SII-SWORD/CoKE huggingface dataset:
Pfam PF17999: Pullulanase N1-terminal domain (domain)
This is the N-terminal domain found in debranching enzyme such as Pullulanase (PulA)from Anoxybacillus sp. LM18-11. The PulA structure comprises four domains (N1, N2, A, and C). This is the N1 domain which has been identified as a carbohydrate-binding motif. Two maltotriose or maltotetraose molecules were found between the N1 domain and a loop of the A domain in the PulA-maltotriose or PulA-maltotetraose structures. These carbohydrates are bound in a parallel binding mode close to each other and form hydrogen bonds.  The sugar moieties bound to the N1 domain are not immediately adjacent to the active site, but the enzyme might use N1 binding to attract and grab the substrate. Functional analysis indicate that N1 is important for catalytic activity and thermostability in addition to assisting substrate binding. The structure of the N1 domain reveals a classic distorted beta-jelly roll fold consisting of two anti-parallel beta-sheets, forming a concave and a convex surface. On the concave side of N1 domain there is a cleft to accommodate two molecules of maltotriose or maltotetraose.
Pfam PF19628: Family of unknown function (DUF6132) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 74 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 PF13604: AAA domain (domain)
This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
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 PF07021: Methionine biosynthesis protein MetW (family)
This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalysed by the products of the metXW genes and is equivalent to the first step in enterobacteria, gram-positive bacteria and fungi, except that in these microorganisms the reaction is catalysed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in gram-positive bacteria and certain fungi, the second and third steps are a direct sulfhydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells.
Pfam PF01497: Periplasmic binding protein (domain)
This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).
Pfam PF24786: RXYLT1 N-terminal domain (domain)
This domain is found in human Ribitol-5-phosphate xylosyltransferase 1 (RXYLT1) and related proteins. RXYLT1 acts as an UDP-d-xylose,ribitol-5-phosphate beta1,4-xylosyltransferase in the biosynthetic pathway of O-mannosyl glycan. This domain has a detectable similarity to domains members of P-loop_NTPase clan and it is predicted to adopt similar structure.
Pfam PF16438: Domain of unknown function (DUF5035) (family)
This family consists of several uncharacterized proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12060: Domain of unknown function (DUF3541) (repeat)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 230 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 PF14125: Domain of unknown function (DUF4292) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 243 and 287 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 PF13932: tRNA modifying enzyme MnmG/GidA C-terminal helical bundle (domain)
The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, last three being rather short and forming small bundle and are represented in this entry. GidA is a tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis the C-terminal helices have been suggested to be implicated in binding of the D-stem of tRNA and, specifically this domain, to be responsible for the interaction with protein MnmE. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, [pfam:PF12631].
Pfam PF05939: Phage minor tail protein (family)
This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.
Pfam PF04283: Chemotaxis signal transduction system protein F from archaea (family)
This is a family of proteins that are archaea-specific components of the bacterial-like chemotaxis signal transduction system of archaea. In H. salinarum, the CheF proteins interact with the chemotaxis proteins CheY, CheD and CheC2 as well as the flagella-accessory proteins FlaCE and FlaD, and are essential for any tactic response. CheF probably functions at the interface between the bacterial-like chemotaxis signal transduction system and the archaeal flagellar apparatus.
Pfam PF10122: Mu-like prophage protein Com (family)
Members of this family of proteins comprise the translational regulator of mom.
Pfam PF19021: CRISPR system CMR subunit Cmr7 1 (family)
The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA. In the CRISPR-Cas system, RNA is targeted by the CMR complex. In Sulfolobus solfataricus this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse "payload" of targeting crRNA. This entry represent the Cmr7 subunit of the CMR complex.
Pfam PF19835: Putative endonuclease segE, GIY-YIG domain (domain)
This domain family is found in viruses. Proteins containing this domain are typically between 147 and 298 amino acids in length. They have a GIY-YIG domain at the N-terminal, which suggests they are likely to be endonucleases. Included in this family is the Putative endonuclease segE from Bacteriophage T4.
Pfam PF04856: Securin sister-chromatid separation inhibitor (family)
Securin is also known as pituitary tumour-transforming gene product. Over-expression of securin is associated with a number of tumours, and it has been proposed that this may be due to erroneous chromatid separation leading to chromosome gain or loss.
Pfam PF04662: Luteovirus P0 protein (family)
This family of proteins may be involved in suppression of PTGS a plant defence mechanism.
Pfam PF17705: Family of unknown function (DUF5551) (family)
This is a family of unknown function found in primates.
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 PF08647: BRE1 E3 ubiquitin ligase (coiled_coil)
BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions.
Pfam PF08335: GlnD PII-uridylyltransferase (family)
This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification ([ec:2.7.7.59]) of the regulatory protein P-II, or GlnB (e.g. [swissprot:P05826], [pfam:PF00543]). In response to nitrogen limitation, these transferases (e.g. [swissprot:P27249]) catalyse the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme. Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species. The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain ([pfam:PF01909]), and N-terminal to an HD domain ([pfam:PF01966]) and two ACT domains ([pfam:PF01842]).
Pfam PF24162: Protein root UVB sensitive 6, N-terminal (domain)
This domain is found at the N-terminal of Protein root UVB sensitive 6 from Arabidopsis thaliana (RUS6) and similar sequences from plants. RUS6 is required for normal embryo development. This domain is normally found associated with [pfam:PF04884] and [pfam:PF24160].
Pfam PF00062: C-type lysozyme/alpha-lactalbumin family (domain)
Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds.
Wikipedia: In molecular biology, glycoside hydrolase family 22 is a family of glycoside hydrolases. EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF17563: Cupiennin (family)
Cupiennin are small cationic alpha-helical peptides from the venom of the ctenid spider Cupiennius salei which are characterized by high bactericidal as well as hemolytic activities. Family members such as cupiennin 1a exert both cytolytic and antibacterial effects. The cytolytic activity of the cupiennin peptides depends primarily on the amphipathic N-terminus, which is capable of inserting into the membrane, and is modulated by the C-terminus via electrostatic interactions with the cell surface.
Pfam PF09295: ChAPs (Chs5p-Arf1p-binding proteins) (repeat)
ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi.    They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other.
Pfam PF17359: Family of unknown function (DUF5385) (family)
This is a family of unknown function found in Mycoplasmataceae. Family members are predicted to have one trans-membrane region.
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 PF03224: V-ATPase subunit H (repeat)
The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer.  This domain corresponds to the N terminal domain of the H subunit of V-ATPase.  The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation.
Wikipedia: Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pumps protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
Pfam PF08632: Activator of mitotic machinery Cdc14 phosphatase activation C-term (domain)
This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions. The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release.
Pfam PF08724: Rep protein catalytic domain like (domain)
Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration.  The catalytic domain has DNA binding and endonuclease activity.
Pfam PF24963: Domain of unknown function (DUF7768) (domain)
This entry represents a domain found in uncharacterised bacterial proteins. It has a detectable similarity to domains members of N-(deoxy)ribosyltransferase-like superfamily and is predicted to adopt similar structure.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17960: TIG domain (domain)
This entry represents an TIG or IPT domain (Ig domain shared by Plexins and Transcription factors) found in plexins.
Pfam PF15591: Immunity protein 31 (family)
A predicted immunity protein with a mostly all-beta fold and a conserved GxS motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox17 or Ntox7 families.
Pfam PF24263: Domain of unknown function (DUF7464) (domain)
This entry represents a small family of uncharacterised phage proteins. The family includes the gene 83 from the mycobacterial phage Bxb1 [swissprot:Q9B038]. This family shows structural similarity to [pfam:PF09926]. These proteins have an SH3 like barrel 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 PF15475: Transmembrane protein C12orf23, UPF0444 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 119 amino acids in length.
Pfam PF23887: Phage L5 gene 47-like protein (domain)
This entry represents the gene 47 protein found in Mycobacterium phage L5. This protein forms a small globular beta domain that is related to LSM superfamily proteins such as Hfq. AlphaFold modelling suggests this protein forms an unusual octameric arrangement. Based on similarity to LSM proteins these proteins may bind to RNA.
Pfam PF12199: Extracellular fibrinogen binding protein C terminal (domain)
This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved in complement regulation. This motif binds to complement and changes its conformation to a form which cannot activate downstream components of the complement cascade.
Pfam PF12726: SEN1 N terminal (family)
This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes. The N terminal of SEN1, unlike the C terminal, is not required for growth.
Pfam PF00960: Neocarzinostatin family (domain)
This family is comprised of antitumour antibiotic chromoproteins, as represented by neocarzinostatin . These chromoproteins consist of a noncovalently bound, labile enediyne chromophore and its stabilising carrier apoprotein. The protein component of the chromophore displays an unusual bicyclic dienediyne structure. The chromoprotein inter-chelates the DNA, where its cycloaromatisation produces a biradical intermediate that has the ability to abstract hydrogens from the sugar moiety of DNA. This causes single- and double-strand breaks in the DNA . In addition to their ability to cleave DNA at sites specific for each chromophore, results indicate that these chromoproteins also possess proteolytic activity against histones, with histone H1 as the preferred substrate .

Neocarzinostatin has 2 disulphide bridges and is kidney-shaped with 2 defined domains that hold a binding cavity. The larger domain forms a 7-stranded antiparallel Î²-barrel and the smaller domain consists of 2 anti-parallel strands of Î² sheet that are perpendicular to each other . Other members of this family include macromycin, actinoxanthine, kedarcidin , and C-1027 .
Pfam PF07807: RED-like protein C-terminal region (family)
This family contains sequences that are similar to the C-terminal region of Red protein ([swissprot:Q13123]). This and related proteins are thought to be localised to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences. The function of Red protein is unknown,  but efficient sequestration to nuclear bodies suggests that its  expression may be tightly regulated or that the protein self-aggregates extremely efficiently.
Pfam PF08623: TATA-binding protein interacting (TIP20) (repeat)
TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription.
Pfam PF18513: Prodomain subtilisin 2 (domain)
Plasmodium subtilisin 2 (Sub2) is a multidomain protein that plays an important role in malaria infection. This domain is a conserved region of the inhibitory prodomain of Sub2 from Plasmodium falciparum, termed prosub2 which has structural similarity to bacterial and mammalian subtilisin-like prodomains.
Pfam PF24463: Domain of unknown function (DUF7577) (domain)
This entry represents a domain found in uncharacterised proteins from prokaryotes. It contains two pairs of conserved cysteines that are likely involved in metal coordination. This domain is predicted to structurally resemble Zinc beta-ribbon 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 PF12206: Domain of unknown function (DUF3599) (domain)
This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This domain is the phage-like element pbsx protein xkdh.
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 PF18960: Family of unknown function (DUF5702) (family)
This family is mostly 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 PF23948: ARM-like repeat (repeat)
This entry represents an array of alpha solenoid repeats found in a large family of fungal proteins. This domain is generally found at the N-terminus of the proteins followed by a NACHT domain [pfam:PF05729].