SII-SWORD/CoKE huggingface dataset:
Pfam PF04961: Formiminotransferase-cyclodeaminase (family)
Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes [ec:4.3.1.4]. This domain is found in  the C-terminus of the bifunctional animal members of the family.
Wikipedia: In molecular biology, enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain acts as a formimidoyltetrahydrofolate cyclodeaminase, which catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it acts as a methenyltetrahydrofolate cyclohydrolase, which catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate, as shown in reaction (2).
Pfam PF00262: Calreticulin family (family)
The calreticulin family is a family of calcium-binding ER chaperonesthat includes calreticulin, calnexin and camlegin .

Calreticulin (calregulin)  is a high-capacity calcium-binding protein which is present in most tissues and located at the periphery of the endoplasmic (ER) and the sarcoplamic reticulum (SR) membranes. It probably plays a role in the storage of calcium in the lumen of the ER and SR and it may well have other important functions.

Structurally, calreticulin is a protein of about 400 amino acid residues consisting of three domains:
 * An N-terminal, probably globular, domain of about 180 amino acid residues (N-domain).
 * A central domain of about 70 residues (P-domain) which contains three repeats of an acidic 17 amino acid motif. This region binds calcium with a low-capacity, but a high-affinity.
 * A C-terminal domain rich in acidic residues and in lysine (C-domain). This region binds calcium with a high-capacity but a low-affinity.


Calreticulin is evolutionarily related to several other calcium-binding proteins, including Onchocerca volvulus antigen RAL-1, calnexin  and calmegin .
Wikipedia: In molecular biology, the calreticulin protein family is a family of calcium-binding proteins. This family includes calreticulin, calnexin and camlegin.
Pfam PF19671: Family of unknown function (DUF6174) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 151 and 236 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 PF10709: Protein of unknown function (DUF2511) (family)
This family is conserved in bacteria. The function is not known.
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 PF23309: Domain of unknown function (DUF7083) (domain)
This is a presumed domain found at the N-terminal of the uncharacterised protein K02A2.6 from C.elegans and similar worm sequences. This domain may adopt a fold similar to retrotransposons.
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 PF24542: TPPC8 C-terminal Ig-like domain (domain)
This entry represents an Ig-like domain found at the C-terminal of TPPC8, a protein that plays a role in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. Together with TBC1D14, it maintains the cycling pool of ATG9 required for initiation of autophagy. It is one of the TRAPPIII complex specific subunits.
Pfam PF20805: Integrin alpha Ig-like domain 2 (domain)
This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of [pfam:PF01839] repeats and to the N-terminus of the [pfam:PF00357] cytoplasmic region. This region is composed of an immunoglobulin-like domain.
Wikipedia: Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
Pfam PF05561: Borrelia burgdorferi protein of unknown function (DUF764) (family)
This family consists of proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete).
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 PF08270: M protein trans-acting positive regulator (MGA) PRD domain (family)
Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This corresponds to the PRD like region.
Pfam PF21150: Ribosomal RNA small subunit methyltransferase F, pre-PUA domain (domain)
This domain is found in Ribosomal RNA small subunit methyltransferase F from Escherichia coli (YebU) and similar proteins mainly from proteobacteria. YebU requires S-adenosyl-l-methionine (SAM) to specifically methylate the cytosine at position 1407 of assembled 30 S rRNA subunits. This proteins is organized into two distinct structural domains: the N-terminal MTase domain (catalytic domain), which can be divided in [pfam:PF17125] and [pfam:PF01189], and the C-terminal, also consisting of two subdomains. This entry represents the first of these subdomains, which is found N-terminal to the PUA- like domain ([pfam:PF13636]). The pre-PUA domain has six beta-strands that form a central sheet in an anti-parallel fashion, and three alpha-helices packing against the edges of the sheet.
Pfam PF13386: Cytochrome C biogenesis protein transmembrane region (family)
Urease is a nickel containing metalloenzyme that hydrolyses urea into ammonia . This entry represents a transmembrane domain found in UreH, an urease accessory protein . In Helicobacter pylori, UreH is part of the UreG/UreF/UreH complex that may be responsible for delivery of nickel ions into the urease active site .

This entry also includes Chloroplast protein FOR GROWTH AND FERTILITY 1/2 from Arabidopsis, transmembrane proteins essential for supporting female gametogenesis and embryogenesis, probably by securing local energy supply .
Pfam PF03756: A-factor biosynthesis hotdog domain (domain)
The AfsA family are key enzymes in A-factor biosynthesis, which is essential for streptomycin production and resistance. This domain is distantly related to the thioester dehydratase FabZ family and therefore has a HotDog domain.
Pfam PF03151: Triose-phosphate Transporter family (family)
This family includes transporters with a specificity for triose phosphate.
Pfam PF07158: Dicarboxylate carrier protein MatC N-terminus (family)
This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier.
Pfam PF20391: Family of unknown function (DUF6686) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 102 and 118 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 PF14967: FAM70 protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 241 and 349 amino acids in length. The function of this family is unknown.
Pfam PF07267: Nucleopolyhedrovirus capsid protein P87 (family)
This family consists of several Nucleopolyhedrovirus capsid protein P87 sequences. P87 is expressed late in infection and concentrated in infected cell nuclei.
Pfam PF02240: Methyl-coenzyme M reductase gamma subunit (domain)
Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha ([pfam:PF02249]), 2 beta ([pfam:PF02241]), and 2 gamma (this family)  subunits with two identical nickel porphinoid active sites.
Pfam PF03174: Chitobiase/beta-hexosaminidase C-terminal domain (domain)
This short domain represents the C terminal domain in chitobiases and beta-hexosaminidases [ec:3.2.1.52]. It is composed of a beta sandwich structure. The function of this domain is unknown.
Pfam PF06072: Alphaherpesvirus tegument protein US9 (family)
This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb.
Pfam PF04878: Baculovirus P48 protein (family)
This family comprises the Baculovirus P48 proteins. They contain two possible membrane-spanning domains and a cysteine-rich domain that are conserved in all of the proteins. The Bombyx mori (Silk moth) nuclear polyhedrosis virus protein, O92463, has been described as a putative DNA helicase.
Pfam PF12697: Alpha/beta hydrolase family (domain)
This family contains alpha/beta hydrolase enzymes of diverse specificity.
Wikipedia: The alpha/beta hydrolase superfamily is a superfamily of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function that share a common fold. The core of each enzyme is an alpha/beta-sheet, containing 8 beta strands connected by 6 alpha helices. The enzymes are believed to have diverged from a common ancestor, retaining little obvious sequence similarity, but preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best-conserved structural features of the fold.
Pfam PF06572: Protein of unknown function (DUF1131) (family)
This family consists of several hypothetical bacterial proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16391: Domain of unknown function (family)
This family around 200 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Parabacteroides species. The function of this family   remains unknown.
Pfam PF23938: Domain of unknown function (DUF7273) (domain)
This entry represents a small family of uncharacterised mycobacterium phage proteins. These proteins adopt a compact three helical bundle 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 PF11988: Retrograde transport protein Dsl1 N terminal (repeat)
Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum. It is localised to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles. It is comprised primarily of alpha helical bundles. It complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein.  A central disorganised region between the N and C termini of Dsl1 contains binding sites for coatomer. The C terminus of Dsl1 contains a binding site to the Sec39 subunit of the Dsl1p complex.
Pfam PF20379: Family of unknown function (DUF6674) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 259 and 297 amino acids in length. There are two conserved sequence motifs: AMKIP and SMN.
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 PF01324: Diphtheria toxin, R domain (domain)
C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis.
Wikipedia: Diphtheria toxin is an exotoxin secreted mainly by Corynebacterium diphtheriae but also by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, the pathogenic bacterium that causes diphtheria. The toxin gene is encoded by a prophage called corynephage β.
The toxin causes the disease in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis.
Pfam PF17252: Family of unknown function (DUF5319) (family)
This is a family of unknown function mostly found in 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 PF19725: DNA-directed RNA polymerase III subunit RPC5 C-terminal (domain)
This is the C-terminal domain of DNA-directed RNA polymerase III subunit RPC5 (POLR3E). PolIII is a complex consisting of 17 subunits and transcribes small RNAs, such as 5S rRNA and tRNA, that is involved in innate immune system as it senses viral DNA to produce non-self RNA polymerase III transcripts, which induce type I interferon and NF-Kappa-B. RPC5 forms a subcomplex with RPC4 which is close to the polymerase active centre that enables open promoter complex formation and facilitates termination and reinitiation. Mutations in this subunit are associated with impaired induction of type I IFN and increased susceptibility to viral infections.
Pfam PF15798: Proline-rich AKT1 substrate 1 (family)
This domain family is found in eukaryotes, and is typically between 117 and 132 amino acids in length. PRAS domain family is found in eukaryotes, and is typically between 117 and 132 amino acids in length. It is a proline-rich family that can be phosphorylated by AKT, and in the phosphorylated state binds to 14-3-3. The AKT signalling pathway contributes to regulation of apoptosis after a variety of cell death stimuli, and PRAS is found to be a substrate. PRAS plays an important role in regulating cell survival downstream of the PI3-K/Akt pathway after re-perfusion injury after transient focal cerebral ischemia. Copper/zinc-SOD (SOD1), a cytosolic isoenzyme of superoxide dismutase, SOD, is highly protective against ischemia and re-perfusion injury after transient focal cerebral ischemia, and SOD1 thus contributes to the inhibition of direct oxidation of PRAS and the activation of its signalling pathway. PRAS is also a mTOR binding partner, and PRAS phosphorylation by AKT and its association with 14-3-3, a cytosolic anchor protein, are crucial for insulin to stimulate mTOR (mammalian target of rapamycin).
Pfam PF17251: Protochlamydia outer membrane protein (domain)
This family represents an outer membrane protein found in environmental chlamydia. The protein shows porin function.
Pfam PF06577: Envelope integrity protein A (family)
This family includes envelope integrity protein A (EipA), a protein required for B. abortus envelope stress resistance and infection. It's gene expression is directly activated by CtrA which binds to the promoter region. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded beta-barrel fold.
Pfam PF09565: NgoFVII restriction endonuclease N-terminal PLD domain (domain)
This family includes the NgoFVII (recognises GCSGC but cleavage site unknown) restriction endonuclease.
Pfam PF08967: Putative type 4B encapsulin shell protein (domain)
Proteins in this entry may be the encapsulin shell protein in a type 4 A-domain encapsulin nanocompartment system. It has been shown that bacterial/archaeal encapsulin-like systems and HK97-type viruses share a common ancestor and it is likely that encapsulins have evolved from HK97-type phages.
Pfam PF17928: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the TetR Transcriptional Repressor present in sco1712 proteins from Streptomyces coelicolo which act as a regulator of antibiotic production.
Pfam PF07424: TrbM (family)
This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulfonate (TSA) degradation. This family also includes MPFK and its functional homologue kikA, which are required for efficient conjugative transfer in IncP-9 plasmids.
Pfam PF20821: Streptococcus virus C1, PlyCB (family)
PlyCB is one of the two components of the potent endolysin PlyC, an enzyme specific for streptococcal species. PlyC consists of a single PlyCA catalytic subunit in complex with eight PlyCB molecules arranged in a planar octameric ring. One surface of the PlyCB octamer is quite planar, whereas the other is more convex in shape. The bacterial cell wall binding is achieved through a cleft on PlyCB, which interacts strongly with phosphatidylserine so that PlyC can cross the epithelial cell membrane.
Pfam PF21412: TEP1, second CUB domain (domain)
Thioester-containing protein 1 (TEP1) is a central component in the innate immune response of Anopheles gambiae to Plasmodium infection.  TEP1 has a series of eight macroglobulin (MG) domains and the beta-sheet CUB domain which is flanking the alpha-helical TED domain. The CUB domain can be divided in two sections, one at the N-terminal and the second at the C-terminal of the TED domain. This entry represents the second part of the CUB domain.
Pfam PF15531: Bacterial toxin 27 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold and conserved aspartate and glutamate residues, and an RxW motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion systems.
Pfam PF05710: Coiled coil (coiled_coil)
This region is found in a group of Dictyostelium discoideum proteins.  It is likely to form a coiled-coil. Some of the proteins are regulated by cyclic AMP and are expressed late in development ().
Pfam PF15641: Metallopeptidase toxin 5 (family)
A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems.
Pfam PF20884: MUM1-like, PWWP domain (domain)
PWWP domain-containing DNA repair factor 3A (also known as EXPAND1 or MUM1) is a nucleosome-binding protein that contributes to the maintenance of chromatin state. Through its interaction with 53BP1, it serves as an accessory factor in the DNA damage response pathway to promote chromatin change in response to DNA damage. MUM1 promotes cell survival following DNA damage, suggesting that it may facilitate DNA repair by regulating the organisation of chromatin structure. This entry represents the PWWP (named after the a conserved Pro-Trp-Trp-Pro motif), a small domain consisting of 100-150 amino acids, found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Pfam PF12681: Glyoxalase-like domain (domain)
This domain is related to the Glyoxalase domain [pfam:PF00903].
Pfam PF02407: Putative viral replication protein (family)
This is a family of viral ORFs from various plant and animal ssDNA circoviruses.  Published evidence to  support the annotated function "viral replication  associated protein" has not be found.
Pfam PF22947: Leucine--tRNA ligase, ubiquitin-like domain (domain)
This domain is found in human Leucine--tRNA ligase (LARS1) and related metazoan proteins. LARS1 is aminoacyl-tRNA synthetase that catalyses the specific attachment of leucine to its cognate tRNA (tRNA(Leu)). It also mediates activation of leucine- dependent mechanistic target of rapamycin complex 1 (mTORC1). In the presence of leucine, LARS1 is translocated to the lysosome and facilitates the conversion of RagD-GTP to RagD-GDP form, resulting in mTORC1 activation. The domain represented by this entry is predicted to adopt Ubiquitin-like fold with similarity to SPN domain of SHANK3. This domain is usually found in combination with domains that are typical for Leucyl-tRNA ligases.