SII-SWORD/CoKE huggingface dataset:
Pfam PF17797: RL domain (domain)
The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase PAPD1. It contributes to PAPD1 dimerization and has a fold similar to RNP-type RBDs.
Pfam PF12281: Nucleotidyltransferase (family)
This is a family of bacterial proteins that have a nucleotidyltransferase fold. The fold-prediction is backed up by conservation of three highly characteristic sequence motifs found in all other nucleotidyl transferases: i) pDhDhhh(h/p), where p is a polar residue and h is a hydrophobic residue; ii) upstream of the first, a GG/S; iii) a conserved D/E in a hydrophobic surround. In the classification of nucleotidyltransferases proposed in this is a group XVIII NTP-transferase. Many of these sequences were classified in the COG database as COG5397. The exact function is not known.
Pfam PF06138: Chordopoxvirus E11 protein (family)
This family consists of several Chordopoxvirus E11 proteins. The E11 gene of vaccinia virus encodes a 15-kDa polypeptide. Mutations in the E11 gene makes the virus temperature-sensitive due to either the fact that virus infectivity requires a threshold level of active E11 protein or that E11 function is conditionally essential.
Pfam PF16168: Adhesin of bacterial autotransporter system, probable stalk (repeat)
The AIDA repeat is found on bacterial autotransporter proteins. As the repeat is short and occurs multiple times, it is likely to be the region of the transporter that acts as the stalk between the beta-barrel inserted into the membrane and the N-terminal head domain.
Pfam PF09958: Uncharacterized protein conserved in archaea (DUF2192) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15884: MICOS complex subunit MIC13, QIL1 (family)
Mic13 (also known as Qil1) is a component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Mic13 is required for MICOS complex stability and cristae morphology. Family members such as C19orf70/QIL1 from human are orthologous to the yeast MIC12 [pfam:PF17050].
Pfam PF12728: Helix-turn-helix domain (domain)
This domain is a DNA-binding helix-turn-helix domain.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF21813: Family of unknown function (DUF6882) (family)
This family of bacterial proteins is 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 PF09047: MEF2 binding (domain)
The myocyte enhancer factor-2 (MEF2) binding domain, predominantly found in the calcineurin-binding protein CABIN 1, adopts an amphipathic alpha-helical structure, which allows it to bind a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription.
Pfam PF03613: PTS system mannose/fructose/sorbose family IID component (family)
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS)  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.

The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).
Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Mannose (Man) family is unique in several respects among PTS permease families.


 * It is the only PTS family in which members possess a IID protein.
 * It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue.
 * Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars.


The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine.
Pfam PF04927: Seed maturation protein (family)
Plant seed maturation protein.
Pfam PF18310: Domain of unknown function (DUF5605) (domain)
This domain is found in the C-terminal region of proteins carrying [pfam:PF16586] and [pfam:PF13204]. The C-terminal domain is carried by species such as Bacteroides vulgatus.
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 PF14130: Cap4, dsDNA endonuclease domain (domain)
This domain family corresponds to the N-terminal of CD-NTase associated protein 4 (Cap4) from bacteria and archaea. CD-NTase-associated protein 4 (Cap4) is a nucleotide second messenger sensor that functions is CBASS immunity. This is the effector domain which has dsDNA nuclease activity, sharing structural homology with type II restriction endonucleases and it has the putative active-site conserved residues required for divalent metal coordination. This domain is inactive as a monomer; after Cap4 signal recognition through its C-terminal SAVED domain ([pfam:PF18145]), it oligomerises to closely locate two nuclease effector domains. This domain does not participates in ligand specificity and it has a promiscuous DNA cleavage response.
Pfam PF14228: Cell morphogenesis central region (family)
This family is the conserved central region of proteins that are involved in cell morphogenesis.
Pfam PF14733: AP2-coincident C-terminal (family)
This family is found at the C-terminus of apicomplexan proteins containing the AP2 domain ([pfam:PF00847]).
Wikipedia: The AP2-Coincident Domain mainly at the Carboxy-terminus, or ACDC domain, is a protein domain that occurs in proteins from apicomplexan parasites.
Pfam PF13914: Phostensin PP1-binding and SH3-binding region (domain)
Phostensin has been identified as a PP1 regulatory protein binding PP1 at the KISF motif. The domain also appears to carry an incomplete incomplete SH3-binding domain PxRxP further upstream. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton. Phostensin binds to actin and decreases the elongation and depolymerisation rates of actin filament pointed ends.
Pfam PF09167: Domain of unknown function (DUF1942) (domain)
Members of this family of bacterial proteins assume a beta-sandwich structure consisting of two antiparallel beta-sheets similar to an immunoglobulin-like fold, with an additional small, antiparallel beta-sheet. The longer-stranded beta-sheet is made up of four antiparallel beta-strands. The shorter-stranded beta-sheet consists of five beta-strands, four of these beta-strands form an antiparallel beta-sheet. The exact function of this family of proteins is unknown, though a putative role includes involvement in host-bacterial interactions involved in endocytosis or phagocytosis, possibly during bacterial internalisation.
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 PF22849: CATSPERE Ig-like domain (domain)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. These are multidomain proteins which share a similar domain organisation. This entry represents the Ig-like domain of CATSPERE (epsilon subunit).
Pfam PF15533: Bacterial toxin 33 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold and [DN]xHxxK and DxxxD motifs. It is usually exported by the Type 2 secretory system.
Pfam PF09442: Domain of unknown function (DUF2018) (domain)
Acid-adaptive protein possibly of physiological significance when H.pylori colonises the human stomach, which adopts a unique four alpha-helical triangular conformations. The biologically active form is thought to be a tetramer. The protein is expressed along with six other proteins, some of which are related to iron storage and haem biosynthesis.
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 PF20303: YEATS-Like-Associating Three TM (domain)
This is a conserved, three transmembrane helix-containing domain found fused to certain prokaryotic YEATS domain. Genome context displacement patterns predict an effector role for this domain, as a membrane-perforating, cell-suicide response-enacting domain.
Pfam PF17392: Urocanase C-terminal domain (domain)
This entry represents the C-terminal domain found in Urocanase. It is found also in S-methyl thiourocanate hydratase which cannot use urocanate or thiourocanate as substrate and catalyses the conversion of S-methyl thiourocanate, to S-methyl-thiohydantoin-5-propanoate .
Urocanase  (also known as imidazolonepropionate hydrolase or urocanate hydratase) is the enzyme that catalyses the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate:

urocanate + H2O = 4,5-dihydro-4-oxo-5-imidazolepropanoate

Urocanase is found in some bacteria (gene hutU) , in the liver of many vertebrates, and has also been found in the plant Trifolium repens (white clover). Urocanase is a protein of about 60 Kd, it binds tightly to NAD+and uses it as an electrophil cofactor. A conserved cysteine has been found to be important for the catalytic mechanism and could be involved in the binding of the NAD+.
Wikipedia: Urocanase is the enzyme that catalyzes the second step in the degradation of histidine, the hydration of urocanate into imidazolonepropionate.
Pfam PF17102: Stealth protein CR3, conserved region 3 (family)
Stealth_CR3 is the third of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins.  The domain is found in tandem with CR1, CR2 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases.  The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system.
Pfam PF17704: Family of unknown function (DUF5550) (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 PF12810: ALK/LTK, Glycine-rich domain (domain)
This entry represents the glycine-rich domain (GRD) from the Anaplastic lymphoma kinase (ALK), the closely related leukocyte tyrosine kinase (LTK) and similar proteins. ALK and LTK have been recently deorphanized receptor tyrosine kinases. They are involved in neural development, cancer and autoimmune diseases. ALK activity is associated with learning and memory and controls energy expenditure, and inhibition of ALK can prevent diet-induced obesity. This is an extracellular domain that regulates receptor activity by binding to activating peptides. This domain consists of fourteen long polyglycine type II (pGII) helices tightly packed into a honeycomb-like lattice. This entry also includes proteins from Trichomonas vaginalis and some uncharacterised bacterial sequences.
Pfam PF16489: GPCR-Autoproteolysis INducing (GAIN) domain (domain)
The GAIN a domain of alpha-helices and beta-strands that is found in cell-adhesion GPCRs and precedes the GPS motif where the autoproteolysis occurs, family, [pfam:PF01825]. The full GAIN domain, comprises the GPS and the GAIN, in cell-adhesion GPCRs, and is the functional unit for autoproteolysis. The GPS motif at the end of the GAIN domain is an ancient domain that exists in primitive ancestor organisms, and the full GAIN + GPS is conserved in all cell-adhesion GPCRs and all PKD1-related proteins.
Pfam PF16425: Domain of unknown function (DUF5022) (family)
This family consists of several uncharacterized proteins around 350 in length and is mainly found in various Firmicutes 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 PF00101: Ribulose bisphosphate carboxylase, small chain (domain)
RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The small subunits induce conformational changes in the large subunits enhancing its catalytic rate. Studies in Oryza sativa demonstrate that the availability of the small subunit upregulates the transcript levels of the large subunit . While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome , which results in RuBisCO being more abundant during the day when it is required.
The RuBisCo small subunit consists of a central four-stranded Î²-sheet, with two helices packed against it .
Wikipedia: Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Pfam PF04431: Pectate lyase, N terminus (family)
This region is found N terminal to the pectate lyase domain ([pfam:PF00544]) in some plant pectate lyase enzymes.
Pfam PF08165: FerA (NUC095) domain (domain)
This is central domain A in proteins of the Ferlin family.
Pfam PF09026: Centromere protein B dimerisation domain (domain)
The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation.
Pfam PF19580: Endonuclease/Exonuclease/phosphatase family (domain)
This domain appears to be related to [pfam:PF03372].
Pfam PF10345: Cohesin loading factor (repeat)
Cohesin_load is a common cohesin loading factor protein that is conserved in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes but dispensable in G2 when cohesion has been established. It is referred to as both Ssl3, in pombe, and Scc4, in S.cerevisiae. It complexes with Mis4.
Pfam PF19752: Family of unknown function (DUF6239) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the kedarcidin biosynthetic gene cluster from Streptoalloteichus  sp. ATCC 53650.
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 PF05013: N-formylglutamate amidohydrolase (family)
Formylglutamate amidohydrolase (FGase) catalyses the terminal reaction in the five-step pathway for histidine utilisation in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolysed to produce L-glutamate plus formate.
Pfam PF05687: BES1/BZR1 plant transcription factor, N-terminal (family)
This family consists of the N terminal regions of several plant transcription factors. It is classified as BES1/BZR1, a plant-specific transcription factor that cooperates with transcription factors such as BIM1 to regulate brassinosteroid-induced genes.
Pfam PF01991: ATP synthase (E/31 kDa) subunit (family)
This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit.
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 PF14479: Prion-inhibition and propagation (domain)
This N-terminal region, HeLo, has a prion-inhibitory effect in cis on its own prion-forming domain (PFD) and in trans on HET-s prion propagation. The domain is found exclusively in the fungal kingdom. Its structure, as it occurs in the HET-s/HET-S proteins, consists of two bundles of alpha-helices that pack into a single globular domain.  The domain boundary determined from its structure and from protease-resistance experiments overlaps with the C-terminal prion-forming domain of HET-s (PF11558. The HeLo domains of HET-s and HET-S are very similar and their few differences (and not the prion-forming domains) determine the compatibility-phenotype of the fungi in which the proteins are expressed. The mechanism of the HeLo domain-function in heterokaryon-incompatibility is still under investigation, however the HeLo domain is found in similar protein architectures as other cell death and apoptosis-inducing domains. The only other HeLo protein to which a function has been associated is LopB from L. maculans.  Although its specific role in L. maculans is unknown, LopB- mutants have impaired ability to form lesions on oilseed rape. The HeLo domain is not related to the HET domain (PF06985) which is another domain involved in heterokaryon incompatibility.
Pfam PF14737: Domain of unknown function (DUF4470) (family)
This family is conserved from fungi to Metazoa and includes plants.  The function is not known, but several members have zinc-finger domain, zf-MYND, [pfam:PF01753], at their very C-terminus. Others are also associated with DUF1279, [pfam:PF06916].
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.