SII-SWORD/CoKE huggingface dataset:
Pfam PF11219: Protein of unknown function (DUF3014) (family)
This family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF18160: SMODS and SLOG-associating 2TM effector domain family 5 (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 contains an additional C-terminal alpha-helix, and strictly associates with a reverse transcriptase domain, part of a predicted retroelement with diversity-generating potential.
Pfam PF01757: Acyltransferase domain (domain)
This family includes a range of acyltransferase enzymes. This domain is found in a wide range of acyltransferase enzymes, including, mainly, bacterial proteins which catalyse the transfer of acyl groups, other than amino-acyl, from one compound to another, such as Glucans biosynthesis protein C (OPGC) or protein OatA from Listeria monocytogenes serovar 1/2a and Staphylococcus aureus, an integral membrane protein which is responsible for O-acetylation at the C6-hydroxyl group of N-acetylmuramyl residues, forming the corresponding N,6-O-diacetylmuramic acid of the peptidoglycan, a modification that determines lysozyme resistance. This domain is also present in eukaryotic proteins, namely O-acyltransferase like protein (OACYL) from mouse and RHY1 (Regulator of hypoxia-inducible factor 1) and NRF6 (Nose resistant to fluoxetine protein 6) from Caenorhabditis elegans.
Pfam PF09234: Domain of unknown function (DUF1963) (domain)
This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been described.
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 PF18709: Dynamin-like helical domain (domain)
This helical domain is found in bacterial proteins such as labile enterotoxin output A (LeoA), a large GTPase (64.2 kDa) with a putative involvement in membrane vesicle (MV) secretion in Escherichia coli. The crystal structure of LeoA reveals a fold with all the hallmarks of a dynamin-like protein (DLP).
Pfam PF19218: Coronavirus replicase NSP3, C-terminal (family)
This family represents the C-terminal region of non-structural protein NSP3 (also known as nsp3). NSP3 is the product of ORF1a. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins. It is a multifunctional protein comprising up to 16 different domains and regions. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins and participates in polyprotein processing.
Pfam PF10984: Protein of unknown function (DUF2794) (family)
This is a bacterial family of proteins with 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 PF04265: Thiamin pyrophosphokinase, vitamin B1 binding domain (domain)
Family of thiamin pyrophosphokinase ([ec:2.7.6.2]). Thiamin pyrophosphokinase (TPK) catalyses the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Pfam PF20885: Nuclear pore complex-interacting protein B13-like, MII repeat (repeat)
This entry represents the MII repeat found in Nuclear pore complex-interacting protein family member B13 (NPB13), NPB12, NPB11, NPB3, NPB4 and NPB5. These repeats may arrange in a beta-solenoid structure. Members of this entry have the repeated sequence MIISRHLPSV.
Pfam PF14277: Domain of unknown function (DUF4364) (family)
This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 180 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 PF07632: Cellulose-binding Sde182, nucleoside hydrolase-like domain (domain)
This Rossmann-related domain is found at the N-terminal end of the C-terminal domain region of the cellulose-binding protein Sde182 from Saccharophagus degradans ([swissprot:Q21PD3]), which seems to have capacity to bind plant carbohydrates. This domain shows an alpha/beta configuration with a central beta-sheet of eight beta-strands and 12 alpha-helices. It is structurally similar to pyrimidine-specific ribonucleoside hydrolases (NH). This domain is also found in other uncharacterised bacterial and fungal proteins.
Pfam PF20004: FtsH ternary system domain X6 (domain)
Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF20295: ABC-three component (ABC-3C) system Middle Component 8 (family)
Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC8 is a MC unifiable with the HTH fold.
Pfam PF01341: Glycosyl hydrolases family 6 (domain)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
The 1,4-beta cellobiohydrolase family plays a central role in the recycling of plant biomass. The biological conversion of cellulose to glucose generally requires three types of hydrolytic enzymes: Endoglucanases, which cut internal beta-1,4-glucosidic bonds; exocellobiohydrolases that cut the dissaccharide cellobiose from the non-reducing end of the cellulose polymer chain; and beta-1,4-glucosidases, which hydrolyze the cellobiose and other short cello-oligosaccharides to glucose.
Wikipedia: In molecular biology, glycoside hydrolase family 6 is a family of glycoside hydrolases EC 3.2.1., which are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of &gt;100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Pfam PF10969: Protein of unknown function (DUF2771) (family)
This bacterial family of proteins has no known 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 PF24109: Family of unknown function (DUF7384) (family)
This is a group of uncharacterised sequences from archaea which are related to VapC (virulence-associated protein C) family of proteins. Members of this entry may adopt a PIN-like 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 PF11766: Agglutinin-like protein, N-terminal domain (domain)
This entry represents the N-terminal domain of yeast alpha-agglutinin and agglutinin-like (ALS) proteins. The ALS glycoproteins have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. The N-terminal domains of Candida albicans ALS3 and ALS9 were shown to be involved in peptide binding. The ligand recognition of these domains relies on a motif capable of binding the flexible C terminus of peptides in extended conformation. In baker's yeast alpha-agglutinin, this domain was implicated in high affinity binding to a-agglutinin that mediates cell-cell contact during mating.
Pfam PF21075: Glutamate dehydrogenase, ACT1 domain (domain)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation. This is the first ACT-like domain (ACT1) found at the N-terminal of GDH. The ACT domains of these proteins differ from the archetypal ACT fold in that strand strand beta1 is located in the position usually occupied by strand beta4 creating an ACT-like topology with a beta1-4 antiparallel sheet.
Pfam PF15122: TMEM206 protein family (family)
The function of this family of transmembrane proteins, TMEM206, has not, as yet, been determined. Members of this family are remain uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are approximately 350 amino acids in length.
Pfam PF04407: Protein of unknown function (DUF531) (family)
Family of hypothetical archaeal 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 PF14845: beta-acetyl hexosaminidase like (domain)
This entry represents the N-terminal domain of the eukaryotic beta-hexosaminidases. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor.
Pfam PF04534: Herpesvirus UL56 protein (family)
In herpes simplex virus type 2, UL56 is thought to be a tail-anchored type II membrane protein involved in vesicular trafficking.  The C terminal hydrophobic region is required for association with the cytoplasmic membrane, and the N terminal proline-rich region is important for the translocation of UL56 to the Golgi apparatus and cytoplasmic vesicles.
Pfam PF06268: Fascin domain (domain)
This family consists of several eukaryotic fascin or singed proteins.  The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles. The cortical structures, which include filopodia, spikes, lamellipodial ribs, oocyte microvilli and the dendrites of dendritic cells, have roles in cell-matrix adhesion, cell interactions and cell migration, whereas the cytoplasmic actin bundles appear to participate in cell architecture.                 Dictyostelium hisactophilin, another actin-binding protein, is a submembranous pH sensor that signals slight changes of the H+ concentration to actin by inducing actin polymerisation and binding to microfilaments only at pH values below seven.  Members of this family are histidine rich, typically contain the repeated motif of HHXH.
Pfam PF09346: SMI1 / KNR4 family (SUKH-1) (domain)
Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems.
Pfam PF01347: Lipoprotein amino terminal region (repeat)
This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100.  These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.
Wikipedia: Vitellogenin is a precursor of egg yolk that transports protein and some lipid from the liver through the blood to the growing oocytes where it becomes part of the yolk. Normally, it is only found in the blood or hemolymph of females, and can therefore be used as a biomarker in vertebrates of exposure to environmental estrogens which stimulate elevated levels in males as well as females. "Vitellogenin" is a synonymous term for the gene and the expressed protein. The protein product is classified as a glycolipoprotein, having properties of a sugar, fat and protein. It belongs to a family of several lipid transport proteins.
Pfam PF03789: ELK domain (family)
This domain is required for the nuclear localisation of these proteins.  All of these proteins are members of the Tale/Knox homeodomain family, a subfamily within homeobox [pfam:PF00046].
Pfam PF02288: Dehydratase medium subunit (domain)
This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.
Pfam PF15961: Domain of unknown function (DUF4764) (family)
This domain is found in eukaryotes. Its function is not 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 PF05743: UEV domain (domain)
This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer. This family is related to the ubiquitin conjugating enzymes.
Pfam PF21315: FAN1, HTH domain (domain)
FAN1 is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). It maintains genomic stability and prevents tissue decline in several organs. This protein possesses preferential endonuclease activity toward 5' flap structures. FAN1 is present in most eukaryotes and some bacterial sequences. It consists of four characterised domains: UBZ, SAP, TPR and VRR nuclease ([pfam:PF08774]). However, monocellular eukaryote and bacterial homologues lack the UBZ domain. The N-terminal helical domain of FAN1 can be subdivided in a winged-helix (WH) DNA-binding domain, represented in this entry, and a SAP domain (bacterial [pfam:PF18081] and eukaryotic [pfam:PF21169]).
Pfam PF04198: Putative sugar-binding domain (domain)
This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix [pfam:PF00325] that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates.
Pfam PF18038: FERM N-terminal domain (domain)
This entry represents the FERM N-terminal domain found in focal adhesion kinases.
Pfam PF03527: RHS protein (repeat)
RHS (Rearrangement hotspot) proteins are distantly related to the wall-associated protein A (WapA) and mediate intercellular competition. The protein sequences comprise highly conserved 141kDa domain containing multiple tandem 22-residue repeats, the YD-peptide repeats that define this protein family. Rhs/YD-repeat proteins are widely distributed suggesting that they play a fundamental role in biology. Rhs C-terminal regions (Rhs-CT) are highly divergent . Rhs-CT regions share sequence identity with toxic effector domains of contact-dependent growth inhibition (CDI) systems, which shows that these proteins inhibit the growth of neighboring cells in a contact-dependent manner .
Pfam PF09007: EBP50, C-terminal (domain)
This C terminal domain allows interaction of EBP50 with FERM (four-point one ERM) domains, resulting in the activation of Ezrin-radixin-moesin (ERM), with subsequent cytoskeletal modulation and cellular growth control. It includes a disordered section between two reasonably well conserved hydrophobic regions.
Pfam PF21557: Alpha-L-rhamnosidase, domain D2 (domain)
This domain is found in Alpha-L-rhamnosidase from Bacillus sp. (RhaB), a member of glycoside hydrolase (GH) family 78 that catalyses the hydrolytic release of rhamnose from polysaccharides and glycosides, degrading the bacterial biofilm gellan. RhaB is organised into five domains: [pfam:PF08531], this entry, [pfam:PF05592], [pfam:PF17389] and [pfam:PF17390]. This domain shows a beta-sandwich structure with 13 beta-strands and two short helices.
Pfam PF03063: Prismane/CO dehydrogenase family (family)
This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster.  The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested. The prismane protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe.  The CO dehydrogenase contains a Ni-3Fe-2S-3O centre.
Pfam PF14331: IcmF-related N-terminal domain (family)
This domain is found in bacterial IcmF (intracellular multiplication and human macrophage-killing) proteins. It is found to the N-terminus of the IcmF-related domain, [pfam:PF06761].
Pfam PF03564: Protein of unknown function (DUF1759) (family)
This is a family of proteins of unknown function. Most of the members are gag-polyproteins.
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 PF06687: SUR7/PalI family (family)
This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homologue of human endophilin, suggesting a function for both in endocytosis. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane.  Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localise with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation. This family also includes PalI which is part of a pH signal transduction cascade.  Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH.
Pfam PF09678: Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) (family)
Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis.
Pfam PF20213: Family of unknown function (DUF6573) (family)
This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Proteobacteria. Proteins in this family are approximately 130 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 PF00381: PTS HPr component phosphorylation site (domain)
This entry represents a structural domain found in both the histidine-containing phosphocarrier protein HPr, as well as its structural homologues, which includes the catabolite repression protein Crh found in Bacillus subtilis . This domain has a Î±+Î² structure found in two layers with an overall architecture of an open faced Î²-sandwich in which a Î²-sheet is packed against three Î±-helices.
Wikipedia: Histidine-containing phosphocarrier protein (HPr) is a small cytoplasmic protein that is a component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS).