SII-SWORD/CoKE huggingface dataset:
Pfam PF20471: Putative glycosyltransferase (DUF6716) (family)
This entry represents a group of uncharacterised proteins that belong to the GT- superfamily of glycosyltransferases.
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 PF17977: RING/Ubox like zinc-binding domain (domain)
This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes.
Wikipedia: In molecular biology, a RING (short for Really Interesting New Gene) finger domain is a protein structural domain of zinc finger type which contains a C3HC4 amino acid motif which binds two zinc cations (seven cysteines and one histidine arranged non-consecutively). This protein domain contains 40 to 60 amino acids. Many proteins containing a RING finger play a key role in the ubiquitination pathway. Conversely, proteins with RING finger domains are the largest type of ubiquitin ligases in the human genome.
Pfam PF20746: Endo-beta-N-acetylglucosaminidase F2, Ig-like domain (domain)
This domain is found in Endo-beta-N-acetylglucosaminidase F2 (EndoS) from Streptococcus pyogenes ([swissprot:Q48RM3]) and similar sequences predominantly found in Firmicutes. EndoS is an immunomodulatory enzyme secreted by the bacteria to remove carbohydrates from IgG antibodies in a highly specific manner, which gives the pathogen a survival advantage over its host. This protein is composed of five distinct protein domains. The domain located at the base of the V-shaped EndoS structure (this entry), also named hybrid Ig domain, is composed of two subdomains. The smaller one is inserted within the loop that connects the LRR domain to the second and third beta strands of the larger subdomain. The latter is a typical Ig domain structurally similar to the interleukin-4 receptor.
Pfam PF06646: Extracytoplasmic thiamine-binding lipoprotein (family)
Thiamine-binding lipoprotein (Cypl) and related proteins are specific to Mycoplasma species. Cypl, also known as p37, whose gene is part of an operon encoding two additional proteins, which are highly similar to components of the periplasmic binding-protein-dependent transport systems of Gram-negative bacteria. It has been suggested that p37 is part of a homologous, high-affinity transport system in Mycoplasma hyorhinis, a Gram-positive bacterium. Its structure indicates that it is a thiamine pyrophosphate-binding protein. The monomer is a mixed alpha/beta fold split into two globular domains (domains I and II) connected by two linker regions and the C-terminal helix.
Pfam PF10350: THADA/TRM732, DUF2428 (repeat)
This conserved domain is found in Thyroid adenoma-associated proteins (THADA) and the yeast homologue, TRM732. Trm732 forms a complex with the methyltransferase Trm7 to 2'- O-methylate tRNA residue 32 (Nm32), being required for Trm7 methylation activity. In humans, mutations of the Trm7 homologue FTSJ1, which interacts with THADA, impair Nm32 modifications, associated with non-syndromic X-linked intellectual disability. It has been suggested that these proteins may play a role in additional biological processes not related to translation. This domain contains a RRSAGLP conserved motif that is required for tRNA modification activity (Funk HM et.al., Preprint from bioRxiv, 03 Jun 2021 DOI: 10.1101/2021.06.03.446962).
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 PF10945: Cellulose biosynthesis protein BcsR-like (family)
Cellulose is necessary for biofilm formation in bacteria and is synthesized by the bacterial cellulose biosynthesis complex (Bcs) which is widespread among beta and gamma proteobacteria. CBP_BcsR is a small subunit of this complex, essential for cellulose secretion. It may play a regulatory role together with BcsQ subunit as they form a subcomplex with chaperone-like function toward each other. BcsR stabilizes BcsQ to form monodisperse BcsR2Q2 heterotetramers in solution and BcsQ may play a role in the folding and subsequent stability of BcsR.
Pfam PF24202: Family of unknown function (DUF7427) (family)
This entry represents a family of uncharacterised phage proteins. Family members are largely found in mycobacterial phage.
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 PF08491: Squalene epoxidase (family)
This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria.                    SE was first cloned from Saccharomyces cerevisiae where it was named ERG1. It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway.  Putative transmembrane regions are found to the protein's C-terminus.
Pfam PF16991: Sir4 SID domain (domain)
This is the Sir2 interaction domain (SID domain) of silent information regulator 4 (Sir4).
Pfam PF16163: Domain of unknown function (DUF4869) (family)
This family consists of uncharacterized proteins around 150 residues in length. Its members are found in human gut Firmicutes and are also abundant in human gut metagenomics datasets.  The function of this family is unknown.
Pfam PF04064: Domain of unknown function (DUF384) (family)
This entry represents a domain within Protein HGH1, of unknown function. It is found C-terminal to another domain of unknown function (IPR007205).
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 PF10158: Tumour suppressor protein (family)
This is a region of 130 amino acids that is the most conserved region of hypothetical proteins involved in loss of heterozygosity and thus tumour suppression. The exact function of family members is not known. This region is also found in subunit 5 of the BLOC-1-related complex, which is also found in the BORC complex. BLOC-1 is important for the biogenesis of lysosome-related organelles, and BORC is important for the positioning of the lysosome in the cytoplasm. The BORC complex associates with the lysosomal membrane where it recruits the small GTPase Arl8, which leads in turn to the kinesin-dependent movement of lysosomes toward the plus ends of microtubules in the peripheral cytoplasm.
Pfam PF08730: Rad33 (family)
Rad33 is involved in nucleotide excision repair (NER).  NER is the main pathway for repairing DNA lesions induced by UV. Cells deleted for RAD33 display intermediate UV sensitivity that is epistatic with NER.
Pfam PF02463: RecF/RecN/SMC N terminal domain (domain)
This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics.                 This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.
Pfam PF01437: Plexin repeat (family)
A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin ([swissprot:P70206]). Two copies of the repeat are found in mahogany protein.  A related C. elegans protein ([swissprot:Q19981]) contains four copies of the repeat.  The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).
Pfam PF13045: Protein of unknown function (DUF3905) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Pfam PF22257: GPR128, N-terminal domain (domain)
GRP128, also known as Adhesion G-protein coupled receptor G7 (AGRG7), is an orphan receptor of the adhesion family (subclass B2) that belongs to class B GPCRs. Expression of GPR128 was detected in the mouse intestinal mucosa and is thought to be involved in energy balance. This entry represents the N-terminal domain of GPR128, which, according to structure prediction and comparison using Foldseek, it adopts a fold similar to the hormone receptor domain (HormR, [pfam:PF02793]) which is usually found preceding the stalk region of the GAIN domain in cell-adhesion GPCRs.
Pfam PF08644: FACT complex subunit (SPT16/CDC68) (domain)
Proteins in this family are subunits the FACT complex.  The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin.
Pfam PF16047: Frog antimicrobial peptide (family)
This family includes the antimicrobial peptides Grahamin and Nigrocin which are secreted from frog skin.
Pfam PF02825: WWE domain (domain)
The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems.
Pfam PF00020: TNFR/NGFR cysteine-rich region (domain)
A number of proteins, some of which are known to be receptors for growth factors, have been found to contain a cysteine-rich domain of about 110 to 160 amino acids in their N-terminal part, that can be subdivided into four (or in some cases, three) modules of about 40 residues containing 6 conserved cysteines. Some of the proteins containing this domain are listed below :


 * Tumor Necrosis Factor type I and type II receptors (TNFR). Both receptors bind TNF-alpha and TNF-beta, but are only similar in the cysteine-rich region. TNFR contains four cysteine-rich domain modules (CRDs), termed CRD1 through CRD4. CRD2 and CRD3 are known as TNF-binding domains .
 * Shope fibroma virus soluble TNF receptor (protein T2)
 * Lymphotoxin alpha/beta receptor
 * Low-affinity nerve growth factor receptor (LA-NGFR) (p75)
 * CD40 (Bp50), the receptor for the CD40L (or TRAP) cytokine
 * CD27, the receptor for the CD27L cytokine
 * CD30, the receptor for the CD30L cytokine
 * T-cell protein 4-1BB, the receptor for the 4-1BBL putative cytokine
 * FAS antigen (or APO-1), the receptor for FASL, a protein involved in apoptosis (programmed cell death)
 * T-cell antigen OX40, the receptor for the OX40L cytokine
 * Wsl-1, a receptor (for a yet undefined ligand) that mediates apoptosis
 * Vaccinia virus protein A53 (SalF19R)


It has been shown  that the six cysteines all involved in intrachain disulphide bonds. A schematic representation of the structure of the 40 residue module of these receptors is shown below:

                  +-------------+    +--------------+
                  |             |    |              |
                 xCxxxxxxxxxxxxxCxCxxCxxxxxxxxxCxxxxCxx
                                  |            |
                                  +------------+

'C': conserved cysteine involved in a disulphide bond.
Wikipedia: The tumor necrosis factor receptor superfamily (TNFRSF) is a protein superfamily of cytokine receptors characterized by the ability to bind tumor necrosis factors (TNFs) via an extracellular cysteine-rich domain. With the exception of nerve growth factor (NGF), all TNFs are homologous to the archetypal TNF-alpha. In their active form, the majority of TNF receptors form trimeric complexes in the plasma membrane. Accordingly, most TNF receptors contain transmembrane domains (TMDs), although some can be cleaved into soluble forms, and some lack a TMD entirely. In addition, most TNF receptors require specific adaptor protein such as TRADD, TRAF, RIP and FADD for downstream signalling. TNF receptors are primarily involved in apoptosis and inflammation, but they can also take part in other signal transduction pathways, such as proliferation, survival, and differentiation. TNF receptors are expressed in a wide variety of tissues in mammals, especially in leukocytes.
Pfam PF04716: ETC complex I subunit conserved region (family)
Family of eukaryotic NADH-ubiquinone oxidoreductase subunits ([ec:1.6.5.3]) ([ec:1.6.99.3]) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N-terminus of the member proteins.
Pfam PF12099: Protein of unknown function (DUF3575) (family)
This family of proteins are functionally uncharacterised. This family is only found in bacteria.  Proteins in this family are typically between 187 to 236 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 PF16655: PhoD-like phosphatase, N-terminal domain (domain)
This domain is found at the N-terminus of proteins in the PhoD family [pfam:PF09423].
Pfam PF06833: Malonate decarboxylase gamma subunit (family)
This family consists of several bacterial malonate decarboxylase gamma subunit proteins. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyses the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcD and E together probably function as malonyl-S-ACP decarboxylase.
Pfam PF20043: Family of unknown function (DUF6445) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 229 and 242 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 PF01722: BolA-like protein (family)
This family consist of the morphoprotein BolA from E. coli and its various homologues. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during  cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of  growth and may have a general role in stress response.  It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5.
Wikipedia: In molecular biology, the BolA-like protein family consists of the morpho-protein BolA from Escherichia coli, the Fra2 protein from Saccharomyces cerevisiae, and various homologs. The BolA protein is a DNA-binding regulator; the Fra2 protein is an iron sulfur cluster protein that binds Grx3/4 and is involved in regulating iron levels
.
Pfam PF13636: RNA-binding PUA-like domain of methyltransferase RsmF (family)
Methyltranf_PUA is the second of two C-terminal domains found on bacterial methyltransferase RsmF that modifies the 16S ribosomal RNA. It has some structural similarity to the RNA-binding PUA domains suggesting that it is involved in RNA recognition. It lies downstream of the catalytic centre of this methyltransferase, family [pfam:PF01189].
Pfam PF13252: Protein of unknown function (DUF4043) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 369 and 424 amino acids in length. There is a single completely conserved residue G that may be functionally important.
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 PF22087: CT0912-like, C-terminal domain (domain)
This domain is found at the C-terminal end of [swissprot:Q8KDY2] from Chlorobaculum tepidum (CT0912), a functionally uncharacterised protein with a ferredoxin-like domain repeat. This domain shows an alpha-beta configuration.
Pfam PF12964: Protein of unknown function (DUF3853) (family)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences.
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 PF15275: PEHE domain (family)
This domain was first identified in drosophila MSL1 (male-specific lethal 1). In drosophila it binds to the histone acetyltransferase males-absent on the first protein (MOF) and to protein male-specific lethal-3 (MSL3).
Pfam PF23578: Diacylglycerol kinase iota-like domain (domain)
This domain is found in human Diacylglycerol kinase iota (DGKI), which converts diacylglycerol/DAG into phosphatidic acid /phosphatidate/PA and regulates the respective levels of these two bioactive lipids. It is found C-terminal to [pfam:PF00781] and [pfam:PF00781].
Pfam PF22592: FCaBP EF-hand domain (domain)
This entry represents a EF-hand domain found in homologues of flagellar calcium-binding protein (FCaBP). This protein contains two EF-hand domains, the first of which is represented by this entry. FCaBP is targeted to the flagella where it regulates flagellar function and assembly.
Pfam PF14724: Mitochondrial-associated sphingomyelin phosphodiesterase (family)
The GO annotation for this family indicates that it is a single-pass membrane protein, and it appears to be found in mitochondrial membranes. Sphingolipids play important roles in regulating cellular responses, and although mitochondria contain sphingolipids, direct regulation of their levels in mitochondria or mitochondria-associated membranes is mostly unclear. Sphingomyelin phosphodiesterases catalyse the hydrolysis of sphingomyelin to ceramide and phosphocholine, and these metabolites are involved in signalling pathways.
Pfam PF02965: Vitamin B12 dependent methionine synthase, activation domain (domain)
Vitamin B12 dependent methionine synthase 2.1.1.13 (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step inde novomethionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin.

In Escherichia coli, methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate, the third module binds the B12 cofactor (IPR003759, IPR006158), and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain . The activation domain adopts an unusual Î±/Î² fold.
Pfam PF18555: MobL relaxases (family)
This family includes members of relaxase enzymes. These enzymes initiate bacterial conjugation contributing to the spread of antibiotic resistance.  These MobL relaxases are found mainly in Firmicutes. It is suggested that MobL type relaxases play a prominent role in horizontal gene transfer in Firmicutes bacteria. Family members carry a stretch of relaxase motif III 'HUH' sequence that is characteristic of the HUH endonuclease superfamily essential for enzymatic activity.
Pfam PF09629: YorP protein (domain)
YorP is a 71 residue protein found in bacteria. As it is also found in a bacteriophage it might be of viral origin. The structure is of an alpha helix between two of five beta strands. The function is unknown.
Pfam PF06306: Beta-1,4-N-acetylgalactosaminyltransferase (CgtA) (family)
This family consists of several beta-1,4-N-acetylgalactosaminyltransferase proteins from Campylobacter jejuni.
Pfam PF01804: Penicillin amidase (family)
Penicillin amidase or penicillin acylase [ec:3.5.1.11] catalyses the hydrolysis of benzylpenicillin to phenylacetic acid and 6-aminopenicillanic acid (6-APA) a key intermediate in the the synthesis of penicillins. Also in the family is cephalosporin acylase [swissprot:P07662] and  [swissprot:P29958] aculeacin A acylase which are involved in the synthesis of related peptide antibiotics.