SII-SWORD/CoKE huggingface dataset:
Pfam PF11757: Suppressor of RNA silencing P21-like N-terminal domain (domain)
This domain can be found at the N-terminal region of is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins. C-terminal domain entry found under [pfam:PF11479].
Pfam PF19097: Snu56-like U1 small nuclear ribonucleoprotein component (family)
This family is a component of the U1 snRNP particle, which recognises  and binds the 5'-splice site of pre-mRNA. Together with other  non-snRNP factors, U1 snRNP forms the spliceosomal commitment complex, which targets pre-mRNA to the splicing pathway.
Pfam PF22594: GTP-eEF1A C-terminal domain-like (domain)
This entry represents a beta-barrel domain that is found C-terminal in homologues of elongation factor eEF1A.
Wikipedia: EF-Tu is a prokaryotic elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA (aa-tRNA) to the ribosome. It is a G-protein, and facilitates the selection and binding of an aa-tRNA to the A-site of the ribosome. As a reflection of its crucial role in translation, EF-Tu is one of the most abundant and highly conserved proteins in prokaryotes. It is found in eukaryotic mitochondria as TUFM.
Pfam PF15390: WD repeat and coiled-coil-containing protein family (repeat)
This family includes WD repeat and coiled-coil-containing protein (WDCP, previously known as C2orf44), which is found in eukaryotes and consists of around 721 amino acids. The N-terminal contains two WD (tryptophan-aspartic acid) repeats (WD1 and WD2). WD repeats may be involved in a range of biological functions including apoptosis, transcriptional regulation and signal transduction. The C-terminal contains a proline-rich sequence (PPRLPQR), and is predicted to have leucine-rich coiled coil region (CC). WDCP was identified in a proteomic screen to find signalling components that interact with Hck (hematopoietic cell kinase), a  non-receptor tyrosine kinase. WDCP was shown to bind tightly and specifically to the SH3 domain of Hck in U937 human monocytic cells. WDCP was also shown to exist as an oligomer when expressed in mammalian cells. While the function of WDCP is unknown, it has been identified in a gene fusion event with anaplastic lymphoma  kinase (ALK) in colorectal cancer patients.
Pfam PF05322: NINE Protein (family)
This family consists of NINE proteins from several bacteriophages and from E. coli.
Pfam PF02283: Cobinamide kinase / cobinamide phosphate guanyltransferase (domain)
This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF14863: Alkyl sulfatase dimerisation (repeat)
This domain is found in alkyl sulfatases such as the Pseudomonas aeruginosa SDS hydrolase ([swissprot:Q9I5I9]), where it acts as a dimerisation domain
Pfam PF04072: Leucine carboxyl methyltransferase (family)
Family of leucine carboxyl methyltransferases [ec:2.1.1.-] . This family may need divides a the full alignment contains a significantly shorter mouse sequence.
Pfam PF02568: Thiamine biosynthesis protein (ThiI) (family)
ThiI is required for thiazole synthesis, required for thiamine biosynthesis.
Pfam PF20871: BTB/POZ domain-containing protein KCTD1/15, C-terminal domain (domain)
This entry represents the C-terminal domain of BTB/POZ domain-containing proteins 1 and 15 (KCTD1/15), characterised by beta-sheets surrounded by alpha-helices. Structural similarities of the C-terminal domain of KCTD proteins allowed their classification in clades and subclades described in.
Pfam PF22922: NLP protein GAF domain (domain)
This entry represents a GAF-like domain found in plant NLP proteins. Several NLP proteins contain two copies of this domain family. Members of the NLP family all contain an amino-terminal GAF domain, an intermediate RWP-RK domain, and a carboxy-terminal Phox and Bem1 (PB1) domain. Additionally, a nuclear export signal domain is predicted in the N-terminus.
Pfam PF00808: Histone-like transcription factor (CBF/NF-Y) and archaeal histone (domain)
This family includes archaebacterial histones and histone like transcription factors from eukaryotes.
Pfam PF16003: Domain of unknown function (DUF4776) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 444 and 485 amino acids in length. There is a conserved TLR sequence motif.
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 PF01346: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase (domain)
This family is only found at the amino terminus of [pfam:PF00254]. This entry represents the N-terminal domain found in FKBP-type peptidylprolyl isomerases (PPIase). The N-terminal domain forms the dimer interface by the mutual exchange of two beta-strands between monomers.
Pfam PF11818: C-terminal domain of tail specific protease (DUF3340) (family)
This presumed domain is found at the C-terminus of tail specific proteases. Its function is unknown. This family is found in bacteria and eukaryotes.  This presumed domain is typically between 88 to 187 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 PF01531: Glycosyl transferase family 11 (family)
This family contains several fucosyl transferase enzymes.
Pfam PF22297: PccH Cytochrome c (domain)
This entry represents the PccH protein, a unique cytochrome c (GSU3274) found in Geobacter sulfurreducens. PccH is a small (15 kDa) cytochrome that contains a single c-type heme and plays an essential role in electron transfer from graphite electrodes to fumarate, the terminal electron acceptor, in G. sulfurreducens. The crystal structure of PccH, reveals a distinct fold characterized by two lobes with the heme located in a cleft between them. Notably, PccH exhibits a low reduction potential of -24 mV at pH 7, which is unusual for monoheme cytochromes. Based on structural and phylogenetic analyses, PccH represents a novel subclass of class I monoheme cytochromes. The unique structural features and low reduction potential of PccH likely enable its redox activity within the typically negative potential range encountered by G. sulfurreducens. Although located in the periplasm, PccH is not involved in the initial electron transfer from the electrode but is believed to participate in downstream electron transport events in the periplasm.
Pfam PF13240: zinc-ribbon domain (domain)
This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. [pfam:PF12773].
Pfam PF14133: Domain of unknown function (DUF4300) (family)
This family of lipoproteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 281 and 303 amino acids in length. There are two conserved sequence motifs: NCR and PYQ.
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 PF13681: Type IV pilus assembly protein PilX C-term (domain)
This family is likely to be the C-terminal region of type IV pilus assembly PilX or PilW proteins.
Pfam PF17624: Family of unknown function (family)
This is a family of unknown function found in Cytomegalovirus. One of the family members US30 is a putative membrane glycoprotein with one predicted trans-membrane region.
Pfam PF16825: IGP family C-type lectin domain (domain)
This C-type lectin domain is present in the IGP 'invariant glycoprotein' family of proteins from Trypanosoma and Leishmania.
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 PF17087: Herpesvirus US34A protein family (family)
Proteins in this human cytomegalovirus (HHV-5 )family contain a transmembrane domain.
Pfam PF18714: DNA polymerase II intein Domain IV (domain)
This domain can be found in the hyperthermophilic archaeon Thermococcus kodakaraensis Pol-2 intein. It is suggested to be a potential DNA binding domain.
Pfam PF06580: Histidine kinase (domain)
This entry represents a long helical region within bacterial histidine kinase enzymes which connects the C-terminal kinase domain to the other domains composing the protein. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain [pfam:PF02518] and/or [pfam:PF00672].
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 PF04786: ssDNA binding protein (family)
Family of Baculovirus ssDNA binding proteins.
Pfam PF03036: Perilipin family (family)
The perilipin family includes lipid droplet-associated protein (perilipin), adipose differentiation-related protein (adipophilin) and TIP47, also known as perilin-3, altogether form the PAT family of proteins. They predominantly localise to the surface of intracellular neutral lipid droplets. Perilipin is a modulator of adipocyte lipid metabolism and adipophilinis and  are involved in the development and maintenance of adipose tissue. This family appears to share some similarity with [pfam:PF08618].
Wikipedia: Perilipin, also known as lipid droplet-associated protein, perilipin 1, or PLIN, is a protein that, in humans, is encoded by the PLIN gene. The perilipins are a family of proteins that associate with the surface of lipid droplets. Phosphorylation of perilipin is essential for the mobilization of fats in adipose tissue.
Pfam PF15360: APJ endogenous ligand (family)
Apelin is among the most potent stimulators of cardiac contractility known. The apelin-APJ signaling pathway is an important novel mediator of cardiovascular control. Apelin is an adipokine secreted by adipocytes where it is co-expressed with apelin receptor (APJ) in adipocytes.  It suppresses adipogenesis through MAPK kinase/ERK dependent pathways and prevents lipid droplet fragmentation, thereby inhibiting basal lipolysis through AMP kinase dependent enhancement of perilipin expression. It also inhibits hormone-stimulated acute lipolysis through decreasing perilipin phosphorylation. Apelin induces a decrease of free fatty acid release via its dual inhibition on adipogenesis and lipolysis. As a vaso-active and vascular cell growth-regulating peptide Apelin is a target of the BMP pathway, the TGF-beta/bone morphogenic protein (BMP) system - a major pathway for angiogenesis.
Pfam PF05290: Baculovirus immediate-early protein (IE-0) (family)
The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. It is thought that that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites.
Pfam PF05374: Mu-Conotoxin (family)
Mu-conotoxins are peptide inhibitors of voltage-sensitive sodium channels.
Wikipedia: A conotoxin is one of a group of neurotoxic peptides isolated from the venom of the marine cone snail, genus Conus.
Pfam PF17786: Mannosidase Ig/CBM-like domain (domain)
This domain corresponds to domain 4 in the structure of Bacteroides thetaiotaomicron beta-mannosidase, BtMan2A. This domain has an Ig-like fold.
Pfam PF22391: Family of unknown function (DUF6975) (family)
This family of uncharacterised proteins is found in Proteobacteria. It shares significant sequence similarity with enzymes members of Heme oxygenase-like superfamily and are predicted to adopt similar structure consisting of a bundle of six alpha-helices.
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 PF05964: F/Y-rich N-terminus (family)
This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.
Pfam PF13072: Mother cell inhibitor of FtsZ (family)
This family of proteins is found in bacteria. Family members are approximately 40 amino acids in length. There is a conserved GKAW sequence motif. There is a single completely conserved residue G that may be functionally important. Family members include the Bacillus subtilis cell-division inhibitor, MciZ (mother cell inhibitor of FtsZ) which blocks the assembly of FtsZ. FtsZ (filamentation temperature-sensitive Z) is the bacterial homolog of tubulin. Crystal structure reveals that MciZ binds to the C-terminal polymerization interface of FtsZ, the equivalent of the minus end of tubulin, causing shortening of protofilaments and blocking the assembly of higher-order FtsZ structures. Hence, MciZ provides a capping-based regulatory mechanism for FtsZ.
Pfam PF17025: Domain of unknown function (DUF5099) (family)
This is a family of microsporidia-specific sequences 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 PF00510: Cytochrome c oxidase subunit III (family)
This entry represents a structural domain found in cytochrome c and ubiquinol oxidase subunit III. The overall structure of these enzymes is similar .
Cytochrome c oxidase (7.1.1.9) is the terminal enzyme of the respiratory chain of mitochondria and many aerobic bacteria. It catalyses the transfer of electrons from reduced cytochrome c to molecular oxygen:

4 cytochrome c+2 + 4 H+ + O2 --> 4 cytochrome c+3 + 2 H2O

This reaction is coupled to the pumping of four additional protons across the mitochondrial or bacterial membrane .

Cytochrome c oxidase is an oligomeric enzymatic complex that is located in the mitochondrial inner membrane of eukaryotes and in the plasma membrane of aerobic prokaryotes. The core structure of prokaryotic and eukaryotic cytochrome c oxidase contains three common subunits, I, II and III. In prokaryotes, subunits I and III can be fused and a fourth subunit is sometimes found, whereas in eukaryotes there are a variable number of additional small polypeptidic subunits . The functional role of subunit III is not yet understood.

As the bacterial respiratory systems are branched, they have a number of distinct terminal oxidases, rather than the single cytochrome c oxidase present in the eukaryotic mitochondrial systems. Even though the cytochrome o complex oxidises quinol (ubiquinol) and does not catalyse the oxidation of reduced cytochrome c, they belong to the same haem-copper oxidase superfamily as cytochrome c oxidases. Members of this family share sequence similarities in all three core subunits: subunit I is the most conserved subunit, whereas subunit II is the least conserved .
Wikipedia: Cytochrome c oxidase subunit III (COX3) is an enzyme that in humans is encoded by the MT-CO3 gene. It is one of main transmembrane subunits of cytochrome c oxidase. It is also one of the three mitochondrial DNA (mtDNA) encoded subunits of respiratory complex IV. Variants of it have been associated with isolated myopathy, severe encephalomyopathy, Leber hereditary optic neuropathy, mitochondrial complex IV deficiency, and recurrent myoglobinuria.
Pfam PF17596: Family of unknown function (DUF5492) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF21984: DnaD N-terminal domain (domain)
DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. The DnaD N-terminal domain has a scaffold-forming activity. This domain adopts classical winged helix fold decorated with extensions at both termini.
Pfam PF06585: Haemolymph juvenile hormone binding protein (JHBP) (family)
This family consists of several insect-specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone regulates embryogenesis, maintains the status quo of larval development and stimulates reproductive maturation in the adult insect. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph. The crystal structure of the JHBP from Galleria mellonella shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance. This family now includes DUF233, [pfam:PF03027].
Wikipedia: In molecular biology, the haemolymph juvenile hormone-binding protein (JHPB) family of proteins consists of several insect specific haemolymph juvenile hormone binding proteins. Juvenile hormone (JH) has a profound effect on insects. It regulates embryogenesis, maintains the status quo of larva development and stimulates reproductive maturation in the adult forms. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph. The crystal structure of the JHBP from Galleria mellonella shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organisation of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance.
Pfam PF22345: GLMA, C-terminal (domain)
This entry represents a beta-sandwich domain found at the C-terminal of exo-beta-D-glucosaminidase GLMA from Thermococcus kodakarensis and similar archaeal proteins. It is an exo-type enzyme that specifically cleaves the non-reducing terminal glycosidic bond of chitooligosaccharides, being involved in chitin degradation.
Pfam PF13525: Outer membrane lipoprotein (repeat)
This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex.
Pfam PF20895: PsV, capsid protein (family)
Capsid protein (CP) from Penicillium stoloniferum virus (PsV) associates only with itself in forming capsids, forming a quasi- symmetrical dimeric fold. 60 dimers associate to form the capsid shell. CP is organized into two domains: the shell domain, which form the continuous capsid, and the arch domain, responsible for the dimeric surface protrusions.