SII-SWORD/CoKE huggingface dataset:
Pfam PF16014: Histone deacetylase complex subunit SAP130 C-terminus (family)
SAP130 (Sin3-associated protein 130) is a component of the histone deacetylase-dependent co-repressor complex mSin3A that acts as a transcriptional repressor. It may function in the assembly and/or enzymatic activity of mSin3A or in mediating interactions between the complex and other regulatory complexes .
This entry represents the C-terminal domain of SAP130.
Wikipedia: Histone deacetylase complex subunit SAP130 is an enzyme that in humans is encoded by the SAP130 gene.
Pfam PF13485: Peptidase MA superfamily (domain)
This entry represents a domain found in a group of putative bacterial peptidases belonging to the MA clan.

Clan MA is one of two zinc-dependent metallopeptidases that contain the HEXXH motif. The two histidines are zinc ligands. The structures of this clan show the active site is between its two sub-domains.
Pfam PF16530: Infectious hypodermal and haematopoietic necrosis virus, capsid (domain)
IHHNV_capsid is the single capsid protein of infectious hypodermal and haematopoietic necrosis virus, found particularly in shrimp densovirus. Densoviruses are a subfamily of the parvoviruses.  The capsid protein has an eight-stranded anti-parallel beta-barrel 'jelly roll' motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the IHHNV coat protein adopts a 'domain-swappe' conformation relative to its twofold-related neighbour.  The loops connecting the strands of the structurally conserved jelly roll motif differ considerably in structure and length from those of other parvoviruses. IHHNV was first reported as a highly lethal disease of juvenile shrimp in 1983, and has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein is the smallest parvoviral capsid protein reported thus far. The small size of the PstDNV capsid protein makes the system attractive as a model for studying assembly mechanisms of icosahedral virus capsids.
Pfam PF22815: Alpha-1,3-glucanase catalytic domain D1 (domain)
This entry represents a domain found in the homologues of Alpha-1,3-glucanase. This domain is found N-terminal in the catalytic domain (CatAgl-FH1). It folds into a beta-sandwich that bears similarity to CBM35 domains and is thought to possess carbohydrate-binding function.
Pfam PF10831: Protein of unknown function (DUF2556) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
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 PF11762: L-arabinose isomerase C-terminal domain (domain)
This is a family of L-arabinose isomerases, AraA, [ec:5.3.1.4]. These enzymes catalyse the reaction: L-arabinose  L-ribulose. This reaction is the first step in the pathway of L-arabinose utilisation as a carbon source after entering the cell L-arabinose is converted into  L-ribulose by the L-arabinose isomerases enzyme. This is a C-terminal non catalytic domain.
Pfam PF15851: Domain of unknown function (DUF4723) (domain)
This domain is found in mammalian proteins. There are a number of conserved cysteines but it is unlikely to be a zinc-finger family. This entry includes PATE4 from mice. According to structure predictions (AlphaFold models and DALI server), this domain is structurally similar to members of the uPar/Lys6 domain superfamily.
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 PF00107: Zinc-binding dehydrogenase (domain)
Alcohol dehydrogenase (1.1.1.1) (ADH) catalyses the reversible oxidation of alcohols to their corresponding acetaldehyde or ketone with the concomitant reduction of NAD:

alcohol + NAD = aldehyde or ketone + NADH

Currently three structurally and catalytically different types of alcohol dehydrogenases are known:

 * Zinc-containing 'long-chain' alcohol dehydrogenases.
 * Insect-type, or 'short-chain' alcohol dehydrogenases.
 * Iron-containing alcohol dehydrogenases.

Zinc-containing ADH's  are dimeric or tetrameric enzymes that bind two atoms of zinc per subunit. One of the zinc atoms is essential for catalytic activity while the other is not. Both zinc atoms are coordinated by either cysteine or histidine residues; the catalytic zinc is coordinated by two cysteines and one histidine. Zinc-containing ADH's are found in bacteria, mammals, plants, and in fungi. In many species there is more than one isozyme (for example, humans have at least six isozymes, yeast have three, etc.). A number of other zinc-dependent dehydrogenases are closely related to zinc ADH  and are included in this family:


 * Sorbitol dehydrogenase (1.1.1.14)
 * L-threonine 3-dehydrogenase (1.1.1.103)
 * Glutathione-dependent formaldehyde dehydrogenase (1.1.1.284)
 * Mannitol dehydrogenase (1.1.1.255)


In addition, this family includes NADP-dependent quinone oxidoreductase (1.6.5.5), an enzyme found in bacteria (gene qor), in yeast and in mammals where, in some species such as rodents, it has been recruited as an eye lens protein and is known as zeta-crystallin . The sequence of quinone oxidoreductase is distantly related to that other zinc-containing alcohol dehydrogenases and it lacks the zinc-ligand residues. The torpedo fish and mammalian synaptic vesicle membrane protein vat-1 is related to qor.

This entry represents the cofactor-binding domain of these enzymes, which is normally found towards the C terminus. Structural studies indicate that it forms a classical Rossman fold that reversibly binds NAD(H) .
Pfam PF18756: Nucleotide modification associated domain 4 (domain)
An alpha+beta fold domain typically associated with DNA methylases and likely to be involved in modified nucleotide biosynthesis.
Pfam PF00512: His Kinase A (phospho-acceptor) domain (domain)
Dimerisation and phospho-acceptor domain of histidine kinases.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF06847: Archaeal Peptidase A24 C-terminus Type II (domain)
This region is of unknown function but is found in some archaeal [pfam:PF01478]. It is predicted to be of mixed alpha/beta secondary structure by Prof.
Pfam PF11871: Domain of unknown function (DUF3391) (domain)
This functionally uncharacterised, N-terminal domain is found in a number of bacterial proteins, including Cyclic di-GMP phosphodiesterase PA4108 ([swissprot:Q9HWS0]). It is often found associated with the HD domain [pfam:PF13328].
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 PF20392: Family of unknown function (DUF6687) (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 342 and 363 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 PF22716: Short NACHT-associated C-Terminal domain, family 11 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF22046: Enoyl-acyl carrier protein reductase FabMG (family)
This entry, previously known as DUF6936, represents FabMG enoyl-acyl carrier protein reductase (ENR) and related proteins. This enzyme is a FabI-type ENR that employs NADH as a coenzyme and mediates resistance to triclosan. FabMG adopts an alpha/beta structure, with a central parallel beta-sheet elaborated with alpha-helices on both sides. FabMG differs from other related ENRs in sequence and structure. These differences, in particular in the substrate-binding loop and pocket regions in which triclosan binds, could be responsible for the triclosan resistance.
Pfam PF03800: Nuf2 family (family)
Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, [swissprot:Q9C953]. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region.
Pfam PF00264: Common central domain of tyrosinase (domain)
This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to [pfam:PF00372].
Wikipedia: Tyrosinase is an oxidase that is the rate-limiting enzyme for controlling the production of melanin. The enzyme is mainly involved in two distinct reactions of melanin synthesis otherwise known as the Raper–Mason pathway. Firstly, the hydroxylation of a monophenol and secondly, the conversion of an o-diphenol to the corresponding o-quinone. o-Quinone undergoes several reactions to eventually form melanin. Tyrosinase is a copper-containing enzyme present in plant and animal tissues that catalyzes the production of melanin and other pigments from tyrosine by oxidation. It is found inside melanosomes which are synthesized in the skin melanocytes. In humans, the tyrosinase enzyme is encoded by the TYR gene.
Pfam PF19064: Family of unknown function (DUF5760) (family)
This is a family of uncharacterised proteins of unknown function found in Phycodnaviridae and Mimiviridae.
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 PF15261: Jhy protein (family)
Jhy protein is the protein product of the gene Jhy (previously known as 4931429I11Rik). This protein family is found in eukaryotes, and is approximately 120 amino acids in length. In humans, the gene encoding this protein lies in the position chromosome 11 open reading frame 63.
Pfam PF07197: Protein of unknown function (DUF1409) (family)
This family represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa 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 PF06120: Tail length tape measure protein (family)
This family consists of the tail length tape measure protein from bacteriophage HK97 and related sequences from Escherichia coli O157:H7.
Pfam PF08053: Tryptophanase operon leader peptide (family)
This family consists of the tryptophanase (tna) operon leader peptide. Tna catalyses the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilise tryptophan as a source of carbon, nitrogen and energy.  The tna operon of E. coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon.
Pfam PF23112: U-box protein 62/63 C-terminal (domain)
This is a domain found at the C-terminal of Plant U-Box 62/63 (PUB62/63) from Arabidopsis thaliana and similar proteins from plants. The U-box mediates interaction with the ubiquitin-conjugating enzyme (E2), which is the signature domain for plant U-box type E3 ligases (PUBs). According to structure predictions, this domain may adopt a SH3-like barrel fold.
Wikipedia: The SRC Homology 3 Domain is a small protein domain of about 60 amino acid residues. Initially, SH3 was described as a conserved sequence in the viral adaptor protein v-Crk. This domain is also present in the molecules of phospholipase and several cytoplasmic tyrosine kinases such as Abl and Src. It has also been identified in several other protein families such as: PI3 Kinase, Ras GTPase-activating protein, CDC24 and cdc25. SH3 domains are found in proteins of signaling pathways regulating the cytoskeleton, the Ras protein, and the Src kinase and many others. The SH3 proteins interact with adaptor proteins and tyrosine kinases. Interacting with tyrosine kinases, SH3 proteins usually bind far away from the active site. Approximately 300 SH3 domains are found in proteins encoded in the human genome. In addition to that, the SH3 domain was responsible for controlling protein-protein interactions in the signal transduction pathways and regulating the interactions of proteins involved in the cytoplasmic signaling.
Pfam PF02627: Carboxymuconolactone decarboxylase family (family)
Carboxymuconolactone decarboxylase (CMD) [ec:4.1.1.44] is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins (e.g. [swissprot:O67982]) CMD represents the C-terminal domain, [pfam:PF00561] represents the  N-terminal domain.
Pfam PF03856: Beta-glucosidase (SUN family) (family)
Members of this family include Nca3, Sun4 and Sim1. This is a family of yeast proteins, involved in a diverse set of functions (DNA replication, aging,  mitochondrial biogenesis and cell septation). BGLA from Candida wickerhamii has been characterised as a Beta-glucosidase [ec:3.2.1.21].
Pfam PF08894: Protein of unknown function (DUF1838) (family)
This family of proteins are functionally uncharacterised.
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 PF09794: Transport protein Avl9 (family)
Avl9 is a protein involved in exocytic transport from the Golgi. It has been speculated that Avl9 could play a role in deforming membranes for vesicle fission and/or in recruiting cargo.
Pfam PF02525: Flavodoxin-like fold (domain)
This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) [ec:1.6.99.2].  These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species.          This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor  NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase [ec:3.1.4.14]. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to [pfam:PF03358] and [pfam:PF00258].
Pfam PF16641: CLIP1 zinc knuckle (family)
This zinc knuckle domain is found tandemly repeated at the C-terminal of the cytoplasmic linker protein CLIP1 (CLIP170). It forms a complex with the CAP-Gly domain of Dynactin.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF22666: Glycosyl hydrolase 2 galactose-binding domain-like (domain)
This domain is found in a number of proteins belonging to glycosyl hydrolase 2 family.
Pfam PF21916: Mtd second domain (domain)
This entry represents the second domain of Mtd. The major tropism determinant (Mtd, 40 kDa), the receptor-binding protein of Bordetella bacteriophage, varies greatly in sequence. Variation in Mtd depends on a phage-encoded retroelement that belongs to a family of retroelements implicated in generating sequence diversity in various phage and bacterial genomes. The second domain forms a beta sandwich structure.
Pfam PF20212: Family of unknown function (DUF6572) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 107 and 214 amino acids in length. These proteins may have a threefold symmetric beta-trefoil fold, a symmetric protein structure thought to be conserved in protein evolution.
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 PF10790: Protein of Unknown function (DUF2604) (family)
Family of bacterial proteins with undetermined 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 PF25018: Importin-9 central HEAT repeats (repeat)
Importin-9 is a nuclear transport receptor that mediates nuclear import of proteins, such as histones, proteasome and actin. It consists of 20 tandem HEAT repeats. This entry represents a central segment of HEAT repeats which includes repeats 7-8 that are part of interface 2 that interacts with a five-residue segment of the H2B N-terminal tail described in.
Pfam PF16731: Glutamic acid/alanine-rich protein of Trypanosoma (domain)
GARP, or glutamic acid/alanine-rich protein, is one of a subset of major surface molecules on Trypanosoma species.  They are all surface-orientated, immunodominant, and highly charged. GARP is interesting as ts expression coincides with the loss and gain of variant surface glycoprotein (VSG) molecules in the tsetse vector. It has an extended helical bundle structure that is homologous to the core surface structure of VSG, suggesting that it might replace the bloodstream VSG as the trypanosomes differentiate inside the tsetse vector after a blood-meal.
Pfam PF13184: NusA-like KH domain (domain)
This entry represents K homology (KH) domains of the type found in NusA transcription termination factors. KH domains bind RNA, and can function in RNA recognition . NusA binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures .
Wikipedia: The K Homology (KH) domain is a protein domain that was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. An evolutionarily conserved sequence of around 70 amino acids, the KH domain is present in a wide variety of nucleic acid-binding proteins. The KH domain binds RNA, and can function in RNA recognition. It is found in multiple copies in several proteins, where they can function cooperatively or independently. For example, in the AU-rich element RNA-binding protein KSRP, which has 4 KH domains, KH domains 3 and 4 behave as independent binding modules to interact with different regions of the AU-rich RNA targets. The solution structure of the first KH domain of FMR1 and of the C-terminal KH domain of hnRNP K determined by nuclear magnetic resonance (NMR) revealed a beta-alpha-alpha-beta-beta-alpha structure. Autoantibodies to NOVA1, a KH domain protein, cause paraneoplastic opsoclonus ataxia. The KH domain is found at the N-terminus of the ribosomal protein S3. This domain is unusual in that it has a different fold compared to the normal KH domain.