SII-SWORD/CoKE huggingface dataset:
Pfam PF06299: Protein of unknown function (DUF1045) (family)
This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12149: Herpes simplex virus virion protein 16 C terminal (domain)
This domain is found in viruses, and is about 30 amino acids in length. It is found in association with [pfam:PF02232]. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.
Pfam PF07748: Glycosyl hydrolases family 38 C-terminal domain (domain)
Glycosyl hydrolases are key enzymes of carbohydrate metabolism.
Wikipedia: In molecular biology, glycoside hydrolase family 38 is a family of glycoside hydrolases.
Pfam PF04099: Sybindin-like family (family)
Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses.
Pfam PF13446: A repeated domain in UCH-protein (domain)
This is a repeated domain found in de-ubiquitinating proteins. It's exact function is not known although it is likely to be involved in the binding of the Ubps in the complex with Rsp5 and Rup1.
Pfam PF14940: Transmembrane 219 (family)
This protein belongs to a family found in eukaryotes.  Proteins in this family are typically between 240 and 315 amino acids in length. The domains in this family vary in length from 202 to 249 amino acids. Its exact function remains unknown, however, it is thought to have a role as a transmembrane protein. More specifically, it is possible that this transmembrane protein may have a role as an insulin-like growth factor binding protein 3-receptor (IGFBP-3R). This receptor binds to the ligand, insulin growth factor 3, which is a p53-induced, apoptosis factor important for cancer prevention.
Pfam PF18347: Domain of unknown function (DUF5606) (domain)
This is a domain of unknown function found at the N-terminal region of bacterial proteins.
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 PF15707: Mitochondrial coiled-coil domain protein 1 (family)
This is a family of uncharacterised proteins known as mitochondrial  coiled-coil domain protein 1.
Pfam PF07568: Histidine kinase (domain)
This is the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with [pfam:PF00512] and [pfam:PF07536]. It is usually found adjacent to a C-terminal ATPase domain ([pfam:PF02518]). This domain is found in a wide range of Bacteria and also several Archaea.
Wikipedia: In molecular biology, a two-component regulatory system serves as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions. Two-component systems typically consist of a membrane-bound histidine kinase that senses a specific environmental stimulus, and a corresponding response regulator that mediates the cellular response, mostly through differential expression of target genes. Although two-component signaling systems are found in all domains of life, they are most common by far in bacteria, particularly in Gram-negative and cyanobacteria; both histidine kinases and response regulators are among the largest gene families in bacteria. They are much less common in archaea and eukaryotes; although they do appear in yeasts, filamentous fungi, and slime molds, and are common in plants, two-component systems have been described as "conspicuously absent" from animals.
Pfam PF20147: Crinkler effector protein N-terminal domain (domain)
Phytophthora sojae encodes hundreds of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling- and necrosis-inducing proteins (CRN) or Crinkler. Their functions and mechanisms in pathogenesis are mostly unknown. This N-terminal domain contains a ubiquitin-like fold.
Pfam PF24724: Family of unknown function (DUF7676) (family)
This entry represents a family of bacterial proteins that based on structural similarities are likely to bind to heme or a related derivative molecule. Structural modelling suggests these proteins are likely to form homodimers and that this complex can bind to two heme-like molecules. Each heme binding site is composed of parts of both subunits.
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 PF23802: Family of unknown function (DUF7178) (family)
This entry describes a family of identified in phage metagenomic datasets. The family contains proteins from a variety of phages that infect actinobacteria, particularly Mycobacterium, Gordonia, and Streptomyces.  The exact specificity and function of this metagenomic family is currently unknown. Some members are described as N-glycosylases but the source of that information is uncertain.
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 PF03495: Clostridial binary toxin B/anthrax toxin PA Ca-binding domain (domain)
This domain is a calcium binding domain in the anthrax toxin protective antigen.
Wikipedia: The AB toxins are two-component protein complexes secreted by a number of pathogenic bacteria, though there is a pore-forming AB toxin found in the eggs of a snail. They can be classified as Type III toxins because they interfere with internal cell function. They are named AB toxins due to their components: the "A" component is usually the "active" portion, and the "B" component is usually the "binding" portion. The "A" subunit possesses enzyme activity, and is transferred to the host cell following a conformational change in the membrane-bound transport "B" subunit. T
Pfam PF05038: Cytochrome Cytochrome b558 alpha-subunit (family)
Cytochrome b-245 light chain (p22-phox) is one of the key electron transfer elements of the NADPH oxidase in phagocytes.
Pfam PF16944: Fungal potassium channel (family)
KHC is a family of fungal proteins carrying three transmembrane domains. It is a member of the fungal potassium channel family of transporters, and includes a pair of homologous sequences that localise to distinct zones of the yeast plasma membrane and are induced during the response to mating pheromones. Together KCH1 and KCH2 promote low-affinity K+ uptake and are essential for K+-dependent activation of HACS - a high-affinity Ca2+ influx system that activates calcineurin and is essential for cell survival - in S. cerevisiae cells responding to mating pheromones.
Pfam PF12356: Baculoviral IAP repeat-containing protein 6 (family)
BIRC6 is an anti-apoptotic protein which can  regulate cell death by controlling caspases  and by acting as an E3 ubiquitin-protein ligase.
Pfam PF17794: Major Vault Protein repeat domain (domain)
This short domain is found repeated numerous times in the Major Vault Protein. This entry is related to [pfam:PF01505].
Pfam PF07659: Nucleotide modification associated domain 1 (domain)
An alpha helical domain with conserved polar residues suggestive of enzymatic function. The domain is associated with the 5-hydroxymethyl uridine synthase and is predicted to play a role in modified base biosynthesis pathways.
Pfam PF10420: Cytokine interleukin-12p40 C-terminus (domain)
IL12p40_C is the largely beta stranded C-terminal, D3, domain of interleukin-12p40 or interleukin-12B. This interleukin is produced on stimulation by macrophage-engulfed micro-organisms and other stimuli, when it dimerises with interleukin-12p35 to form a heterodimer which then binds to receptors on natural killer cells to activate them to destroy the micro-organisms. This domain contains two disulfide bridges, one of which serves to bind p40 to p35 and the other to hold the beta strands within the domain together. The cupped shape of the p35 binding interface matches the elbow-like bend between D2 and D3 in p40. The domain is often associated with family fn3, [pfam:PF00041].
Pfam PF13689: YfiR/HmsC-like (family)
This family of proteins is found in bacteria and includes YfiR from E. coli. YfiR has been shown to regulate YfiN, a diguanylate cyclase and a bifunctional protein that produces c-di-GMP in response to reductive stress and then dynamically relocates to the division site to arrest cell division in response to envelope stress in Escherichia coli. YfiR may serve as a periplasmic redox sensor that regulates YfiN activity in response to reducing conditions. HmsC in Yersinia Pestis is the orthologue of YfiR from E. coli. HmsC is a periplasmic protein that interacts directly with the periplasmic domain (PD) of HmsD and causes proteolytic degradation of HmsD, which in turn negatively regulates Y. pestis biofilm formation.
Pfam PF22700: Diphosphomevalonate decarboxylase-like N-terminal domain (domain)
This entry represents the N-terminal domain of Diphosphomevalonate decarboxylases whoch catalyse the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Members of this entry function in the mevalonate pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis.
Pfam PF09611: CRISPR-associated protein (Cas_Csy1) (family)
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1.
Pfam PF09430: ER membrane protein complex subunit 7, beta-sandwich domain (domain)
This is the beta-sandwich domain found in ER membrane protein complex subunit 7 (EMC7), which is an integral membrane component of the EMC. EMC is widely conserved and involved in membrane protein biogenesis. It mediates the insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins in an energy-independent manner, both post-translational insertions of tail-anchored proteins  and co-translational insertion of multipass membrane proteins. This entry includes UPF0620 protein C83.10 from S. pombe, an orthologue of animal EMC7. This domain is also found in nodal modulators, which have been identified as part of a protein complex that participates in the nodal signalling pathway during vertebrate development.
Pfam PF12797: 4Fe-4S binding domain (domain)
This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF21127: ATG1-like, MIT domain 2 (domain)
Members of this entry are serine/threonine-protein kinases and includes  Atg1 from yeasts, Unc-51 from C. elegans and ULK1-2 from humans. Atg1 is required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway. Unc-51 is important for axonal elongation and axonal guidance and ULK1-2 are involved in autophagy in response to starvation. They consist of a kinase domain at the N-terminal ([pfam:PF00069]) and two tandem microtubule interacting and transport (MIT) domains (tMIT) at the C-terminal which, in ATG1, mediates the interaction with ATG13. In ULK1-2, MIT domain control the regulatory function and localization of the proteins and also mediate interactions with additional autophagy proteins. This is the C-terminal MIT domain (MIT2).
Pfam PF11575: FhuF 2Fe-2S C-terminal domain (domain)
This family consists of several bacterial ferric iron reductase protein (FhuF) sequences.                 FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B. This domain is the C-terminal domain that contains 4 conserved cysteine residues that are found to be part of a 2Fe-2S cluster.
Pfam PF01015: Ribosomal S3Ae family (family)
A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. This family represents the small ribosomal subunit protein eS1, previously known as S1 in yeast and S3A in archaea and mammals , which consists of proteins that have from 220 to 250 amino acids.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF24383: Family of unknown function (DUF7539) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt a mainly alpha structure.
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 PF07174: Fibronectin-attachment protein (FAP) domain (domain)
This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.
Pfam PF04038: Dihydroneopterin aldolase (family)
This domain contains a strongly conserved YPLM motif and it is found at the C terminus of archaeal specific 7,8-dihydroneopterin aldolase (DHNA) MtpD, an enzyme involved in the synthesis of 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) . 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin.
Wikipedia:  The enzyme dihydroneopterin aldolase catalyzes the chemical reaction2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8- dihydropteridine  2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine + glycolaldehyde
Pfam PF13530: Sterol carrier protein domain (domain)
This domain is found in enhanced intracellular survival protein eis from Mycobacterium tuberculosis. It shares protein sequence similarity with the SCP2 sterol-binding domain.
Pfam PF14456: Alpha-helical domain 2 (family)
An alpha-helical domain found in gene neighborhoods encoding genes  containing bacterial homologs of components of the ubiquitin  modification pathway such as the E1, E2, Ub and JAB peptidase  proteins.
Pfam PF04339: Peptidogalycan biosysnthesis/recognition (family)
FemAB_like is a family of both baterial and Viridiplantae proteins with responsibility for building interpeptide bridges in peptidoglycan. Such a function is feasible for bacteria but less likely for the plant members of this family. Perhaps the plant-members are using homologous proteins to recognise bacterial peptidoglcans as part of their innate immune system.
Pfam PF10747: Sporulation inhibitor of replication protein SirA (family)
This entry represents the Sporulation inhibitor of  replication (sirA) family of proteins from Bacillus sp.  Induction of sporulation in rapidly growing cells inhibits  replication; this is thought to be through the action of SirA protein and independent of phosphorylated Spo0A;  however SirA protein synthesis is induced by Spo0A.
Pfam PF09043: D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit (domain)
Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as co-factors.  The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl co-factor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state. This is a TIM-barrel domain.
Wikipedia: In enzymology, D-lysine 5,6-aminomutase is an enzyme that catalyzes the chemical reactionD-lysine  2,5-diaminohexanoate
Pfam PF02137: Adenosine-deaminase (editase) domain (family)
Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and  are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc.
Wikipedia: Adenosine deaminase is an enzyme involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues.
Pfam PF15799: Coiled-coil domain-containing protein 48 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 575 amino acids in length.
Pfam PF00306: ATP synthase alpha/beta chain, C terminal domain (domain)
Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis .

In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit .

In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.
The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal Î²-barrel, a central domain containing the nucleotide-binding site and a C-terminal Î± bundle domain of 7 and 6 helices, respectively, in the alpha and beta subunits . This entry represents the C-terminal domain of the alpha subunit.
Wikipedia: The alpha and beta subunits are found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively, as well as flagellar (T3SS) ATPase and the termination factor Rho. The subunits make up a ring that contains the ATP-hydrolyzing catalytic core. The F-ATPases, V-ATPases and A-ATPases are composed of two linked complexes: the F1, V1 or A1 complex containsthat synthesizes/hydrolyses ATP, and the Fo, Vo or Ao complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis.
Pfam PF02112: cAMP phosphodiesterases class-II (family)
Cyclic-AMP phosphodiesterase (3.1.4.17) (PDE) catalyses the hydrolysis of cAMP to the corresponding nucleoside 5' monophosphate. On the basis of sequence similarity, most PDEs can be grouped together , but some enzymes lie apart from the main family and represent a second distinct class  that includes PDEs from Dictyostelium and yeast.

This entry contains class-II cyclic-AMP phosphodiesterases.