SII-SWORD/CoKE huggingface dataset:
Pfam PF01315: Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain (domain)
Aldehyde oxidase (1.2.3.1) catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase (1.1.1.204) catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase (1.1.3.22) activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups.

The aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain is an evolutionary conserved protein domain .

This entry includes also the a/b hammerhead domain of the Nicotine 6-hydroxylase ndhL that is involved in the degradation of nicotine .
Wikipedia: IN, In or in may refer to:
Pfam PF17166: Domain of unknown function (DUF5126) (family)
This domain lies C-terminal to DUF4959, [pfam:PF16323].
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 PF02118: Srg family chemoreceptor (family)
G protein-coupled receptors (GPCRs) constitute a vast protein family that encompasses a wide range of functions, including various autocrine, paracrine and endocrine processes. They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups . The term clan can be used to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence . The currently known clan members include rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) . GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice . Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs .
The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli . Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' . Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr . Many of these proteins have homologues in Caenorhabditis briggsae.
This entry represents serpentine receptor class g (Srg) from the Srg superfamily . Srg receptors contain seven hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.
Pfam PF07073: Modulator of Rho-dependent transcription termination (ROF) (family)
This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo.
Pfam PF24340: DBL homology domain (DH-domain) (domain)
This domain is found in uncharacterised fungal proteins. It shares significant sequence similarity to known DBL homology domains (DH-domains) and it is predicted to adopt similar structure. Proteins containing this domain also contain a PH-domain located upstream the DH-domain and are likely members of the Dbl family of guanine nucleotide exchange factors.
Pfam PF23899: Phage SU10 portal protein (family)
This entry represents the portal protein of Escherichia coli phage SU10.  The portal protein, encoded by gp6, forms a dodecameric complex that replaces a pentamer of capsid proteins at one vertex of the prolate SU10 capsid. The portal complex enables packaging of the viral genome into the capsid as well as attachment of the phage tail. The portal protein contains wing, stem, clip, crown and barrel domains. The wing domain interacts with the viral DNA and the capsid proteins. The clip domain enables attachment of the adaptor protein complex.
Pfam PF21419: RoxA-like, cytochrome c-like (domain)
This entry represents a cytochrome c-like domain described in RoxA from Xanthomonas sp, one of only two known enzymes able to catalyse the oxidative cleavage of latex for biodegradation. This domain contains the second heme-binding motif. This domain is found in the uncharacterised proteins y4iM and Y4IJ from Sinorhizobium fredii.
Pfam PF01291: LIF / OSM family (domain)
On the basis of functional and structural similarities, the small cytokines leukemia inhibitory factor (LIF) and oncostatin (OSM) can be classified into a single family .

It has been said  that LIF and OSM can be included in the IL-6 family of cytokines, but while all these cytokines seem to be structurally related, the sequence similarity is not high enough to allow the use of a single consensus pattern.
Pfam PF22940: CCR4-NOT transcription complex subunit 1, N-terminal domain (repeat)
This domain is found at the N-terminal end of human CCR4-NOT transcription complex subunit 1 (CNOT1) and similar sequences from animals. CNOT1 is a scaffolding component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. This domain adopts the structure of an helical HEAT-repeat.
Pfam PF10185: Chaperone for wingless signalling and trafficking of LDL receptor (family)
Mesd is a family of highly conserved proteins found from nematodes to humans. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs). The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation).
Pfam PF12713: Domain of unknown function (DUF3806) (domain)
This family represent the C-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1ma7 whose C-terminal domain is a phage integrase, [pfam:PF00589].
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 PF22059: Glucuronosyltransferase GumK, N-terminal domain (domain)
Beta-1,2-glucuronosyltransferase GumK is a membrane- associated protein that is involved in the biosynthesis of xanthan. The GumK enzyme is the founding member of the glycosyltransferase family 70 of carbohydrate-active enzymes, which is composed of bacterial glycosyltransferases involved in exopolysaccharide synthesis. This protein consists of two domains, N-terminal of which is represented by this entry.
Pfam PF05409: Coronavirus endopeptidase C30 (family)
This Coronavirus (CoV) domain, peptidase C30, is also known as 3C-like proteinase (3CL-pro), or CoV main protease (M-pro) domain. CoV M-pro (alsp known as non-structural protein 5, NSP5) is a dimer where each subunit is composed of three domains I, II and III. Domains I and II consist of six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin, and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad. In contrast to serine proteinases and other cysteine proteinases, which have a catalytic triad, there is no third catalytic residue present. This peptidase is involved in viral polyprotein processing during replication.
Wikipedia: The 3C-like protease (3CLpro) or main protease (Mpro), formally known as C30 endopeptidase or 3-chymotrypsin-like protease, is the main protease found in coronaviruses. It cleaves the coronavirus polyprotein at eleven conserved sites. It is a cysteine protease and a member of the PA clan of proteases. It has a cysteine-histidine catalytic dyad at its active site and cleaves a Gln–(Ser/Ala/Gly) peptide bond.
Pfam PF08187: Myoactive tetradecapeptides family (family)
This family consists of myoactive tetradecapeptides that are isolated from the gut of earthworms, Eisenia foetida and Pheretima vitata. These peptides were termed ETP and PTP respectively. Both peptides showed a potent excitatory action on spontaneous contractions of the anterior gut. These peptides show similarity to Molluscan tetradecapeptides and arthropodan tridecapeptides.
Pfam PF13175: AAA ATPase domain (domain)
This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
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 PF01585: G-patch domain (family)
This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains.  This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.
Pfam PF14336: D-glutamate cyclase-like, C-terminal (domain)
This entry represents the C-terminal domain of mitochondrial D-glutamate cyclase, which converts D-glutamate to 5-oxo-D-proline. This is a conserved domain also found in uncharacterised proteins from bacteria and archaea. Structural studies of the hypothetical protein TON_0340 from Thermococcus onnurineus revealed an active-site cavity harbouring a metal-binding site containing six invariant aspartate and glutamate residues that adopts an alpha/beta-structure. Biochemical and mutational analysis show that TON_0340 is a Mn+2-dependent phosphatase.
Pfam PF04102: SlyX (coiled_coil)
The SlyX protein has no known function.  It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure.
Pfam PF16103: Domain of unknown function (DUF4822) (domain)
A lipocain-like domain found in functionally uncharacterised bacterial proteins, often as a repeat of two domains. Proteins with this domain  are found in a wide range of bacteria and are often annotated as S-layer proteins, but the origin of this annotation is not clear
Pfam PF18634: RXLR phytopathogen effector protein WY-domain (domain)
Filamentous plant pathogens cause devastating diseases of crops. Phytophthora infestans, the Irish potato famine pathogen, facilitates disease on its hosts by delivering effector proteins that modulate host cell processes to the benefit of the parasite, a strategy used by many biotrophic plant pathogens. The Phytophthora infestans RXLR-type effector PexRD54 binds potato ATG8 via its ATG8 family-interacting motif (AIM) and perturbs host-selective autophagy. The N-terminal region of PexRD54 contains 5 tandem WY domains. The WY domain is a conserved structural unit consisting of three alpha-helices and two characteristic hydrophobic amino acids, frequently W (Trp) and Y (Tyr), which contribute to a stable hydrophobic core. Deletion analysis show that the WY domains of PexRD54 are dispensable for ATG8CL binding suggesting an alternative function for these domains.
Pfam PF13307: Helicase C-terminal domain (domain)
This domain is found at the C-terminus of DEAD-box helicases.
Pfam PF03904: Domain of unknown function (DUF334) (family)
Staphylococcus aureus plasmid proteins with no characterised 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 PF05794: T-complex protein 11 (family)
This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants.
Pfam PF00973: Paramyxovirus nucleocapsid protein (family)
The nucleocapsid protein is referred to as NP.  NP is is the major structural component of the nucleocapsid. The protein is approx. 58 kDa. 2600 NP molecules go to tightly encapsidate the RNA. NP interacts with several other viral encoded proteins, all of which are involved in controlling replication. {NP-NP, NP-P, NP-(PL), and NP-V}.
Pfam PF21610: Flagellar protein FlgA, N-terminal domain-like (domain)
This domain is found at the N-terminal end of Flagellar protein FlgA, putative from Thermotoga maritima ([swissprot:Q9X1M7]). It adopts an alpha-beta structure.
Pfam PF04370: Domain of unknown function (DUF508) (family)
This is a family of uncharacterised proteins from C. elegans.
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 PF18850: Large polyvalent protein associated domain 30 (domain)
This is an alpha and beta fold domain that is found in polyvalent proteins of conjugative elements.
Pfam PF17076: SBE2, C-terminal domain (domain)
This entry represents a domain found C-terminal in Sbe2 and its paralogue, Sbe22 from budding yeast. These proteins are involved in bud growth and yeast cell wall formation. They may be also involved in the transport of cell wall components from the Golgi apparatus to the cell surface periphery. This domain is predicted to adopt a globular structure with similarity to TBC domains.
Pfam PF00141: Peroxidase (domain)
This entry represents the first type of haem peroxidases found predominantly in bacteria, fungi, plants.
Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme:Fe3++ H2O2-->R' (Compound I) + H2O R' + substrate -->R (Compound II) + oxidised substrate R + substrate -->Fe3++ H2O + oxidised substrate

In this mechanism, the enzyme reacts with one equivalent of H2O2to give R' (compound I). This is a two-electron oxidation/reduction reaction where H2O2is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl  intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical .

Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes. Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress .

Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+serves as the reducing substrate . Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites.

Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes.
Wikipedia: Haem peroxidases (or heme peroxidases) are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme:Fe3+ + H2O2  [Fe4+=O]R' (Compound I) + H2O[Fe4+=O]R' + substrate --&gt; [Fe4+=O]R (Compound II) + oxidized substrate[Fe4+=O]R + substrate --&gt; Fe3+ + H2O + oxidized substrate
Pfam PF03598: CO dehydrogenase/acetyl-CoA synthase complex beta subunit (domain)
The carbon monoxide dehydrogenase alpha subunit (1.2.7.4) catalyses the interconversion of CO and CO2 and the synthesis of acteyl-coA from the methylated corrinoid/iron sulphur protein, CO and CoA. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Pfam PF01308: Chlamydia major outer membrane protein (domain)
The major outer membrane protein of Chlamydia contains four symmetrically spaced variable domains (VDs I to IV).  This protein is believed to be an integral part to the pathogenesis, possibly adhesion. Along with the lipopolysaccharide, the major out membrane  protein (MOMP) makes up the surface of the elementary body cell.   The MOMP is the protein used to determine the different serotypes.
Pfam PF22856: Peptide tarsal-less 1A/2A (family)
This protein family includes the short small open-reading frames (smORF) peptides Peptide tarsal-less 1A/2A from Drosophila melanogaster (Tal-1A_2A), which are involved in several developmental processes.
Pfam PF17013: Putative acetyl-transferase (family)
This is a family of microsporidial proteins which may be distantly related to acetyl-transferase.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF19669: Family of unknown function (DUF6172) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 116 amino acids in length. There is a conserved KRER sequence motif.
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 PF09598: Stm1 (family)
This region is found at the N terminal of the Stm1 protein. Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein.  It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with CDC13, and is known to associate with ribosomes and nuclear telomere cap complexes.
Pfam PF23718: Family of unknown function (DUF7160) (family)
This protein family includes a group of uncharacterised short sequences from actinobacteria.
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 PF10913: Protein of unknown function (DUF2706) (family)
This family of proteins with unknown function appears to be restricted to Rickettsia 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 PF18492: Open reading frame 2 N-terminal domain (domain)
This is the N-terminal domain found in ORF 2 (open reading frame 2), a protein encoded just downstream of asp (A. sobria serine protease). The ORF 2 N-terminal domain is essential for proper ASP folding. This domain is intrinsically disordered but forms some degree of secondary structure upon binding ASP.
Pfam PF10380: Transcription factor CRF1 (family)
CRF1 is a transcription factor that co-represses ribosomal genes with FHL1 via the TOR signalling pathway and protein kinase A.