SII-SWORD/CoKE huggingface dataset:
Pfam PF02145: Rap/ran-GAP (domain)
Structural domains comprising this superfamily share the structure of two shown to be homologous GTPase activating proteins for Rap and Ran. Both are Ras-like guanine-nucleotide-binding proteins (GNBPs) involved in a variety of signal-transduction processes and their activity is regulated by GEFs and GAPs.

Rap small G proteins have been implicated in various cellular processes such as exocytosis, cAMP signalling, cell adhesion and cell proliferation. Rap proteins acts as molecular switches, with an active GTP-bound form and an inactive GDP-bound form . The inactive GDP bound form is promoted by GTPase-activating proteins (GAPs). GAP proteins specific for Rap contain a conserved region of around 200 amino-acid residues, the RapGAP domain. This domain can accelerate the GTP hydrolysis activity of Rap by five orders of magnitude .

Ran, also known as GTP-binding nuclear protein, is on the other hand essential for the translocation of RNA and proteins through the nuclear pore complex and has been implicated in the control of DNA synthesis and cell cycle progression.
Pfam PF17741: Family of unknown function (DUF5578) (family)
This is a family of unknown function 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 PF17693: Family of unknown function (DUF5539) (family)
This is a family of unknown function found in primates.
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 PF07949: YbbR-like protein (family)
The members of this family are are all hypothetical bacterial proteins of unknown function, and are  similar to the YbbR protein expressed by Bacillus  subtilis ([swissprot:O34659], [swissprot:O87088]). One member ([swissprot:Q97EN2]) is annotated as an uncharacterized secreted protein, whereas another member ([swissprot:P43521]) is described as a hypothetical protein in the 5'region  of the def gene of Thermus thermophilus, which encodes a deformylase, but no further information was found  in either case. This region is found repeated up to four times in many members of this family.
Pfam PF22099: Magnesium transporter MRS2-like (family)
This entry represents eukaryotic membrane transporters distantly related to prokaryotic CorA transporters, including the inner mitochondrial membrane Mg2+ transporters Mfm1p/Lpe10p and Mrs2p from yeast, MRS2/MRSL from human and the homologues from plants.
Pfam PF09206: Alpha-L-arabinofuranosidase B, catalytic (domain)
Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyses the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan.
Pfam PF20823: CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain (domain)
The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the conserved Zn binding subdomain included in the first RMM domain (D1 domain) of Cmr2. This region shows two alpha-helices.
Pfam PF17046: SesB domain on fungal death-pathway protein (family)
SesB is a short conserved domain found on fungal proteins that are part of the cell death or heterokaryon incompatibility pathway.
Pfam PF04297: Putative helix-turn-helix protein, YlxM / p13 like (family)
Members of this family are predicted to contain a helix-turn-helix motif,  for example residues 37-55 in Mycoplasma mycoides p13 ([swissprot:O05290]). Genes encoding family members are often part of operons that encode  components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway.
Pfam PF24877: Dihydroxy-acid/6-phosphogluconate dehydratase C-terminal (domain)
This is the C-terminal domain of Ilv/ED dehydratase protein family which includes dihydroxy-acid/6-phosphogluconate dehydratases,  and pentonate dehydratases. Members of this entry are involved in various biosynthetic and carbohydrate metabolic pathways. Dihydroxy-acid dehydratase catalyses the fourth step in the biosynthesis of isoleucine and valine, the dehydratation of 2,3-dihydroxy-isovaleic acid into alpha-ketoisovaleric acid. 6-Phosphogluconate dehydratase catalyses the first step in the Entner-Doudoroff pathway, the dehydratation of 6-phospho-D-gluconate into 6-phospho-2-dehydro-3-deoxy-D-gluconate. They consist of two domains, N- and C-terminal, the latter contains residues (Ser490 and Thr492) that participate in the formation of the substrate binding site. This domain is composed of a beta-sheet consisting of six parallel and two anti-parallel beta-strands that are arranged like a beta-barrel.
Pfam PF04220: Der GTPase activator (YihI) (family)
YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor.  The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI.
Pfam PF24748: Galaxin-like repeats (repeat)
These entry represents a repetitive region found in galaxins and related proteins. These proteins share common structural features such as the presence of repetitive motifs containing di-cysteine residues. These pairs of cysteines are predicted to reside on beta-hairpins and to form a disulfide bonds each with the pair located downstream and upstream of them, forming a continuum. This probably is essential for the function of galaxins which have a role in the formation of calcium carbonate skeletons in marine organisms, such as corals.
Pfam PF05871: ESCRT-II complex subunit (family)
This family of conserved eukaryotic proteins are subunits of the endosome associated complex ESCRT-II which recruits transport machinery for protein sorting at the multivesicular body (MVB).  This protein complex transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo.
Wikipedia: Vacuolar protein-sorting-associated protein 25 is a protein that in humans is encoded by the VPS25 gene.
Pfam PF13548: Domain of unknown function (DUF4126) (domain)
This presumed domain is functionally uncharacterised.
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 PF08827: Domain of unknown function (DUF1805) (domain)
This domain is found in bacteria and archaea and has an N terminal tetramerisation region that is composed of beta sheets.
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 PF18729: STY4199-like HEPN (domain)
STY4199-like HEPN nuclease domain.
Pfam PF22726: NACHT C-terminal Alpha/Beta 2 (domain)
This is a domain containing alpha-helices and beta-strands, found at the C-terminus of certain bacterial NACHT conflict systems.
Pfam PF05326: Seminal vesicle autoantigen (SVA) (family)
This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19-kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP, has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4.
Pfam PF08345: Flagellar M-ring protein C-terminal (domain)
This is the RBM3/beta-collar domain found in bacterial flagellar M-ring (FliF) proteins which also have the YscJ/FliF domain ([pfam:PF01514]) at the N-terminal.
Pfam PF04252: Protein arginine N-methyltransferase SFM1-like (family)
This family of proteins includes Protein arginine N-methyltransferase SFM1 from Saccharomyces cerevisiae and similar proteins from fungi and archaea. Sfm1 is a S-adenosyl-L-methionine-dependent protein- arginine N-methyltransferase that monomethylates ribosomal protein S3 (RPS3) at 'Arg-146'.
Pfam PF20433: PKAT, KLD domain (domain)
This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and TMEM130, which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers. This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family PMEL and GPNMB share overlapping phenotype and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma.
Pfam PF12271: Chitin synthase export chaperone (family)
This family of proteins is found in eukaryotes, and are typically between 288 and 332 amino acids in length. Family members include the Saccharomyces cerevisiae Chs7, an integral membrane protein located in the ER which is directly involved in chitin synthesis through the regulation of chitin synthase III (CSIII) activity. In the absence of CHS7 gene product, Chs3p, but not other secreted proteins, is retained in the ER, leading to a severe defect in CSIII activity and consequently, to a reduced rate of chitin synthesis. In addition, chs7 null mutants show the yeast phenotypes associated with a lack of chitin: reduced mating efficiency and lack of the chitosan ascospore layer, clear indications of Chs7p function throughout the S. cerevisiae biological cycle. Hence, Chs7 is involved in the regulation of CSIII activity by controlling Chs3p export from the ER.
Pfam PF20964: DNA polymerase III subunit tau, C-terminal domain (domain)
This domain is found at the C-terminal end of the subunit tau of bacterial DNA polymerase III (DnaX). It binds to the C terminus of the alpha subunit of the same complex through its C-terminal helix and the adjacent loop.
Pfam PF19270: F-box only protein C-terminal region (family)
This entry represents the C-terminal region of several F-box only proteins. These proteins are the substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. This family includes yeast HRT3 protein as well as human F-box only 9 protein.
Pfam PF08463: EcoEI R protein C-terminal (family)
The restriction enzyme EcoEI recognises 5'-GAGN(7)ATGC-3' and is composed of the three proteins R, M, and S. The domain described here is found at the C-terminus of the R protein (HsdR) which is required for both nuclease and ATPase activity.
Wikipedia: In molecular biology, the EcoEI R protein C-terminal domain is a protein domain found at the C-terminus of both the R subunit of type I restriction enzymes and the Res subunit of type III restriction enzymes. The type I enzymes include EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity.
Pfam PF19849: Family of unknown function (DUF6324) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two conserved sequence motifs: QIGPT and GMVR.
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 PF07002: Copine (family)
This family represents a conserved region approximately 220 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth.
Pfam PF23315: PEX6 fourth domain (domain)
This domain is found in the yeast Peroxisomal ATPase PEX6 and related proteins. PEX6 is a component of the PEX1-PEX6 AAA ATPase complex, a protein dislocase complex that mediates the ATP-dependent extraction of the PEX5 receptor from peroxisomal membranes, an essential step for PEX5 recycling. The domain represented in this entry is predicted to adopt a globular structure with some topological similarity to AAA ATPase p97.
Pfam PF04613: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD (domain)
UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) catalyses an early step in lipid A biosynthesis: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] -> UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein]. Members of this family also contain a hexapeptide repeat ([pfam:PF00132]).  This family constitutes the non-repeating region of LPXD proteins.
Pfam PF12987: Domain of unknown function, B. Theta Gene description (DUF3871) (family)
Based on Bacteroides thetaiotaomicron gene BT_2984, a putative uncharacterized protein  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture.
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 PF14773: Helicase-associated putative binding domain, C-terminal (family)
The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain.
Pfam PF17819: Testis-specific expressed protein 55 (family)
This family includes testis-specific expressed protein 55 (also known as TSCPA in human), which is involved in normal in normal spermatogenesis.
Pfam PF11011: Protein of unknown function (DUF2849) (family)
This bacterial family of proteins has been suggested to be an electron source for sulfite reductase. This family is usually found upstream of cysI, the beta subunit of this enzyme. This family was also found fused to cysI in Pseudomonas putida GB-1 (See Supplementary note 5 in).
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 PF09666: Sororin protein (family)
Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion. The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex.
Pfam PF15791: Doublesex-and mab-3-related transcription factor C1 and C2 (family)
DMRT-like is a C-terminal domain found on eukaryotic proteins for doublesex-and mab-3-related transcription factors C1 and C2. This is not the DM DNA-binding region. The family is all disorder and low-complexity.
Pfam PF14345: GDYXXLXY protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 171 and 199 amino acids in length.  It contains a conserved GDYXXLXY motif.
Pfam PF05107: CRISPR-associated protein Cas7 (family)
CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defence complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA.
Pfam PF10864: Protein of unknown function (DUF2663) (family)
Some members in this family of proteins are annotated as YpbF however currently no function is known.
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 PF14907: Uncharacterised nucleotidyltransferase (domain)
This family is likely to be an uncharacterised group of nucleotidyltransferases.
Pfam PF16441: Domain of unknown function (DUF5038) (family)
This family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Clostridiales 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 PF12884: Transducer of regulated CREB activity, N terminus (family)
This family includes the N terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerisation domain of CREB (cAMP Response Element-Binding). The proteins display a highly conserved predicted N-terminal coiled-coil domain and an invariant sequence matching a protein kinase A (PKA) phosphorylation consensus sequence (RKXS). The coiled-coil structure interacts with the bZIP domain of CREB. This interaction may occur via ionic bonds because it is disrupted under high-salt conditions. In addition to CREB-binding, the N-terminal region plays a role in the tetramer formation of TORCs, but the physiological function of the multimeric complex has not been clarified yet.
Pfam PF18183: SMODS and SLOG-associating 2TM effector domain 2 (domain)
The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is the only prokaryotic SLATT family to exist as a standalone domain, with no as-yet discernable genome associations.
Pfam PF13864: Calmodulin-binding (family)
This is a family of apparent calmodulin-binding proteins found at high levels in the testis and vomeronasal organ and at lower levels in certain other tissues. Enkurin is a scaffold protein that binds PI3 kinase to sperm transient receptor potential (canonical) (TRPC) channels. The mammalian transient receptor potential (canonical) channels are the primary candidates for the Ca(2+) entry pathway activated by the hormones, growth factors, and neurotransmitters that exert their effect through activation of PLC.  Calmodulin binds to the C-terminus of all TRPC channels, and dissociation of calmodulin from TRPC4 results in profound activation of the channel.
Pfam PF19293: CdaA N-terminal transmembrane domain (family)
This entry represents the amino terminal three helical transmembrane region found in the CdaA diadenylate cyclase enzyme.
Pfam PF04246: Positive regulator of sigma(E), RseC/MucC (family)
This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions). In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonisation in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain [pfam:PF02424], which is itself involved in thiamine biosynthesis.
Pfam PF13069: Protein of unknown function (DUF3933) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.