SII-SWORD/CoKE huggingface dataset:
Pfam PF12161: HsdM N-terminal domain (domain)
This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with [pfam:PF02384]. Mutations in this region of EcoKI methyltransferase [swissprot:P08957] abolish the normally strong preference of this system for methylating hemimethylated substrate.  The structure of this domain has been shown to be all alpha-helical.
Wikipedia: In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Pfam PF12984: Domain of unknown function (DUF3868) (family)
Based on Bacteroides thetaiotaomicron gene BT_1065, 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 PF03807: NADP oxidoreductase coenzyme F420-dependent (family)
Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain and a C-terminal dimerisation domain. This entry represents the N-terminal catalytic domain, which consists of an Î±/Î²/Î± sandwich with a canonical NADP-binding Rossmann fold . This type of NADP-binding domain is also found in F420-dependent NADP reductases .
Pfam PF05901: Excalibur calcium-binding domain (domain)
Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognised and the evolution of EF-hand-like domains is probably more complex than previously appreciated.
Pfam PF11331: EDR4 zinc-ribbon domain (domain)
This zinc beta ribbon domain is found in Protein ENHANCED DISEASE RESISTANCE 4 (EDR4) and related plant proteins. EDR4 mainly localizes to the plasma membrane and endosomal compartments. It plays a negative role in resistance to powdery mildew and this requires salicylic acid signaling. In Arabidopsis, EDR4 associates with CLATHRIN HEAVY CHAIN2 (CHC2) and modulates plant immunity by regulating the relocation of EDR1.
Pfam PF20629: D-galactarate/Altronate dehydratase, C-terminal (domain)
This entry represents the C-terminal domain of Galactarate dehydratase (GarD). GarD catalyses the dehydration of galactarate to 5-dehydro-4-deoxy-D-galactarate. In the crystal structure, GarD forms dimers and each monomer consists of three domains: the N-terminal SAF domain ([pfam:PF08666]) connected to the second domain ([pfam:PF04295]) through a long linker and the C-terminal domain which represents the core of the protein. This domain adopts a variant of a Rossmann fold with an unusual crossover, consisting of seven-stranded parallel beta-sheets surrounded by nine alpha-helices. This domain may contain a catalytic metal binding site.
Pfam PF15634: HYE1 signature containing ADP-ribosyltransferase (family)
A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteristic histidine, tyrosine and glutamate residues that comprise the active site.
Pfam PF23216: Mitochondrial protein cyt-4, winged helix (domain)
This entry represents a winged helix domain found in mitochondrial protein CYT4 from Neurospora crassa and related fungal sequences. CYT4 is required for RNA 5'- and 3'-end processing and splicing.
Pfam PF13579: Glycosyl transferase 4-like domain (domain)
MshA belongs to the GT-B structural family of glycosyltransferases whose members have a two-domain structure with both domains exhibiting a Rossman-type fold . This entry represents the N-terminal domain found in MshA and the subfamily 4 of glycosyltransferases family 1.
Pfam PF06449: ATP synthase YMF19, C-terminal (domain)
This domain represents the C-terminal region of YMF19 of the F0 complex of mitochondrial F-ATPases from plants. This family is found in conjunction with [pfam:PF02326].
Pfam PF14778: Odorant response abnormal 4-like (family)
In C.elegans, odr-4 and odr-8 are required for localising a subset of odorant GPCRs to the cilia of olfactory neurons. Olfactory receptors (ORs) are synthesised in endoplasmic reticulum of the olfactory neurons, trafficked to the cell surface membrane and transported to the tip of the olfactory cilium, where they bind with odorants. Various accessory proteins are required for proper targetting of different ORs to the cell membrane. ODR-4 was the first accessory protein to be described.
Pfam PF19539: Family of unknown function (DUF6063) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 237 and 249 amino acids in length. They contain a central predicted transmembrane helix.
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 PF07275: Antirestriction protein (ArdA) (family)
This family consists of several bacterial antirestriction (ArdA) proteins. ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.
Pfam PF07417: Sigma factor-binding transcriptional regulator Crl (domain)
This family contains the bacterial Sigma factor-binding protein Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria. These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. It was initially suggested that Crl affects transcription initiation in vitro by other sigmas, such as sigma-70 and sigma-32. However, it is now established that Crl binds specifically to the alternative sigma factor S/RpoS and favors its association with the core RNAP (RNA polymerase), thereby increasing its activity, which in turn regulates general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. Furthermore, sigma S factor/RpoS plays important roles in biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium.
Pfam PF07862: Nif11 domain (family)
This domain is found mainly in the Cyanobacteria and in Proteobacteria such as the nitrogen-fixing bacterium Azotobacter vinelandii. It is found in Nif11, a protein described in Azotobacter as linked to nitrogen fixation. It also constitutes a leader peptide in Nif11-derived peptides (N11P), which are thought to be post-translationally modified microcins derived from a putative nitrogen-fixing protein. N11P sequences have a classic leader peptide cleavage motif, usually Gly-Gly, which marks the end of family-wide similarity area and the beginning of a low-complexity region rich in Cys, Gly and Ser.
Pfam PF13944: Calycin-like beta-barrel domain (domain)
The lipocalin fold is dominated by eight Î²-strands which together form a cup-shaped antiparallel Î²-barrel that encloses an internal ligand-binding site . This entry represents domains with a fold that is related to the to the lipocalin fold.
Pfam PF20448: Family of unknown function (DUF6705) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 170-200 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 PF22405: Sulfolobus turreted icosahedral virus 1-like, major capsid protein (domain)
This entry represents a jelly-roll domain present in the major capsid protein from Sulfolobus turreted icosahedral virus 1. The structure of this domain is similar to major capsid protein structures of the  eukaryotic Paramecium bursaria Chlorella virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenovirus.
Pfam PF20601: Domain of unknown function (DUF6797) (domain)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, and is around 100 amino acids in length. This domain is found in association with [pfam:PF13442]. There is a conserved sequence motif GPLP.
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 PF22235: Fatty acid synthase subunit beta, insertion domain (domain)
This entry represents the insertion domain in the thioesterase of fatty acid synthases from fungi and related sequences.
Pfam PF03399: SAC3/GANP family (family)
This family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins.  The family includes the yeast nuclear export factor Sac3 [swissprot:P46674], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle.
Pfam PF11632: Lactococcin G-beta (family)
This family of proteins is LcnG-beta, which with LcnG-alpha constitute the two-peptide bacteriocin lactococcin G (LcnG). This family of proteins represents the N terminal domain which has an alpha-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure.
Pfam PF24260: Family of unknown function (DUF7461) (family)
This entry represents a small uncharacterised family of mycobacterial phage proteins. The family includes gene 71 from phage Bxb1 [swissprot:Q9B050]. Structure prediction suggests this protein may form a pair of alpha helices that form a helical hairpin 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 PF05990: Alpha/beta hydrolase of unknown function (DUF900) (family)
This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold.
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 PF08985: DP-EP family (domain)
The DP-EP family of proteins, formerly known as DUF1888 have been shown to catalyse a cleavage of an internal peptide bond.
Pfam PF25045: Ro60 vWA domain (domain)
This entry represents the vWA domain of RNA-binding protein RO60 which is found after the TROVE domain at the N-terminal. This domain closes the ring from by the TROVE domain.
Pfam PF24700: Vein beta-barrel (domain)
This entry includes vein protein form Drosophila, a secreted neuregulin-like EGFR ligand. It may play a role in the global proliferation of wing disc cells and the larval patterning. This entry represents a beta-barrel domain found in vein, which is similar to that found in Tissue inhibitors of metalloproteinases (TIMP).
Pfam PF16483: Beta-1,3-glucanase (domain)
Family 64 glycoside hydrolases have beta-1,3-glucanase activity.
Pfam PF12256: Insecticide toxin TcdB middle/N-terminal region (repeat)
This domain family is found in bacteria and archaea, and is typically between 164 and 180 amino acids in length. The family is found in association with [pfam:PF05593]. This family is the N-terminal-sided middle region of the bacterial insecticide toxin TcdB. This region appears related to the FG-GAP repeat [pfam:PF01839].
Pfam PF24121: Type I-B CRISPR Cas8b N-terminal domain (domain)
This entry represents the N-terminal domain of Type I-B CRISPR Synechocystis Cas8b and related proteins. Type I CRISPR-Cas systems employ multi-subunit effector Cascade and helicase-nuclease Cas3 to target and degrade foreign nucleic acids, representing the most abundant RNA-guided adaptive immune systems in prokaryotes. Cas8b subunit displays very low sequence similarity with the large subunits of any other known type I CRISPR systems. Cas8b N-terminal domain is involved in PAM recognition.
Pfam PF15105: TMEM61 protein family (family)
The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 150 and 211 amino acids in length.
Pfam PF17633: Family of unknown function (DUF5514) (family)
This is a family of unknown function found in Bacillus.
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 PF09742: Dyggve-Melchior-Clausen syndrome protein (family)
Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 residues long and present in plants and animals.  Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterised by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus.
Wikipedia: In molecular biology, the Dymeclin protein family is a family of proteins which includes human Dymeclin. Dymeclin contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteristically about 700 amino acids long and present in plants and animals. In humans, mutations in the gene coding for this protein give rise to a disorder called Dyggve-Melchior-Clausen syndrome, which is an autosomal-recessive disorder characterised by the association of spondylo-epi-metaphyseal dysplasia, postnatal onset microcephaly and intellectual disability.
Pfam PF03015: Male sterility protein (family)
This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila.  A sequence-related jojoba acyl CoA reductase is also included.
Pfam PF00944: Alphavirus core protein (domain)
Also known as coat protein C and capsid protein C. This makes the literature very confusing.  Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane.
Pfam PF19826: Family of unknown function (DUF6307) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide.
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 PF05849: Fibroin light chain (L-fibroin) (family)
This family consists of several moth fibroin light chain (L-fibroin) proteins. Fibroin of the silkworm, Bombyx mori, is secreted into the lumen of posterior silk gland (PSG) from the surrounding PSG cells as a molecular complex consisting of a heavy (H)-chain of approximately 350 kDa, a light (L)-chain of 25 kDa and a P25 of about 27 kDa. The H- and L-chains are disulfide-linked but P25 is associated with the H-L complex by non-covalent force.
Wikipedia: Fibroin is an insoluble protein present in silk produced by numerous insects, such as the larvae of Bombyx mori, and other moth genera such as Antheraea, Cricula, Samia and Gonometa. Silk in its raw state consists of two main proteins, sericin and fibroin, with a glue-like layer of sericin coating two singular filaments of fibroin called brins. Silk fibroin is considered a β-keratin related to proteins that form hair, skin, nails and connective tissues.
Pfam PF18583: Aminoarabinose transferase C-terminal domain (domain)
ArnT is a member of the GT-C family of glycosyltransferases, and it has a similar fold to a bacterial oligosaccharyltransferase (OST) from Campylobacter lari (PglB) and to an archaeal OST from Archaeoglobus fulgidus (AglB). This entry represents the C-terminal periplasmic domain of Arnt proteins.
Pfam PF24972: Attractin GBD-like (domain)
This entry represents a domain found towards the C-terminal of attractin (ATRN) and attractin-like proteins. ATRN is involved in the initial immune cell clustering during inflammatory response and may regulate chemotactic activity of chemokines. It may play a role in melanocortin signaling pathways that regulate energy homeostasis and hair color. It was thought to have dipeptidase activity but it was shown later to lack that activity. This domain may adopt a beta-sandwich fold similar to galactose-binding domains.
Pfam PF00675: Insulinase (Peptidase family M16) (family)
This entry represents an N-terminal domain found in metallopeptidases and non-peptidase homologues belonging to MEROPS peptidase family M16 (clan ME), subfamilies M16A, M16B and M16C. Members of this group of proteins include:


 * Insulinase, insulin-degrading enzyme (3.4.24.56)
 * Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64)
 * Pitrilysin, Protease III precursor (3.4.24.55)
 * Nardilysin (3.4.24.61)
 * Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2)
 * Coenzyme PQQ synthesis protein F (3.4.99)


These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown  that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The proteins classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.
Wikipedia: The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain, playing a critical role in biochemical generation of ATP. Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial and the nuclear genomes. Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most bacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits, 2 core proteins and 6 low-molecular weight proteins.
Pfam PF19839: Ribbon-helix-helix protein (domain)
This entry represents a family of Ribbon-helix-helix proteins.
Pfam PF00861: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (family)
This family includes the large subunit ribosomal proteins from bacteria, archaea, the mitochondria and the chloroplast. It does not include the 60S L18 or L5 proteins from Metazoa.
Pfam PF22670: Baseplate wedge protein gp10 domain 3 (domain)
This domain is found in Baseplate wedge protein gp10 and related proteins. This domain folds into a beta-sandwich.
Pfam PF11854: Putative outer membrane beta-barrel porin, MtrB/PioB (family)
MtrB-PioB is a family of bacterial putative outer membrane porins. This family, is secreted as part of the pio (phototrophic iron oxidation) operon that has been found to couple the oxidation of ferrous iron [Fe(II)] to reductive CO2 fixation using light energy. PioABC is found in Rhodopseudomonas palustris and MtrB-PioB is likely to be a beta-barrel porin. Similar to other outer membrane porins, PioB and MtrB are predicted to have long loops protruding into the extracellular space and short turns on the periplasmic side.