SII-SWORD/CoKE huggingface dataset:
Pfam PF01241: Photosystem I psaG / psaK (family)
This entry represents Photosystem I reaction centre subunits V (PsaG) and PsaK from Cyanobacteria, Rhodophyta (red algae) and plants.
Photosystem I (PSI)  is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. It is found in the chloroplasts of plants and cyanobacteria. PSI is composed of at least 14 different subunits, two of which are small hydrophobic proteins of about 7 to 9 Kd and evolutionary related, PsaG (also known as PSI-G) and PsaK (also known as PSI-K), both integral membrane proteins. Cyanobacteria contain only PsaK . While cyanobacterial PSI have phycobilisomes to harvest light, eukaryotic PSI have a membrane-imbedded peripheral antenna .
Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .
Pfam PF00294: pfkB family carbohydrate kinase (domain)
This family includes a variety of carbohydrate and pyrimidine kinases.
Pfam PF21689: Sensor protein TorS, sensor domain (domain)
This entry represents the periplasmic sensor domain of Sensor protein TorS from Escherichia coli and similar proteins predominantly found in proteobacteria. TorS is a sensor histidine kinase that forms a complex with TorT, and TorR, to form the trimethylamine-N-oxide (TMAO) reductase (Tor) pathway, which plays a role in the regulation of this terminal electron receptor in anaerobic respiration.
Pfam PF16191: Ubiquitin-activating enzyme E1 four-helix bundle (domain)
This domain is found in the ubiquitin-activating E1 family enzymes.
Pfam PF11952: XRN-Two Binding Domain, XTBD (family)
XTBD is a family of eukaryotic proteins that act as an XRN2-binding module.  XRN2 is an essential exoribonuclease in eukaryotes that processes and degrades a number of different substrates. XTBD is found on a number of different proteins to link them to XRN, such as PAXT-1.
Pfam PF12672: Protein of unknown function (DUF3793) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 211 amino acids in length. There are two conserved sequence motifs: PHE and LGYP.
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 PF17059: MgtA leader peptide (family)
MGTL is a bacterial protein that makes mgtA transcription sensitive to intracellular proline levels. When the levels of proline are low, this protein is not able to be translated and stem loop'C' forms in the mgt A 5'UTR which enables the transcription of the downstream mgtA gene.
Pfam PF13323: N-terminal domain with HPIH motif (family)
This family is found in fungi on proteins carrying the PAS, [pfam:PF00989], domain. There is a well-conserved characteristic HPIH motif, but the function is not known.
Pfam PF15046: Protein of unknown function (DUF4532) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes.
Pfam PF02714: Calcium-dependent channel, 7TM region, putative phosphate (family)
RSN1_7TM is the seven transmembrane domain region of putative phosphate transporter. The family is the 7TM region of osmosensitive calcium-permeable cation channels.
Pfam PF03504: Chlamydia cysteine-rich outer membrane protein 6 (family)
Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane . They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.

The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane . OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa . MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin .

The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level . Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.
Pfam PF12245: Bacterial Ig-like domain (domain)
This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins.
Pfam PF01637: ATPase domain predominantly from Archaea (domain)
This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family.
Pfam PF15909: C2H2-type zinc ribbon (domain)
This family carries three zinc-fingers in tandem.
Pfam PF14472: Domain of unknown function (DUF4429) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length.  This domain is often found in two tandem copies.
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 PF15809: Simian taste bud-specific gene product family (family)
STG was first isolated from rhesus monkey taste buds. The exact function of STG is not known, but it has been implicated in follicular lymphomas, though not with psoriasis at least in a Swedish population despite lying close to the PSOR1 gene-locus.
Pfam PF08293: Mitochondrial ribosomal subunit S27 (family)
This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes and to subunit S33 in humans. It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome.
Pfam PF05258: Dna[CI] antecedent, DciA (family)
This family contains several actinomycete proteins. Family members such as DciA (dna[CI] antecedent) found in Pseudomonas aeruginosa, has been shown to share a common function with DnaC (in Escherichia coli) and DnaI (in Bacillus subtilis), acting as a replicative helicase. Furthermore, functional analysis revealed that DciA is essential for replication initiation and protein depletion resulted in a blockage of the initiation of replication after the formation of the open complex.
Pfam PF17636: Viral Unique Long protein 21a (family)
Members of this family such as UL21a found in Human cytomegalovirus (HCMV) is required for HCMV to establish efficient productive infection. It is a short-lived cytoplasmic protein that facilitates HCMV replication. It has also been shown to be responsible for APC1, APC4 and APC5 degradation.
Pfam PF04943: Poxvirus F11 protein (family)
The protein F11 is an early virus protein.
Pfam PF15075: Sperm microtubule associated protein 1 (family)
This family (previously DUF4542) represents the homologs of Sperm microtubule associated protein 1 (SPMAP1 also known as C17orf98). These proteins contain a conserved IPPYN sequence motif. The EM structure of sperm DMTs shows that SPMAP1 interacts directly with the tubulin lattice at the A-tubule seam (between protofilaments A09/A10) where outer dense fibers (ODFs) are connected to dynein-decorated doublet microtubules (DMTs).
Pfam PF11458: Membrane-integrating protein Mistic (family)
Mistic is an integral membrane protein that folds autonomously into the membrane.The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations.
Pfam PF01155: Hydrogenase/urease nickel incorporation, metallochaperone, hypA (domain)
HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilise the protein fold.
Pfam PF11232: Mediator complex subunit 25 PTOV activation and synapsin 2 (domain)
Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function.  The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear.
Wikipedia: Mediator of RNA polymerase II transcription subunit 25 is an enzyme that in humans is encoded by the MED25 gene.
Pfam PF14961: Broad-minded protein central region (repeat)
The Broad-minded family proteins are essential for the proper response to Sonic hedgehog (Shh) signaling during neural tube development. Members of the Broad-minded family collaborate with cyclin-dependent kinase 20 (CDK20) to regulate the structure of the primary cilium. They are involved in the coordination of the ciliary membrane and axoneme assembly, which is crucial for the activation of the GLI2 transcription factor in response to Shh signaling.  This entry represents a central series of alpha-solenoid repeats.
Pfam PF10399: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal (conserved_site)
This is the N-terminal region of the E or R chain, Ubiquitinol-cytochrome C reductase Fe-S subunit, of the hetero-hexameric cytochrome bc1 complex. This region is a TAT-signal region. The cytochrome bc1 complex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains.        The enzyme couples the transfer of electrons from ubiquinol to cytochrome c with the the generation of a protein gradient across the membrane. The motif is also associated with Rieske ([pfam:PF00355]), UCR_TM ([pfam:PF02921]) and Ubiq-Cytc-red_N ([pfam:PF09165]).
Pfam PF00998: Viral RNA dependent RNA polymerase (family)
This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.
Pfam PF22486: MATH domain (domain)
This motif has been called the Meprin And TRAF-Homology (MATH) domain.ED   A0A835B747.1/23-123; A0A835B747.1/23-76;
Pfam PF04399: Glutaredoxin 2, C terminal domain (domain)
Glutaredoxins are a multifunctional family of glutathione-dependent disulphide oxidoreductases.  Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase.  Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, [swissprot:P39811]), which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. Grx2 is structurally similar to glutathione-S-transferases (GST), but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own.  Both domains are needed for correct folding and activity of Grx2. It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress.
Wikipedia: In molecular biology, the glutaredoxin 2 family is a family of bacterial glutaredoxins. Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase. Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. Grx2 is structurally similar to glutathione-S-transferases, but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own. Both domains are needed for correct folding and activity of Grx2. It is thought that the primary function of Grx2 is to catalyse reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress.
These enzymes are not related to GLRX2.
Pfam PF02317: NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain (domain)
This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids.
Wikipedia: In molecular biology, the octopine dehydrogenase family of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The family includes octopine dehydrogenase EC 1.5.1.11, nopaline dehydrogenase EC 1.5.1.19, lysopine dehydrogenase EC 1.5.1.16 and opine dehydrogenase EC 1.5.1.-. NADPH is the preferred cofactor, but NADH is also used. Octopine dehydrogenase is involved in the reductive condensation of arginine and pyruvic acid to D-octopine.
Pfam PF22200: ExsA N-terminal regulatory domain (domain)
ExsA is an AraC-type transcriptional activator protein that is regulated through protein-protein interactions rather than small molecule ligands.  Prior to infection, ExsA is inhibited through a direct interaction with the anti-activator ExsD. Upon host cell contact this interaction is disrupted by the anti-antiactivator protein ExsC. The regulatory domain of ExsA mediate ExsD binding and is represented by this entry. The structure of this domain closely resembles those of the regulatory domains of AraC and ToxT, having typical cupin-like fold.
Pfam PF06178: Oligogalacturonate-specific porin protein (KdgM) (family)
This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM ([swissprot:Q934G3]) from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric.
Wikipedia: Oligogalacturonate-specific porins (KdgM) are a family of outer bacterial membrane proteins from Dickeya dadantii. The phytopathogenic Gram-negative bacteria D. dadantii secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. Synthesis of KdgM is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. KdgM seems to be monomeric.
Pfam PF12001: Domain of unknown function (DUF3496) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 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 PF21159: Flagellar hook-associated protein 1, D3 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 has a multidomain fold comprising an elongated alpha-helical scaffold core, and depending on the bacterial species, a variable number of smaller domains. FlgK from Burkholderia pseudomallei (the causing agent of melioidosis) has two beta-sandwich domains protruding from the large alpha-helical core, referred to as D2 and D3 domains in, which the second one (D3) is represented in this entry. FlgK has cytotoxic effects suggesting an important role in pathogenesis and is highly immunogenic. Domains D2 and D3 have been identified as epitopes with increased immunogenic potential for vaccine development.
Pfam PF00440: Bacterial regulatory proteins, tetR family (domain)
This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamilies based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten Î±-helices with connecting turns and loops. The three N-terminal Î±-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.
Pfam PF15529: Bacterial toxin 24 (family)
A predicted RNase toxin found in bacterial polymorphic toxin systems.  The toxin possesses an all-beta fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system.  Interestingly, the toxin is also found in type-II toxin-antitoxin systems.
Pfam PF14959: gamma-Secretase-activating protein C-term (family)
GSAP, or gamma-secretase-activating protein, also known as PION, regulates gamma-secretase activity. The holo-protein is a large, approx 850 residue protein that is rapidly cleaved to an active 16 kDa C-terminal fragment that is the stable, predominant form. GSAP is expressed in inclusion bodies and is important in brain function. It dramatically and selectively increases neurotoxic beta-Amyloid production in the brain through a mechanism involving its interactions with both gamma-secretase and its substrate, the amyloid precursor protein C-terminal fragment (APP-CTF). Accumulation of neurotoxic beta-Amyloid is a major hallmark of Alzheimer's disease.  Formation of beta-Amyloid is catalysed by gamma-secretase, a protease with numerous substrates that catalyses the intra-membrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein).  The secondary structure of GSAP is largely alpha-helical, lacking well-defined tertiary structure. GSAP represents a type of gamma-secretase regulator that directs enzyme specificity by interacting with a specific substrate.
Pfam PF14580: Leucine-rich repeat (repeat)
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF11573: Mediator complex subunit 23 (family)
Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.
Wikipedia: Mediator of RNA polymerase II transcription subunit 23 is an enzyme that in humans is encoded by the MED23 gene.
Pfam PF06186: Protein of unknown function (DUF992) (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.