system superfamily that is one of the largest and possibly one of the oldest gene families. It is represented in all extant phyla, from prokaryotes to humans. ABC transporters belong to translocases.
Pfam PF18146: Damage-inducible protein CinA KH domain (domain)
This domain is found in competence-induced protein A (CinA) present in Thermus thermophiles. CinA is important in the horizontal transfer of genes via competence and may also participate in the pyridine nucleotide cycle, which recycles products formed by non-redox uses of NAD. This domain has a KH-type fold and contains the absolutely conserved Glu-187, which stabilizes the binding of Mg2+ and hence polarizes the P=O bond for hydrolysis. A major feature of the CinA in T. thermophiles structure is the asymmetry in the dimer, which is caused by contact between a KH-type domain on the opposite chain and the bound ADP-ribose. This has the effect of closing the active site, allowing additional recognition of ADP-ribose by residues from the KH-type domain.
Pfam PF22504: Domain of unknown function (DUF6993) (domain)
This entry represents a bacterial domain of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24973: Laminin/attractin EGF domain (domain)
This entry represents the EGF-like domains found in laminin subunits (alpha, beta, gamma), attractin (ATRN), netrin, among others. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color. It was thought to have dipeptidase activity but it was shown later to lack that activity. Laminins are crucial for the formation of stable basement membranes and organising receptor complexes and cytoskeletal components. Netrins control guidance of central nervous system commissural axons and peripheral motor axons, serving as survival factors and regulating apoptosis.
Pfam PF04617: Hox9 activation region (family)
This family constitutes the N termini of the paralogous homeobox proteins HoxA9, HoxB9, HoxC9 and HoxD9.  The N terminal region is found to act as a transcription activation region. Btg1 and Btg2 - the B-cell translocation gene products - may function as cofactors for Hoxb9-mediated transcription. The Btg proteins modulate Hoxb9 transcriptional activity by recruiting a multiprotein Ccr4-like complex.
Pfam PF00680: Viral RNA-dependent RNA polymerase (family)
This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Remdesivir, a recent treatment approved for Covid-19 disease, directly interacts with this region of the RdRp (NSP12) from SARS-CoV-2 and explains its mechanism of action via delayed-chain termination.
Wikipedia: RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to typical DNA-dependent RNA polymerases, which all organisms use to catalyze the transcription of RNA from a DNA template.
Pfam PF19773: Domain of unknown function (DUF6259) (domain)
This domain is found in bacterial proteins and it is functionally uncharacterised. However, some proteins are putative glycoside hydrolases and this domain has some overlaps with clan family members of CL0058. Proteins containing this domain are typically between 678 and 749 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 PF01342: SAND domain (domain)
The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerisation. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri.  This region of RegA is known as the VARL domain.
Wikipedia: In molecular biology, the protein domain SAND is named after a range of proteins in the protein family: Sp100, AIRE-1, NucP41/75, DEAF-1. It is localised in the cell nucleus and has an important function in chromatin-dependent transcriptional control. It is found solely in eukaryotes.
Pfam PF23189: Uncharacterised protein family (UPF0261) C-terminal domain (domain)
This entry represents the C-terminal domain of ToMV resistance protein Tm-1 and the uncharacterised UPF0261 proteins. The tomato resistance protein Tm-1, which inhibits replication complex formation through its binding to tomato mosaic virus (ToMV) replication proteins .
Pfam PF01565: FAD binding domain (domain)
This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme [ec:1.1.1.158].  This enzyme is involved in the biosynthesis of peptidoglycan.
Pfam PF22376: PSV, transcriptional regulator domain (domain)
This domain is found in Transcriptional regulator from Pyrobaculum spherical virus (PSV) and similar viral proteins. It shows a winged-helix configuration.
Pfam PF24641: DEAH11 eukaryotic type KH-domain (domain)
This domain is found in the ATP-dependent RNA helicase DEAH11, DEAH12 from Arabidopsis thaliana and related plant proteins. This domain shares detectable similarity to type I KH domains and is predicted to adopt an alpha/beta structure with similar topology.
Pfam PF21424: Distal tail protein pb9, A domain C-terminal (domain)
This entry includes phage distal tail proteins which form a hexameric ring located at the tail tube end, such as pb9 from bacteriophage T5. pb9 consists of two domains, A and B. Domain A adopts a split barrel  fold and includes residues 1 to 82-172 to 205. This entry covers the C-terminal region of the A domain.
Pfam PF10966: Protein of unknown function (DUF2768) (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 PF10978: Protein of unknown function (DUF2785) (family)
Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family 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 PF24019: Family of unknown function (DUF7332) (family)
This entry represents uncharacterised archaeal 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 PF12809: Eukaryotic metallothionein (family)
This is a family of eukaryotic metallothioneins.
Pfam PF05515: Viral nucleic acid binding (family)
This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding  proteins (NABP).
Pfam PF01397: Terpene synthase, N-terminal domain (repeat)
It has been suggested that this gene family be designated tps (for terpene synthase).  It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase [swissprot:Q39979], 5-epi- aristolochene synthase, [swissprot:Q40577] and (+)-delta-cadinene synthase [swissprot:P93665]. tpsb includes (-)-limonene synthase, [swissprot:Q40322]. tpsc includes kaurene synthase A, [swissprot:O04408]. tpsd includes taxadiene synthase, [swissprot:Q41594], pinene synthase, [swissprot:O24475] and myrcene synthase, [swissprot:O24474]. tpse includes kaurene synthase B. tpsf includes linalool synthase.
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 N terminal domain of the TPS protein.
Pfam PF14432: DYW family of nucleic acid deaminases (domain)
This is the DYW domain found in nucleic acid  deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteristic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems.
Pfam PF14435: SUKH-4 immunity protein (family)
This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems.
Pfam PF02745: Methyl-coenzyme M reductase alpha subunit, N-terminal domain (domain)
Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta ([pfam:PF02241]), and 2 gamma ([pfam:PF02240]) subunits with two identical nickel porphinoid active sites. The N-terminal domain has a ferredoxin-like fold.
Pfam PF05879: Root hair defective 3 GTP-binding protein (RHD3) GTPase domain (domain)
This is the GTPase domain of several eukaryotic root hair defective 3 (RHD3) like GTP-binding proteins, including RHD3 from Arabidopsis and Sey1 from yeast, which are involved in homotypic membrane fusion of the endoplasmic reticulum. This domain binds GTP and forms dimers with other molecule for membrane tethering.
Pfam PF12128: Protein of unknown function (DUF3584) (family)
This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.
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 PF20437: Lon-like LonC helical domain (domain)
This domain represents the helical domain found in the Lon-like LonC protease from Meiothermus taiwanensis, a Lon-like protease with no ATPase activity.
Pfam PF22073: Cep192 domain 4 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the fourth domain of the metazoan Cep192 homologs. This domain along with domain 5 constitutes the so-called Spd2 domain that is ubiquitously present in all SPD2/CEP192 homologues beyond Metazoa and represents the most conserved region amongst them.
Pfam PF12824: Mitochondrial ribosomal protein subunit L20 (domain)
This family is the essential mitochondrial ribosomal protein subunit L20 of fungi.
Pfam PF05610: Protein of unknown function (DUF779) (family)
This family consists of several bacterial proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF04060: Putative Fe-S cluster (domain)
This family includes a domain with four conserved cysteines that probably form an Fe-S redox cluster.
Pfam PF15056: Neuritin protein family (domain)
The domain family Neuritin1 (NRN1) is a GPI-anchored protein expressed in post-mitotic-differentiating neurons in the developing nervous system. NRN1 is a glutamate and neurotrophin receptor target encoding a neuronal protein that functions extracellularly to modulate neurite outgrowth (OMIM:607409).                           This family of proteins is found in eukaryotes. Proteins in this family are typically between and 158 amino acids in length.
Pfam PF12215: beta-glucosidase 2, glycosyl-hydrolase family 116 N-term (family)
This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with [pfam:PF04685]. It is found just after the extreme N terminus. The N-terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO, is a glutamine-335 in the downstream family [pfam:PF04685].
Pfam PF00940: DNA-dependent RNA polymerase (family)
This is a family of single chain RNA polymerases.
Wikipedia: T7 RNA Polymerase is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' direction.
Pfam PF09342: Domain of unknown function (DUF1986) (domain)
This domain is found in serine proteases and is predicted to contain disulphide bonds (see [swissprot:P98159]).
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.