SII-SWORD/CoKE huggingface dataset:
Pfam PF00858: Amiloride-sensitive sodium channel (family)
The apical membrane of many tight epithelia contains sodium channels that are primarily characterised by their high affinity to the diuretic blocker amiloride . These channels mediate the first step of active sodium reabsorption essential for the maintenance of body salt and water homeostasis . In vertebrates, the channels control reabsorption of sodium in kidney, colon, lung and sweat glands; they also play a role in taste perception.

Members of the epithelial Na+channel (ENaC) family fall into four subfamilies, termed alpha, beta, gamma and delta . The proteins exhibit the same apparent topology, each with two transmembrane (TM) spanning segments, separated by a large extracellular loop. In most ENaC proteins studied to date, the extracellular domains are highly conserved and contain numerous cysteine residues, with flanking C-terminal amphipathic TM regions, postulated to contribute to the formation of the hydrophilic pores of the oligomeric channel protein complexes. It is thought that the well-conserved extracellular domains serve as receptors to control the activities of the channels.

Vertebrate ENaC proteins are similar to degenerins of Caenorhabditis elegans : deg-1, del-1, mec-4, mec-10 and unc-8. These proteins can be mutated to cause neuronal degradation, and are also thought to form sodium channels.

Structurally, the proteins that belong to this family consist of about 510 to 920 amino acid residues. They are made of an intracellular N terminus region followed by a transmembrane domain, a large extracellular loop, a second transmembrane segment and a C-terminal intracellular tail .
Wikipedia: Acid-sensing ion channels (ASICs) are neuronal voltage-insensitive sodium channels activated by extracellular protons permeable to Na+. ASIC1 also shows low Ca2+ permeability. ASIC proteins are a subfamily of the ENaC/Deg superfamily of ion channels. These genes have splice variants that encode for several isoforms that are marked by a suffix. In mammals, acid-sensing ion channels (ASIC) are encoded by five genes that produce ASIC protein subunits: ASIC1, ASIC2, ASIC3, ASIC4, and ASIC5. Three of these protein subunits assemble to form the ASIC, which can combine into both homotrimeric and heterotrimeric channels typically found in both the central nervous system and peripheral nervous system. However, the most common ASICs are ASIC1a and ASIC1a/2a and ASIC3. ASIC2b is non-functional on its own but modulates channel activity when participating in heteromultimers and ASIC4 has no known function. On a broad scale, ASICs are potential drug targets due to their involvement in pathological states such as retinal damage, seizures, and ischemic brain injury.
Pfam PF25081: CC142 N-terminal (coiled_coil)
This entry represents the N-terminal coiled-coils of CC142, a protein whose function is still unknown.
Pfam PF08534: Redoxin (domain)
This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins.
Pfam PF16079: Phage holin family Hol44, in holin superfamily V (family)
Phage_holin_V_2 is a family of small hydrophobic proteins with three transmembrane domains of the Hol44 family. These proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. Full activity of the endolysin Lys44 from oenophage fOg44 requires sudden ion-nonspecific dissipation of the proton motive force, undertaken by the fOg44 holin during phage-infection.
Pfam PF06422: CDR ABC transporter (family)
Corresponds to a region of the PDR/CDR subgroup of ABC transporters comprising extracellular loop 3, transmembrane segment 6 and linker region.
Pfam PF14650: FAM75 family (family)
This entry represents a domain found in SPATA31 and FAM205 proteins. Their function is not clear. SPATA31 (spermatogenesis-associated protein 31), also known as Aep1, plays a role in spermatogenesis . Aep1 has been found to interact with beta-actin and syntaxin 1 in vitro .
Pfam PF13619: KTSC domain (domain)
This short domain is named after Lysine tRNA synthetase C-terminal domain. It is found at the C-terminus of some Lysyl tRNA synthetases as well as a single domain in bacterial proteins. The domain is about 60 amino acids in length and contains a reasonably conserved YXY motif in the centre of the sequence. The function of this domain is unknown but it could be an RNA binding domain.
Pfam PF19078: Bacterial Ig-like domain (domain)
Presumed domain found as tandem repeats of high sequence identity in bacterial cell surface proteins.
Pfam PF15534: Bacterial toxin 35 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a conserved histidine residue and a KH motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 secretion system.
Pfam PF23265: KY-like, immunoglobulin-like domain (domain)
This domain is found twice in human Kyphoscoliosis peptidase (KY), a probable cytoskeleton-associated protease required for normal muscle growth. This domain, which is predicted to adopt an immunoglobulin-like structure. Members of this family are mainly found in animals.
Pfam PF14150: YesK-like protein (family)
The YesK-like protein family includes the B. subtilis YesK protein [swissprot:O31514], which is functionally uncharacterised. Its expression is regulated by the sporulation-specific sigma factor sigma-E.  This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length.
Pfam PF07534: TLD (domain)
This domain is predicted to be an enzyme and is often found associated with [pfam:PF01476]. It's structure consists of a beta-sandwich surrounded by two helices and two one-turn helices.
Pfam PF18454: Major tropism determinant N-terminal domain (domain)
This is the N-terminal domain of major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein. Mtd-N forms a three-fold symmetric beta-prism. This resembles the pseudo three-fold-symmetric beta-prisms of monocot lectins, but lacks residues in these lectins identified as binding carbohydrates. The beta-prism and beta-sandwich domains reinforce overall trimeric assembly and therefore may have indirect roles in stabilizing the backbone of the variable region.
Pfam PF22168: Transcriptional regulator DIP2311-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Transcriptional regulator DIP2311 from Corynebacterium diphtheriae ([swissprot:Q6NEG3]) and similar bacterial sequences. This domain, which shows a winged helix fold, is normally found associated to [pfam:PF04326].
Pfam PF18520: Spindle pole body component 110 C-terminal domain (domain)
This is the C-terminal domain found in Spc110 proteins. Spc110 is a spindle pole body component (SPB) protein. The N-terminus is shown to bind to gamma-tubulin small complex (g-TuSC) while this C-terminal domain is essential for calmodulin-binding. The C-terminus of Spc110 is anchored to the SPB via a conserved PACT domain.
Pfam PF05448: Acetyl xylan esterase (AXE1) (domain)
This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan.
Pfam PF06102: rRNA biogenesis protein RRP36 (family)
RRP36 is involved in the early processing steps of the pre-rRNA.
Pfam PF07552: Spore Coat Protein X and V domain (domain)
This family is found in the Bacilliales coat protein X as a tandem repeat and also in coat protein V. The proteins are found in the insoluble fraction.
Pfam PF09726: Macoilin family (family)
The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons.
Pfam PF00089: Trypsin (domain)
This entry represents the active-site-containing domain found in the trypsin family members. The catalytic activity of the serine proteases from the trypsin family is provided by a charge relay system involving an aspartic acid residue hydrogen-bonded to a histidine, which itself is hydrogen-bonded to a serine. The sequences in the vicinity of the active site serine and histidine residues are well conserved in this family of proteases . A partial list of proteases known to belong to the trypsin family is shown below.


 * Acrosin.
 * Blood coagulation factors VII, IX, X, XI and XII, thrombin, plasminogen, and protein C.
 * Cathepsin G.
 * Chymotrypsins.
 * Complement components C1r, C1s, C2, and complement factors B, D and I.
 * Complement-activating component of RA-reactive factor.
 * Cytotoxic cell proteases (granzymes A to H).
 * Duodenase I.
 * Elastases 1, 2, 3A, 3B (protease E), leukocyte (medullasin).
 * Enterokinase (EC 3.4.21.9) (enteropeptidase).
 * Hepatocyte growth factor activator.
 * Hepsin.
 * Glandular (tissue) kallikreins (including EGF-binding protein types A, B, and C, NGF-gamma chain, gamma-renin, prostate specific antigen (PSA) and tonin).
 * Plasma kallikrein.
 * Mast cell proteases (MCP) 1 (chymase) to 8.
 * Myeloblastin (proteinase 3) (Wegener's autoantigen).
 * Plasminogen activators (urokinase-type, and tissue-type).
 * Trypsins I, II, III, and IV.
 * Tryptases.


All the above proteins belong to family S1 in the classification of peptidases  and originate from eukaryotic species. It should be noted that bacterial proteases that belong to family S2A are similar enough in the regions of the active site residues that they can be picked up by the same patterns. These proteases are listed below.


 * Achromobacter lyticus protease I.
 * Lysobacter alpha-lytic protease.
 * Streptogrisin A and B (Streptomyces proteases A and B).
 * Streptomyces griseus glutamyl endopeptidase II.
 * Streptomyces fradiae proteases 1 and 2.
Wikipedia: Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins. Trypsin is formed in the small intestine when its proenzyme form, the trypsinogen produced by the pancreas, is activated. Trypsin cuts peptide chains mainly at the carboxyl side of the amino acids lysine or arginine. It is used for numerous biotechnological processes. The process is commonly referred to as trypsinogen proteolysis or trypsinization, and proteins that have been digested/treated with trypsin are said to have been trypsinized.
Pfam PF18969: Family of unknown function (DUF5708) (family)
This family includes members in Actinobacteria.  All family members present double transmembrane.
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 PF07477: Glycosyl hydrolase family 67 C-terminus (domain)
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C terminal region of alpha-glucuronidase which is mainly alpha-helical. It wraps around the catalytic domain ([pfam:PF07488]), making additional interactions both with the N-terminal domain ([pfam:PF03648]) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer.
Wikipedia: In molecular biology, glycoside hydrolase family 67 is a family of glycoside hydrolases.
Pfam PF14184: Regulatory protein YrvL (family)
YrvL prevents expression and activity of the YrvI sigma factor. It may function as an anti-sigma factor
Pfam PF25007: Dynein axonemal heavy chain 2/5/8 coiled-coil (repeat)
This entry represents a coiled-coil region found in Dynein axonemal heavy chains 2/5/8 which is similar to spectrin repeats. These proteins are involved in sperm motility. DYH2 is part of the axonemal inner dynein arm complex plays a central role in ciliary beat.
Pfam PF14695: Lines C-terminus (family)
This family represents the C-terminus of protein lines. In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator.
Pfam PF02471: Borrelia outer surface protein E (family)
This is a family of outer surface proteins (Osp) from the Borrelia spirochete. The family includes OspE, and OspEF-related proteins (Erp). These proteins are coded for on different circular plasmids in the Borrelia genome.
Pfam PF16203: ERCC3/RAD25/XPB C-terminal helicase (domain)
This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.
Pfam PF02294: 7kD DNA-binding domain (domain)
This family contains members of the hyper-thermophilic archaebacterium  7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the  tightest DNA-binding ability.
Pfam PF13095: Kinetochore Sim4 complex subunit FTA2 (family)
Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1. The equivalent higher eukaryotic protein is CENP-P. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC.
Pfam PF07610: Protein of unknown function (DUF1573) (family)
These hypothetical proteins, from bacteria such as Rhodopirellula baltica, Bacteroides thetaiotaomicron, and Porphyromonas gingivalis, share a region of conserved sequence towards their N-termini.
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 PF08311: Mad3/BUB1 homology region 1 (repeat)
Proteins containing this domain are checkpoint proteins involved in cell division.  This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Pfam PF13298: DNA polymerase Ligase (LigD) (family)
This is the N terminal region of ATP dependant DNA ligase.
Pfam PF09355: Phage protein Gp19/Gp15/Gp42 (domain)
This family of proteins are functionally uncharacterised. They are found in a variety of bacteriophage.
Pfam PF06971: Putative DNA-binding protein N-terminus (family)
This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins.
Pfam PF17226: MTA R1 domain (domain)
The R1 domain is found in the MTA1 protein and its homologues. The domain is composed of 4 alpha helices. It has been shown to bind to the RBBP4 protein. The MTA proteins contain a second partial copy of this domain called R2. The R2 domain is matched by this model for some proteins.
Pfam PF22755: E217 collar protein gp28 (domain)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. The collar protein gp28 is located at the neck of the E217 virion. Gp28 consists of a small beta-barrel decorated by an alpha-helix and two wing-like lateral extensions. Six collar proteins pack under the head-to-tail dodecamer with gp28 N-helix positioned orthogonal to two gp27 subunits. On the opposite side of the gp28 barrel, the wing-like extensions contact two gateway subunits.
Pfam PF11857: Domain of unknown function (DUF3377) (family)
This domain is functionally uncharacterised. This domain is found in eukaryotes. This presumed domain is about 70 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 PF00433: Protein kinase C terminal domain (family)
This domain is found in a large variety of protein kinases with different functions and dependencies. Protein kinase C, for example, is a calcium-activated, phospholipid-dependent serine- and threonine-specific enzyme. It is activated by diacylglycerol which, in turn, phosphorylates a range of cellular proteins. This domain is most often found associated with IPR000719.
Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity :


 * Serine/threonine-protein kinases
 * Tyrosine-protein kinases
 * Dual specificity protein kinases (e.g. MEK -phosphorylates both Thr and Tyr on target proteins)


Protein kinase function is evolutionarily conserved from Escherichia coli to human . Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases .
Wikipedia: In cell biology, protein kinase C, commonly abbreviated to PKC (EC 2.7.11.13), is a family of protein kinase enzymes that are involved in controlling the function of other proteins through the phosphorylation of hydroxyl groups of serine and threonine amino acid residues on these proteins, or a member of this family. PKC enzymes in turn are activated by signals such as increases in the concentration of diacylglycerol (DAG) or calcium ions (Ca2+). Hence PKC enzymes play important roles in several signal transduction cascades.
Pfam PF14563: Domain of unknown function (DUF4444) (family)
This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved LIPL sequence motif. There are two completely conserved G residues that may be functionally important.
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 PF15654: Toxin with a conserved tryptophan and TIP tripeptide motif (family)
A predicted toxin domain with two membrane spanning alpha helices and RxxR, Wx[ST]IP motifs. The domain is present in bacterial polymorphic toxin systems. The toxin is usually exported by the type 2 or Photorhabdus virulence cassette (PVC)-type secretion system.
Pfam PF09390: Protein of unknown function (DUF1999) (family)
This family contains a putative Fe-S binding reductase ([swissprot:Q72J89]) whose structure adopts an alpha and beta fold.
Pfam PF08080: RNPHF zinc finger (domain)
This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F.  The domain is often associated with [pfam:PF00076].
Pfam PF13121: Domain of unknown function (DUF3976) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 40 amino acids in length.
Pfam PF19161: Family of unknown function (DUF5843) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF18436: Helical box domain of E3 ubiquitin-protein ligase HECW1 (domain)
This is a region of 109 amino acids found in HECW1 proteins in Eukaryotes.Polymorphisms in the same region in the C.elegans homologue affects C. elegans behavioural avoidance of a lawn of Pseudomonas aeruginosa.
Pfam PF08589: Autophagy receptor ATG43 (family)
This family represents the autophagy receptor ATG43 from fungi. It is a mitochondrial outer membrane protein which serves as a mitophagy receptor to promote the selective degradation of mitochondria.
Pfam PF03640: Secreted repeat of unknown function (repeat)
This family occurs as tandem repeats in a set of lipoproteins. The alignment contains a Y-X4-D motif.
Pfam PF05018: CFA20 domain (domain)
This domain is characteristic of cilia- and flagella-associated protein 20 (CFA20). CFA20 is a cilium- and flagellum-specific protein that plays a role in axonemal structure organisation and motility. In Chlamydomonas reinhardtii, it stabilises outer doublet microtubules (DMTs) of the axoneme and may work as a scaffold for intratubular proteins, such as tektin and PACRG, to produce the beak structures in DMT1. Other proteins contain a domain with homology to CFA20. WDR90/POC16 contains such a domain in its N terminus, followed by a large C-terminal domain with multiple WD40 repeats. This domain is also present in the N terminus of uncharacterised protein C3orf67.