SII-SWORD/CoKE huggingface dataset:
Pfam PF00465: Iron-containing alcohol dehydrogenase (domain)
Alcohol dehydrogenase (1.1.1.1) (ADH) catalyses the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. 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.


Iron-containing ADH's have been found in yeast (gene ADH4) , as well as in Zymomonas mobilis (gene adhB) . These two iron-containing ADH's are closely related to the following enzymes:


 * Escherichia coli lactaldehyde reductase (also known as propanediol oxidoreductase) (1.1.1.77) (gene fucO) , an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s).
 * Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1) (genes adh1, bdhA and bdhB) , an enzyme which has activity using butanol and ethanol as substrates.
 * E. coli aldehyde-alcohol dehydrogenase (AdhE) , an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10) and pyruvate-formate-lyase deactivase.
 * Bacterial glycerol dehydrogenase (1.1.1.6) (gene gldA or dhaD) .
 * Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61).
 * Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202) (gene dhaT).
 * Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244) .
 * E. coli and Salmonella typhimurium ethanolamine utilization protein eutG.
 * E. coli hypothetical protein yiaY.
Wikipedia: Alcohol dehydrogenases (ADH) (EC 1.1.1.1) are a group of dehydrogenase enzymes that occur in many organisms and facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of nicotinamide adenine dinucleotide (NAD+) to NADH. In humans and many other animals, they serve to break down alcohols that are otherwise toxic, and they also participate in the generation of useful aldehyde, ketone, or alcohol groups during the biosynthesis of various metabolites. In yeast, plants, and many bacteria, some alcohol dehydrogenases catalyze the opposite reaction as part of fermentation to ensure a constant supply of NAD+.
Pfam PF01446: Replication protein (family)
Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin  (dso) of replication.  The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase.
Pfam PF00854: POT family (family)
The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters.
Wikipedia: Proteins of the Proton-dependent Oligopeptide Transporter (POT) Family are found in animals, plants, yeast, archaea and both Gram-negative and Gram-positive bacteria, and are part of the major facilitator superfamily. The transport of peptides into cells is a well-documented biological phenomenon which is accomplished by specific, energy-dependent transporters found in a number of organisms as diverse as bacteria and humans. The proton-dependent oligopeptide transporter (PTR) family of proteins is distinct from the ABC-type peptide transporters and was uncovered by sequence analyses of a number of recently discovered peptide transport proteins. These proteins that seem to be mainly involved in the intake of small peptides with the concomitant uptake of a proton.
Pfam PF07161: LppX_LprAFG lipoprotein (domain)
This entry consists of several lipoproteins mainly from Mycobacterium species, collectively known as the LppX_ LprAFG family. Proteins in this entry include LprG, LppX,  LprF and lprA.
Pfam PF20057: Domain of unknown function (DUF6456) (domain)
This presumed domain is sometimes associated with a helix-turn-helix domain suggesting that it may be a small molecule ligand binding domain.  This family of proteins is 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 PF04620: Flagellar filament outer layer protein Flaa (family)
Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such connective tissue. The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species.
Pfam PF17070: 30S ribosomal protein Thx (family)
Thx forms part of the 30S ribosomal subunit. It fits into a cavity between multiple RNA elements in the top of the 30S subunit head and stabilises the organisation of these elements.
Pfam PF23923: Family of unknown function (DUF7262) (family)
This entry represents uncharacterised proteins found mainly in Halobacteria. They are composed of N-terminal transmembrane helix and alpha/beta globular domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19921: MoxR-vWA-beta-propeller ternary system domain bpX5 (domain)
Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF08368: FAST kinase-like protein, subdomain 2 (family)
This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases ([ec:2.7.1.-]) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Pfam PF00656: Caspase domain (domain)
This domain can be found in caspases (MEROPS family C12A) and metacaspases (MEROPS family C14B). Metacaspases adopt a caspase fold, with active site loops arranged similarly as other caspases .

Caspases (Cysteine-dependent ASPartyl-specific proteASE) are cysteine peptidases . They are tightly regulated proteins that require zymogen activation to become active, and once active can be regulated by caspase inhibitors. Caspases are mainly involved in mediating cell death (apoptosis) . They have two main roles within the apoptosis cascade: as initiators that trigger the cell death process, and as effectors of the process itself. Caspases can have roles other than in apoptosis, such as caspase-1 (interleukin-1 beta convertase) (3.4.22.36), which is involved in the inflammatory process. The activation of apoptosis can sometimes lead to caspase-1 activation, providing a link between apoptosis and inflammation, such as during the targeting of infected cells. Caspases may also be involved in cell differentiation .

Metacaspases are arginine/lysine-specific, in contrast to caspases, which are aspartate-specific. They are found only in plants , fungi  and lower eukaryotes, including the protozoa . While plant metacaspases have been shown to be involved in cell death pathways, in other organisms they have evolved alternative functions .
Wikipedia: Caspases are a family of protease enzymes playing essential roles in programmed cell death. They are named caspases due to their specific cysteine protease activity – a cysteine in its active site nucleophilically attacks and cleaves a target protein only after an aspartic acid residue. As of 2009, there are 12 confirmed caspases in humans and 10 in mice, carrying out a variety of cellular functions.
Pfam PF23526: AprA N-terminal domain (domain)
This entry represents a domain found N-terminal in the homologues of AprA Methyltransferase 1. AprA is an S-adenosylmethionine and Fe3+-dependent dimethyltransferase that acts in the initiation steps of apratoxin A biosynthesis. This domain has similarity to winged helix domains.
Pfam PF18392: COP9 signalosome complex subunit 7a helix I domain (domain)
This is The C-terminal helix I domain found in COP9 signalosome complex subunit 7a. The helix from CSN7 (helix I) contacts CSN6 helices I and II at the base of the bundle, nearest the PCI ring.
Pfam PF17283: SprT-like zinc ribbon domain (domain)
This family represents a domain found in eukaryotes and prokaryotes.  The domain contains a characteristic motif of the zinc ribbon. This family includes the bacterial SprT protein.
Pfam PF11737: Protein of unknown function (DUF3300) (family)
This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
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 PF03764: Elongation factor G, domain IV (domain)
This domain is found in elongation factor G, elongation  factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.
Wikipedia: EF-G is a prokaryotic elongation factor involved in mRNA translation. As a GTPase, EF-G catalyzes the movement (translocation) of transfer RNA (tRNA) and messenger RNA (mRNA) through the ribosome.
Pfam PF13749: Putative ATP-dependent DNA helicase recG C-terminal (domain)
This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
Pfam PF06911: Senescence domain (family)
This is the AAA ATPase senescence domain (SC) found at the C-terminal of plant senescence-associated proteins and spartin. In Hemerocallis, petals a genetically based program that leads to senescence and cell death approximately 24 hours after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program. This domain is also present at the C-terminal of Spartin, a protein from higher vertebrates associated with mitochondrial membranes and transportation along microtubules. Spartin functions presynaptically with endocytic adaptor Eps15 to regulate synaptic growth and function. Mutations in human spartin gene cause Troyer syndrome, a hereditary spastic paraplegia. This AAA ATPase domain, similar to other AAA proteins contain an alpha/beta nucleotide-binding domain (NBD) and a smaller four-helix bundle domain (HBD). Uniquely among  AAA structures, spastin has two helices (N-terminal alpha1 and C-terminal alpha11) hat embrace the NBD.
Pfam PF20397: Family of unknown function (DUF6690) (family)
This presumed domain is functionally uncharacterised. This domain family is found in Planctomycete bacteria, and is approximately 170 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 PF01589: Alphavirus E1 glycoprotein (family)
E1 forms a heterodimer with E2 [pfam:PF00943].  The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus).
Wikipedia: Alphavirus is a genus of RNA viruses, the sole genus in the Togaviridae family. Alphaviruses belong to group IV of the Baltimore classification of viruses, with a positive-sense, single-stranded RNA genome. There are 32 alphavirus species, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. Alphaviruses that can infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and their vertebrate hosts occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical, and have a 40 nm isometric nucleocapsid.
Pfam PF04073: Aminoacyl-tRNA editing domain (family)
This domain is found either on its own or in association with the tRNA synthetase class II core domain ([pfam:PF00587]).  It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro).  The structure of this domain shows a novel fold.
Wikipedia: In molecular biology, this protein domain of unknown function is found in numerous prokaryote organisms. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA.
Pfam PF17998: Cell surface antigen I/II C2 terminal domain (domain)
This is the second domain (C2) located in the C-terminal region found in antigen I/II type adhesin protein AspA from S. pyogenes. Together with C3, these two domains form an elongated structure, each domain adopts the DEv-IgG fold. Similar to the classical IgG folds, it is comprised of two major antiparallel beta-sheets, designated ABED and CFG. For the C2-domain, there are two additional strands on the CFG sheet. Furthermore, sheets ABED and CFG are interconnected by several cross-connecting loops and one alpha-helix (DH1). The side chains of D982 and N996 in the C2-domain are involved in hydrogen bonding with the side chains of R1264 and N1295 in the C3 domain. Main chain hydrogen bonding can also be observed between S992 in C2 and N1189/G1191 in C3, furthermore stabilizing the interaction between the domains. The C2 domain contains one bound metal ion, modelled as Ca2+, and both the C2- and C3-domains are stabilized by conserved isopeptide bonds, which connect the beta-sheets of the central DEv-IgG motifs.Other members of this family include Major cell-surface adhesin PAc from Streptococcus mutans and SspB from Streptococcus gordonii.
Pfam PF02932: Neurotransmitter-gated ion-channel transmembrane region (family)
This family includes the four transmembrane helices that form the ion channel.
Wikipedia: Ligand-gated ion channels (LICs, LGIC), also commonly referred to as ionotropic receptors, are a group of transmembrane ion-channel proteins which open to allow ions such as Na+, K+, Ca2+, and/or Cl− to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand), such as a neurotransmitter.
Pfam PF22986: ELFN1/ELFN2, fibronectin type-III domain (domain)
This domain is found in the homologues of human ELFN1 and ELFN2 proteins. The postsynaptic ELFN1 regulates target-specific presynaptic properties which influences the timing of recruitment of inhibitory neuron subtypes. Both ELFN1 and ELFN2 inhibit the phosphatase activity of protein phosphatase 1 (PP1) complexes. This domain is predicted to adopt a Ig-like beta-sandwich with significant similarity to fibronectin type III domains.
Pfam PF14210: Domain of unknown function (DUF4322) (family)
This presumed domain is functionally uncharacterised. This domain family is found in archaea, and is approximately 60 amino acids in length. There is a conserved QTV 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 PF22011: Family of unknown function (DUF6931) (family)
This is a family of uncharacterised bacterial proteins. They share significant sequence similarity with immunity protein Imm5 and are predicted to adopt similar alpha-helical 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 PF12919: TcdA/TcdB catalytic glycosyltransferase domain (domain)
This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein.
Wikipedia: Clostridioides difficile toxin B (TcdB) is a cytotoxin produced by the bacteria Clostridioides difficile. It is one of two major kinds of toxins produced by C. difficile, the other being a related enterotoxin. Both are very potent and lethal.
Pfam PF11281: Protein of unknown function (DUF3083) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF07816: Protein of unknown function (DUF1645) (family)
These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this.
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 PF11945: WAHD domain of WASH complex (domain)
This domain forms part of the WASH-complex of domains and proteins that activates the Arp2/3 complex, see [pfam:PF04062]. The Arp2/3 complex regulates endocytosis, sorting, and trafficking within the cell. The WAHD domain attaches to the FAM21 proteins via its N-terminal residues and to the microtubules via its C-terminal residues.
Pfam PF12349: Sterol-sensing domain of SREBP cleavage-activation (family)
Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus.
Pfam PF06842: Protein of unknown function (DUF1242) (family)
This family consists of a number of eukaryotic proteins of around 72 residues in length. 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 PF10432: Bacterial phospho-glucose isomerase C-terminal SIS domain (domain)
This is the C-terminal SIS domain of a bacterial phospho-glucose isomerase [ec:5.3.1.9] protein which is similar to eukaryote homologues to the extent that the sequence includes the cluster of threonines and serines that forms the sugar phosphate-binding site in conventional PGI. This domain contributes a good proportion of the active catalytic site residues. This PGI uses the same catalytic mechanisms for both glucose ring-opening and isomerisation for the interconversion of glucose 6-phosphate to fructose 6-phosphate.  It is associated with family SIS, [pfam:PF01380].
Wikipedia: Glucose-6-phosphate isomerase (GPI), alternatively known as phosphoglucose isomerase/phosphoglucoisomerase (PGI) or phosphohexose isomerase (PHI), is an enzyme that in humans is encoded by the GPI gene on chromosome 19.
This gene encodes a member of the glucose phosphate isomerase protein family. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. In the cytoplasm, the gene product functions as a glycolytic enzyme that interconverts glucose-6-phosphate (G6P) and fructose-6-phosphate (F6P). Extracellularly, the encoded protein functions as a neurotrophic factor that promotes survival of skeletal motor neurons and sensory neurons, and as a lymphokine that induces immunoglobulin secretion. The encoded protein is also referred to as autocrine motility factor (AMF) based on an additional function as a tumor-secreted cytokine and angiogenic factor. Defects in this gene are the cause of nonspherocytic hemolytic anemia, and a severe enzyme deficiency can be associated with hydrops fetalis, immediate neonatal death and neurological impairment. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Pfam PF06127: 2-hydroxy-palmitic acid dioxygenase Mpo1-like (family)
Budding yeast Mpo1 is a dioxygenase that catalyzes the alpha-oxidation of a 2-hydroxy fatty acid in an Fe2+-dependent manner. This entry also includes Mpo1 homologues from bacteria, fungi and plants. Their function is not clear.