SII-SWORD/CoKE huggingface dataset:
Pfam PF02035: Coagulin (domain)
Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them . The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C . Gel formation results from interlinking of coagulin molecules. The crystal structure of a coagulogen has been revealed. Coagulogen contains a C-terminal domain that has a NGF-like fold .

Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. It has been shown that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs .
Pfam PF19043: Nuclear cap binding complex subunit CBP66 C-terminal region (family)
This entry represents the CBP66 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP66 is part of the complex that recognises this cap. This domain adopts a beta-grasp like structure.
Pfam PF17728: BsuBI/PstI restriction endonuclease HTH domain (domain)
This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI ([ec:3.1.21.4]). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system.
Wikipedia: In molecular biology, the BsuBI/PstI restriction endonuclease family is a family of type II restriction endonucleases. It includes BsuBI and PstI. The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system.
Pfam PF21158: Flagellar hook-associated protein 1, D2-like domain (domain)
This entry includes Flagellar hook-associated protein 1 (FlgK or HAP1), one of three HAPs that form the hook-filament junction and has structural similarity to flagellin. FlgK is required for normal flagellum assembly. Proteins in this entry have a multidomain fold comprising an elongated alpha-helical scaffold core, and depending on the bacterial species, a variable number of smaller domains. This entry represents a beta-sandwich domain from FlgK proteins; Salmonella typhimurium FlgK ([swissprot:P0A1J5]) has one beta-sandwich domain, while FlgK from Burkholderia pseudomallei has two of them protruding from the alpha-helical core, referred to as D2 and D3 domains in, of which the first one, D2, is covered in this entry. FlgK has cytotoxic effects suggesting an important role in pathogenesis and is highly immunogenic. Domains D2 and D3 from B. pseudomallei have been identified as epitopes with increased immunogenic potential for vaccine development.
Pfam PF09137: Glucodextranase, domain N (domain)
Members of this family, which are uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopt a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilise the domain. Members of this family are mainly concerned with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism.
Pfam PF11679: Protein of unknown function (DUF3275) (family)
This family of proteins with unknown function appear to be restricted to Proteobacteria.
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 PF04717: Type VI secretion system/phage-baseplate injector OB domain (domain)
Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix.
Pfam PF11311: Protein of unknown function (DUF3114) (family)
Some members in this family of proteins with unknown function are annotated as cytosolic proteins. This cannot be confirmed.
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 PF13455: Meiotically up-regulated gene 113 (family)
This is a family of fungal proteins found to be up-regulated in meiosis.
Pfam PF09163: Formate dehydrogenase N, transmembrane (domain)
Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein.
Wikipedia: Formate dehydrogenases are a set of enzymes that catalyse the oxidation of formate to carbon dioxide, donating the electrons to a second substrate, such as NAD+ in formate:NAD+ oxidoreductase (EC 1.17.1.9) or to a cytochrome in formate:ferricytochrome-b1 oxidoreductase (EC 1.2.2.1). This family of enzymes has attracted attention as inspiration or guidance on methods for the carbon dioxide fixation, relevant to global warming.
Pfam PF17089: Uncharacterised protein family (family)
This is a family of bacterial proteins. The function is unknown.
Pfam PF12421: Tip attachment protein J, C-terminal receptor binding domain (domain)
This entry represents the C-terminal receptor binding domain of Tip attachment protein J from Escherichia phage lambda (GpJ) and similar bacterial and viral proteins. J attaches the virion to the host receptor LamB, inducing viral DNA ejection. This domain, which determines the host specificity of the phage, shows an immunoglobulin-like fold. Many of the proteins in this entry are annotated as fibronectin type III. This domain was previously known as DUF3672 and is normally found associated with [pfam:PF09327] and [pfam:PF13550].
Pfam PF15520: Novel toxin 10 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an alpha+beta fold that is usually exported by the type 2 secretion system.
Pfam PF24449: y05I-like putative transcription factor N-terminal domain (domain)
This entry represents the N-terminal domain of family of uncharacterised phage protein that includes T4 y05I protein [swissprot:P39240]. The family also includes homologues from T2 and T6 phage among others. These proteins contain two domains. These domains appear to be related to those found in the eukaryotic PurA transcription factor. This N-terminal presumably single stranded DNA binding domain contains two copies of a PurA-like repeat. The C-terminal domain contains a single copy that may mediate dimerisation in an analogous fashion to PurA.
Pfam PF20773: Immune inhibitor A-like, MAM domain (domain)
Immune inhibitor A (InhA)-type metallopeptidases are potential virulence factors secreted by members of the Bacillus cereus group (BGC) and belong to the thuringilysin family within the metzincin clan of metallopeptidases, M6 in the MEROPS database. The structure revealed four domains: a pro-peptide, a catalytic domain, a domain reminiscent of viral envelope glycoproteins (VEG) and a MAM domain grafted into the latter. This entry represents the MAM domain found in InhA and PrtV peptidases from Vibrio (a slightly more distant thuringilysin family members), which is required for proper protein expression and has certain flexibility. It is a beta-sandwich consisting of two five-stranded antiparallel beta-sheets, grafted between the second and third strands of the upper sheet of VEG. This domain displays closest structural similarity with MAM domains such as the one from the human MP, meprin beta.
Pfam PF14160: Centrosome-associated C terminus (family)
This is the C-terminus of a family of proteins that colocalise with the centrosome/microtubule organisation centre in interphase and at the spindle poles in mitosis.
Pfam PF04288: MukE-like family (family)
Bacterial protein involved in chromosome partitioning, MukE
Pfam PF24183: Family of unknown function (DUF7412) (domain)
This entry represents an uncharacterised protein family found in a range of bacteriophage including Phage T2. These proteins include a beta barrel domain. Many members of the family are annotated as IP4 internal head protein, although the source of evidence for this annotation was not found.
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 PF02256: Iron hydrogenase small subunit (domain)
This family represents the small subunit of the Fe-only hydrogenases [ec:1.18.99.1]. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.
Pfam PF24625: Domain of unknown function (DUF7626) (domain)
This is a HTH-like domain found in uncharacterised sequences from fungi.
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 PF11718: Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term (domain)
This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known.
Pfam PF08869: XisI protein (domain)
The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required.
Pfam PF17602: Family of unknown function (DUF5498) (family)
This is a family of unknown function found in Myoviridae.
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 PF09013: YopH, N-terminal (domain)
The N-terminal domain of YopH is a compact structure composed of four alpha-helices and two beta-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin.
Wikipedia: In molecular biology, YopH, N-terminal  refers to an evolutionary conserved protein domain. This entry represents the N-terminal domain of YopH protein tyrosine phosphatase (PTP).
Pfam PF01105: emp24/gp25L/p24 family/GOLD (domain)
Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains.  This domain corresponds closely to the beta-strand rich GOLD domain described in.    The GOLD domain is always found combined with lipid- or membrane-association domains.
Wikipedia: P24 protein family is a group of transmembrane proteins that are major components of COPI and COPII-coated vesicles. The family is also known as EMP24/GP25L/p24 family and TMP21-like proteins. The latter naming was after transmembrane emp24 domain-containing protein 10 that was found in the human brain. It was claimed to block the beta-amyloid peptide, which is implicated in the pathogenesis of Alzheimer's disease.
Pfam PF11916: Vacuolar protein 14 C-terminal Fig4p binding (domain)
Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. The C-terminal region of Vac14 binds to Fig4p. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system.
Pfam PF19616: Family of unknown function (DUF6121) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 133 and 164 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 PF02114: Phosducin (domain)
The outer and inner segments of vertebrate rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the GTP-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A . The protein is thought to participate in the regulation of visual phototransduction or in the integration of photo-receptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the functional role of the protein is the same in both retina and pineal gland .
This entry represents a domain found in members of the phosducin family. This domain has a thioredoxin-like fold .
Wikipedia: The outer and inner segments of vertebrate retina rod photoreceptor cells contain phosducin, a soluble phosphoprotein that complexes with the beta/gamma-subunits of the guanosine triphosphate-binding protein, transducin. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of phosducin by protein kinase A. The protein is thought to participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism. Similar proteins have been isolated from the pineal gland and it is believed that the function of the protein is the same in both retina and pineal gland.
Pfam PF00375: Sodium:dicarboxylate symporter family (family)
It has been shown  that integral membrane proteins that mediate the uptake of a wide variety of molecules with the concomitant uptake of sodium ions (sodium symporters) can be grouped, on the basis of sequence and functional similarities into a number of distinct families. One of these families is known as the sodium:dicarboxylate symporter family (SDF) .

Such re-uptake of neurotransmitters from the synapses, is thought to be an important mechanism for terminating their action, by removing these chemicals from the synaptic cleft, and transporting them into presynaptic nerve terminals, and surrounding neuroglia. This removal is also believed to prevent them accumulating to the point of reaching neurotoxic .

The structure of these transporter proteins has been variously reported to contain from 8 to 10 transmembrane (TM) regions, although 10 now seems to be the accepted value.

Members of the family include: several mammalian excitatory amino acid transporters, and a number of bacterial transporters. They vary with regards to their dependence on transport of sodium, and other ions.
Wikipedia: It has been shown that integral membrane proteins that mediate the uptake of a wide variety of molecules with the concomitant uptake of sodium ions can be grouped, on the basis of sequence and functional similarities into a number of distinct families. One of these families is known as the sodium:dicarboxylate symporter family (SDF).
Pfam PF10802: Protein of unknown function (DUF2540) (family)
This family of proteins includes the uncharacterized protein MJ0366 from Methanocaldococcus jannaschii and similar proteins predominantly found in Methanococci. This protein adopts the 3-1 trefoil knot conformation.
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 PF04055: Radical SAM superfamily (domain)
Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Wikipedia: Radical SAM enzymes belong to a superfamily of enzymes that use an iron-sulfur cluster (4Fe-4S) to reductively cleave S-adenosyl-L-methionine (SAM) to generate a radical, usually a 5′-deoxyadenosyl radical (5'-dAdo), as a critical intermediate. These enzymes utilize this radical intermediate to perform diverse transformations, often to functionalize unactivated C-H bonds. Radical SAM enzymes are involved in cofactor biosynthesis, enzyme activation, peptide modification, post-transcriptional and post-translational modifications, metalloprotein cluster formation, tRNA modification, lipid metabolism, biosynthesis of antibiotics and natural products etc. The vast majority of known radical SAM enzymes belong to the radical SAM superfamily, and have a cysteine-rich motif that matches or resembles CxxxCxxC. Radical SAM enzymes comprise the largest superfamily of metal-containing enzymes.
Pfam PF21405: Phosphoacetylglucosamine mutase AMG1, domain II (domain)
Phosphoacetylglucosamine mutase (AMG1) catalyses the conversion of GlcNAc-6-P into GlcNAc-1-P during the synthesis of uridine diphosphate/UDP-GlcNAc. It consists of four domains, the first three have the same fold of four beta-strands between two alpha-helices. This entry represents domain II of eukaryotic AMG1, which contains the metal-binding loop.
Pfam PF17401: Family of unknown function (DUF5407) (family)
This is a family of unknown function found in Chlamydiales.
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 PF23123: WDR72, alpha-solenoid domain (repeat)
This entry represents an alpha-solenoid domain found in WD repeat-containing protein 72 (WDR72), a protein that plays a major role in formation of tooth enamel. It is specifically required during the maturation phase of amelogenesis for normal formation of the enamel matrix and clearance of enamel proteins. These proteins have a particular domain architecture comprising one or two beta-propellers followed by an alpha-solenoid, a highly conserved architecture among proteins that form membrane coat complexes, dating back to the early eukaryotic endomembrane system. This entry also includes WDR7, whose function is currently unknown.
Pfam PF16134: THO complex subunit 2 N-terminus (family)
This family represents the N-terminus of THO complex subunit 2.
Pfam PF20356: Family of unknown function (DUF6651) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, eukaryotes and viruses, and is approximately 110 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 PF14324: PINIT domain (domain)
The PINIT domain is a protein domain that is found in PIAS proteins. The PINIT domain is about 180 amino acids in length.
Pfam PF13328: HD domain (family)
HD domains are metal dependent phosphohydrolases.
Pfam PF23645: TRAPP trafficking subunit Trs65 IgD1 (domain)
This entry includes Trp65, an essential subunit of the TRAPP Golgi trafficking complex. TRAPP subunits are found in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII and they function in various vesicle trafficking pathways. TRAPPI mediates transport from endoplasmic reticulum to cis-Golgi by tethering COPII-coated vesicles; TRAPPII interacts with COPI-coated vesicles in mammalian cells and aids in endosome-to-Golgi transport, and TRAPPIII plays a unique role in autophagy. TRAPP complexes act as GEFs and play an essential role in catalysing nucleotide exchange for Ypt/Rab GTPase. The three complexes share a core of six different proteins (Bet3, Bet5, Trs20, Trs23, Trs31, and Trs33) that make up core TRAPPI. TRAPPII contains four additional proteins (Trs120, Trs130, Trs65, and Tca17), and TRAPPIII has one additional Trs85 in yeast. while Trp65 has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPPII is supported by the findings that the protein co-localises with Trs130p, and deletion of Trs65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPPII-specific subunits is modified. Trs65 is essential to the formation of TRAPPII dimer and consists of three Ig-like  domains (IgD1, IgD2 and IgD3). This entry represents IgD1 domain.