SII-SWORD/CoKE huggingface dataset:
Pfam PF00482: Type II secretion system (T2SS), protein F (domain)
The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella. This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats).
Pfam PF17852: Dynein heavy chain AAA lid domain (domain)
This entry corresponds to the extension domain of AAA domain 5 in the dynein heavy chain. This domain is composed of 8 alpha helices.
Pfam PF15861: Partial cleavage stimulation factor domain (domain)
Partial_CstF domain is a protein domain that occurs in proteins from apicomplexan parasites. Currently (as of 2012), little is known about the function of this domain. However, it is homologous to the amino-terminal part of the cleavage stimulation factor, which is thought to be involved with mRNA maturation in mammals.
Wikipedia: The partial cleavage stimulation factor domain, or partial CstF domain, is a protein domain that occurs in proteins from apicomplexan parasites.
Pfam PF01428: AN1-like Zinc finger (family)
Zinc finger at the C-terminus of An1 [swissprot:Q91889], a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues.
Wikipedia: In molecular biology, the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 SWISSPROT, a ubiquitin-like protein in Xenopus laevis. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms.
Pfam PF12546: Blue/Ultraviolet sensing protein C terminal (family)
This domain family is found in eukaryotes, and is typically between 113 and 125 amino acids in length. The family is found in association with [pfam:PF03441], [pfam:PF00875]. Cryptochromes are blue/ultraviolet-A light sensing photoreceptors involved in regulating various growth and developmental responses in plants.
Pfam PF00233: 3'5'-cyclic nucleotide phosphodiesterase (domain)
The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction.

All of these forms contain a catalytic domain of approximately 270 amino acids at the carboxyl terminus. Regulatory domains that vary widely among the PDEase subfamilies flank the catalytic core and include regions that autoinhibit the catalytic domains as well as targeting sequences that control subcellular localization .

PDEase catalytic domains adopt a compact Î±-helical structure consisting of 16 Î±-helices that can be divided into three subdomains. The active site of PDEases is a deep pocket formed by the three subdomains and can be divided into two major subpockets for binding of divalent metals and substrate/inhibitors, respectively. The active site of all PDEase domains contains two divalent metal ions: zinc and probably magnesium .
Wikipedia: 3′,5′-cyclic-nucleotide phosphodiesterases (EC 3.1.4.17) are a family of phosphodiesterases. Generally, these enzymes hydrolyze a nucleoside 3′,5′-cyclic phosphate to a nucleoside 5′-phosphate:nucleoside 3′,5′-cyclic phosphate + H2O = nucleoside 5′-phosphate
Pfam PF12869: tRNA_anti-like (domain)
This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family [pfam:PF01336]. The major characteristic of families like tRNA_anti is their OB-fold, and many of them bind DNA.
Pfam PF04618: HD-ZIP protein N terminus (domain)
This family consists of the N termini of plant homeobox-leucine zipper proteins. Its function is unknown.
Pfam PF07326: Regulator of chromosome segregation 1 (family)
This family consists of several mammalian proteins of around 240 residues in length. Family members include regulator of chromosome segregation 1 (RCS1), also known as FAM64A, CATS or PIMREG (PICALM-interacting mitotic regulator). It is a substrate of APC/C. It may control the metaphase to anaphase transition. It is also a substrate of the Kinase Interacting Stathmin (KIS). RCS1 is highly expressed in cancer cell lines in a cell cycle dependent manner and is induced by mitogens.
Pfam PF12543: Protein of unknown function (DUF3738) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 457 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 PF05056: Protein of unknown function (DUF674) (family)
This family is found in Arabidopsis thaliana and contains several uncharacterised 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 PF08979: Domain of unknown function (DUF1894) (domain)
Members of this family have an important role in methanogenesis. They assume an alpha-beta globular structure consisting of six beta-strands and three alpha-helices forming the secondary structural topological arrangement of alpha1-beta1-alpha2-beta2-beta3-beta4-beta5-beta6-alpha3.
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 PF23190: TRPY1 N-terminal linker helical domain (family)
This domain is found N-terminal in the yeast calcium channel YVC1 (aslo known as TRPY1) and related proteins. YVC1 is a transient receptor potential (TRP) channel that acts as a mechanosensitive osmoregulator. It is non-selective Ca2+ permeable and polymodal cation channel that function similarly to other TRP channels. YVC1 forms a domain-swapped homotetramer with each subunit composed of an N-terminal cytosolic linker helical domain (LHD, represented by this entry) and a transmembrane domain. The LHD domain is composed of eight closely packed alpha-helices and may harbour the docking site for binding partners in the cytosol.
Pfam PF25080: RING zinc finger-like domain (domain)
This domain is found in uncharacterised fungal proteins. It is predicted to fold into a structure with significant similarity to RING/U-box domains. It contains four highly conserved pairs of cysteine residues.
Pfam PF04143: Sulphur transport (family)
This is an integral membrane protein. It is predicted to have a function in the transport of sulphur-containing molecules. It contains several conserved glycines and an invariant cysteine that is probably an important functional residue.
Pfam PF07487: SopE GEF domain (domain)
This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors.
Pfam PF07962: Replication Fork Protection Component Swi3 (family)
Replication fork pausing is required to initiate a recombination events.  More specifically, Swi1 is required for recombination near the mat1 locus.  Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling
Pfam PF24364: Family of unknown function (DUF7520) (family)
This family includes a group of proteins from archaea.
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 PF08503: Tetrahydrodipicolinate succinyltransferase N-terminal (family)
This domain is found at the N-terminus of tetrahydrodipicolinate N-succinyltransferase (DapH) which catalyses the acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate in the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. The N-terminal domain as defined here contains three alpha-helices and two twisted hairpin loops.
Pfam PF08355: EF hand associated (family)
This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis).  The EF hand associated region is found in yeast, vertebrates and plants.
Pfam PF05077: Protein of unknown function (DUF678) (family)
This family contains several poxvirus proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18394: TANK-binding kinase 1 coiled-coil domain 1 (coiled_coil)
This is a coiled-coil domain found in TANK-binding kinase 1 (TBK1), it comprises one of two coiled-coil domains found in the scaffold dimerization region. TBK1 is a serine/threonine kinase and a noncanonical member of the IKK family implicated in diverse cellular functions, including innate immune response as well as tumorigenesis and development. Deletion of the coiled-coil 1 region in TBK1 lead to a severe impairment in TBK1 function even upon over-expression.
Pfam PF21295: Bacterial transglutaminase, N-terminal domain (domain)
This domain is found at the N-terminal end of a group of transglutaminases and similar sequences from bacteria. This domain is often found associated to [pfam:PF01841]. Its structure resembles that of [pfam:PF08379].
Pfam PF05874: Pheromone biosynthesis activating neuropeptide (PBAN) (family)
This family consists of several moth pheromone biosynthesis activating neuropeptide (PBAN) sequences. Female moths produce and release species specific sex pheromones to attract males for mating. Pheromone biosynthesis is hormonally regulated by the Pheromone Biosynthesis Activating Neuropeptide (PBAN) which is biosynthesised in the subesophageal ganglion (SOG).
Pfam PF04895: Archaeal Nre, C-terminal (family)
This conserved region is found in the C-terminal region of archaeal Nre proteins. While most archaeal organisms encode only a single Nre protein, some encode two, NreA  and NreB.
Pfam PF10029: Predicted periplasmic protein (DUF2271) (domain)
This domain, found in various hypothetical bacterial proteins and misannotated lysozyme proteins, it has no known function. This domain contains a [S/T]GA[S/T] conserved motif and serves as a flavinylation substrate for ApbE, and is likely to be involved in extracytosolic redox activities.
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 PF18197: Hypothetical protein TTHB210 (domain)
This domain is found in TTHB210 protein present in Thermus thermophilus. TTHB210 is a Sigma-E factor regulated gene product that forms a homodecamer. This domain is chain G and can be classified with chains A, C, E and I based on its folds.
Pfam PF09251: Salmonella phage P22 tail-spike (repeat)
Members of this family of viral domains adopt a structure consisting of a single-stranded right-handed beta-helix, which in turn is made of parallel beta-strands and short turns. They are required for recognition of the 0-antigenic repeating units of the cell surface, and for subsequent infection of the bacterial cell.
Pfam PF12102: MrcB-like, N-terminal domain (domain)
This model describes the N-terminal domain of a group of mostly uncharacterised proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines)  produced by a broad range of DNA methylases and appears to act  against 5-methylcytosine preceded by a purine residue. The  N-terminal domain of MrcB has been shown to be a DNA-binding domain,  and the crystal structure has been solved.
Pfam PF02731: SKIP/SNW domain (family)
This domain is found in chromatin proteins.
Pfam PF23730: Cartilage intermediate layer protein 1-like domain (domain)
This domain is found in human Cartilage intermediate layer protein 1 (CILP) and similar sequences mainly found in vertebrates. CILP-1 is thought to play a role in cartilage scaffolding. This domain, which is predicted to adopt an all-beta structure, is often found associated to [pfam:PF13927] and [pfam:PF13330].
Pfam PF10133: CO dehydrogenase accessory protein CooT (family)
CooT is an accessory protein required for maturation of Carbon Monoxide Dehydrogenase (CODH). It is a member of a Ni(ii)-binding protein family, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH. Structure analysis indicates that it is a homodimer featuring a fold that resembles an Sm-like domain.
Pfam PF19683: Family of unknown function (DUF6185) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001485) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a  member from the 3-demethylchuangxinmycin biosynthetic gene cluster from Actinoplanes tsinanensis. This family appears to be  predominantly found in Actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF20524: Family of unknown function (DUF6739) (family)
This protein family is functionally uncharacterised. It is found in eukaryotes.
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 PF12443: AT-hook-containing transcription factor (family)
This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.
Pfam PF04491: Poxvirus T4 protein, N terminus (family)
This family of poxvirus proteins are thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C terminal region ([pfam:PF04490]).  M-T4 of myxoma virus ([swissprot:O55698]) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection.
Pfam PF08372: Plant phosphoribosyltransferase C-terminal (family)
This domain is found at the C-terminus of phosphoribosyltransferases and phosphoribosyltransferase-like proteins.  It contains putative transmembrane regions.  It often appears together with calcium-ion dependent C2 domains ([pfam:PF00168]).
Pfam PF08159: NUC153 domain (domain)
This small domain is found in a a novel nucleolar family.
Pfam PF11403: Yeast metallothionein (domain)
Metallothioneins are characterised by an abundance of cysteine residues and a lack of generic secondary structure motifs. This protein functions in primary metal storage, transport and detoxification. For the first 40 residues in the protein the polypeptide wraps around the metal by forming two large parallel loops separated by a deep cleft containing the metal cluster.
Wikipedia: Metallothionein (MT) is a family of cysteine-rich, low molecular weight proteins. They are localized to the membrane of the Golgi apparatus. MTs have the capacity to bind both physiological and xenobiotic heavy metals through the thiol group of its cysteine residues, which represent nearly 30% of its constituent amino acid residues.
Pfam PF16880: N-terminal EH-domain containing protein (family)
EHD_N is a short domain that lies at the very N-terminus of many dynamins and EF-hand domain-containing proteins.
Pfam PF08781: Transcription factor DP (domain)
DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression.  The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer and negatively regulates the G1-S transition.
Wikipedia: In molecular biology, transcription factor DP is a family of proteins which function as transcription factors.
DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer and negatively regulates the G1-S transition.
Pfam PF21904: CAND6/7, N-terminal domain (domain)
This entry represents the N-terminal domain found in CAND6/7 from Arabidopsis and related sequences. These proteins have been predicted to be G-protein coupled receptors that play a role in plants and microbes interactions. They consist of two domains, a GOLD-like domain represented in this entry and a seven transmembrane domain, an architecture shared with GOST (GOLD seven- transmembrane helix) proteins. CAND7 has been described as a G-protein coupled receptor involved in root growth mediated by the bacterial quorum-sensing signals N-acyl-homoserine lactones (AHLs).
Pfam PF09033: DNA Fragmentation factor 45kDa, C terminal domain (domain)
The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40.
Wikipedia: DNA fragmentation factor subunit alpha (DFFA), also known as Inhibitor of caspase-activated DNase (ICAD), is a protein that in humans is encoded by the DFFA gene.
Pfam PF12567: Leukocyte receptor CD45 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 77 and 1130 amino acids in length. The family is found in association with [pfam:PF00041]. CD45 plays a critical role in T-cell receptor (TCR)-mediated signaling. CD45 interacts with SKAP55 which is a transcriptional activator of IL-2.
Pfam PF19919: MoxR-vWA-beta-propeller ternary system domain bpX3 (domain)
Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF08117: Ptu family (family)
This family consists of toxic peptides that are  isolated from the saliva of assassin bugs. The  saliva contains a complex mixture of proteins  that are used by the bug either to immobilise  the prey or to digest it. One of the proteins (Ptu1) has been purified and shown to block reversibly the  N-type calcium channels and to be less specific for  the L- and P/Q- type calcium channels expressed in  BHK cells.
Wikipedia: Insect toxins are various protein toxins produced by insect species. 
Assassin bugs, sometimes known as kissing bugs, are one of the largest and morphologically diverse families of true bugs feeding on crickets, caterpillars and other insects. Some assassin bug species are bloodsucking parasites of mammals, even feed on humans. They can be commonly found throughout most of the world and their size varies from a few millimeters to as much as 3 or 4 centimeters. The toxic saliva of the predatory assassin bugs contains a complex mixture of small and large peptides for diverse uses such as immobilizing and pre-digesting their prey, as well as defense against competitors and predators. Assassin bug toxins are small peptides with disulfide connectivity that target ion channels. They are relatively homologous to the calcium channel blockers omega-conotoxins from marine cone snails and belong to the four-loop cysteine scaffold structural class.
Pfam PF22453: Tubulin/FtsZ-like protein TubZ-like, C-terminal domain (domain)
This entry represents the C-terminal domain of TubZ from Bacillus thuringiensis and related bacteria. TubZ structure consists of an N-terminal GTPase domain and a C-terminal domain. TubZ is part of the polymerizing cytomotive filament, a complex that drives newly replicated plasmids to opposite ends of the dividing cell.
Pfam PF23427: EGF-like domain (domain)
This entry represents an EGF-like domain found in a variety of nematode cell surface proteins.
Pfam PF14943: Mitochondrial ribosome subunit S26 (family)
This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes
Pfam PF08280: M protein trans-acting positive regulator (MGA) HTH domain (domain)
Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.