SII-SWORD/CoKE huggingface dataset:
Pfam PF06912: Protein of unknown function (DUF1275) (family)
This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although most members have 6 TM regions, and may be putative permeases.
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 PF20982: CSS_CxxC domain (domain)
This is a periplasmic sensor domain found at the N-terminal of c-di-GMP phosphodiesterases, which is a variation of the CSS motif sensor [pfam:PF12792]. This domain, apart of the CSS motif, has an additional conserved CxxC motif, which presumably broaden its redox-sensing palette. It has been found in Shewanella spp. and other members of Altermonadales, Vibrionales and in some acidobacteria.
Pfam PF16150: Domain of unknown function (DUF4858) (family)
This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF17000: Accessory secretory protein Sec, Asp5 (family)
Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp5 is found in Firmicutes.
Pfam PF24841: Domain of unknown function (DUF7719) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to fold into three transmembrane helices.
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 PF03256: Anaphase-promoting complex, subunit 10 (APC10) (family)
The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis, such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome .
One of the subunits of the APC that is required for ubiquitination activity is APC10, a one-domain protein homologous to a sequence element, termed the DOC domain, found in several hypothetical proteins that may also mediate ubiquitination reactions, because they contain combinations of either RING finger (see [prositedoc:PDOC00449]), cullin (see [prositedoc:PDOC00967]) or HECT (see [prositedoc:PDOC50237]) domains .

The DOC domain consists of a Î²-sandwich, in which a five-stranded antiparallel Î²-sheet is packed on top of a three stranded antiparallel Î²-sheet, exhibiting a 'jellyroll' fold .

Proteins known to contain a DOC domain include:


 * Eucaryotic Doc1/Apc10.
 * Mammalian protein associated with the transcription factor Myc (PAM).
 * Mouse runty-jerky-sterile (RJS) protein.
 * Human HERC2, the ortholog of RJS.
Pfam PF05187: Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S (family)
Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer.
Pfam PF18401: Thioredoxin-like domain (domain)
This is the second out of four TRXL(thioredoxin-like) domains found in UDP-glucose:glycoprotein glucosyltransferase (UGGT).
Wikipedia: Thioredoxins are small disulfide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulfide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol.
Pfam PF17733: Family of unknown function (DUF5572) (domain)
This domain is found in Peroxisomal membrane protein PEX14 from Arabidopsis thaliana and other eukaryotic proteins. PEX14 is a component of the PEX13-PEX14 docking complex, a translocon channel that specifically mediates the import of peroxisomal cargo proteins bound to PEX5 receptor. This domain carry a highly conserved KPWE sequence at the C-terminal.
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 PF05708: Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family (family)
Amidase_YiiX is a family of permuted papain-like amidases. It has amidase specificity for the amide bond between a lipid and an amino acid (or peptide). From the structure, a tetramer, each monomer is made up of a layered alpha-beta fold with a central, 6-stranded, antiparallel beta-sheet that is protected by helices on either side. The catalytic Cys154 in UniProtKB:Q74NK7, PDB:3kw0, is located on the N-terminus of helix alphaF. The two additional helices located above Cys154 contribute to the formation of the active site, where the lysine ligand is bound.
Pfam PF05538: Campylobacter major outer membrane protein (family)
This family consists of Campylobacter major outer membrane proteins. The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni, may play an important role in the adaptation of the organism to various host environments.
Pfam PF15671: Proline-rich protein family 18 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 297 amino acids in length. The function is not known but there are many highly conserved proline residues.
Pfam PF11519: Protein of unknown function (DUF3222) (family)
This family of proteins with unknown function appears to be restricted to Rhodopseudomonas.
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 PF19731: Family of unknown function (DUF6222) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp..
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 PF13662: Toprim domain (domain)
The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.
Pfam PF12632: Mysoin-binding motif of peroxisomes (family)
Vezatin is a peroxisome transmembrane receptor that is involved in membrane-membrane and cell-cell adhesions. In the movement of peroxisomes it binds to class V and class VIIa myosins to guide the organelle through the microtubules and allow pathogens to internalise themselves into host cells. Vezatin is crucial for spermatozoan production. In mouse cells it interacts with the cadherin-catenin complex bridging it to the C-terminal FERM domain of myosin VIIA.
Pfam PF04537: Herpesvirus UL55 protein (family)
In infected cells, UL55 is associated with the nuclear matrix, and found adjacent to compartments containing the capsid protein ICP35.  UL55 was not detected in assembled virions. It is thought that UL55 may play a role in virion assembly or maturation.
Pfam PF24157: Domain of unknown function (DUF7408) (domain)
This is a domain of unknown function found in a group of uncharacterised sequences from archaea. It may adopt an amidotransferase-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 PF00487: Fatty acid desaturase (domain)
Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase and Cyanobacterial DesA. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme.
Wikipedia: Fatty acid desaturases are a family of enzymes that convert saturated fatty acids into unsaturated fatty acids and polyunsaturated fatty acids. For the common fatty acids of the C18 variety, desaturases convert stearic acid into oleic acid. Other desaturases convert oleic acid into linoleic acid, which is the precursor to alpha-linolenic acid, gamma-linolenic acid, and eicosatrienoic acid.
Pfam PF21273: Sortin nexin 17/27/31, FERM domain, F1 lobe (domain)
Sortin nexin 17/27/31 are known as PX-FERM proteins, a sub-group of the PX superfamily that contain a defining PtdInsP-binding PX domain, and a C-terminal 4.1, ezrin, radixin, moesin (FERM) domain. They are modular peripheral membrane proteins that act as central scaffolds mediating protein-lipid interactions, cargo binding, and regulatory protein recruitment. The FERM domain comprises three lobes termed F1, F2, and F3: F1 adopts a ubiquitin-like fold, F2 is a helical structure similar to acyl-CoA binding protein ([pfam:PF21271]), and F3 is similar to the phosphotyrosine binding (PTB)/pleckstrin homology domain and referred to as atypical FERM domain ([pfam:PF18116]). This entry represents the F1 lobe that folds as a prototypical ubiquitin/Ras association (RA) domain.
Pfam PF18828: Large polyvalent-protein-associated domain 15 (domain)
This is a predicted enzymatic alpha and beta domain. It is found at the N-terminus of polyvalent proteins of conjugative elements.
Pfam PF16054: Transmembrane protein family 72 (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 275 amino acids in length.
Pfam PF16145: Domain of unknown function (DUF4853) (family)
This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Actinomyces species. The function of this family is unknown.
Pfam PF04046: PSP (family)
Proline rich domain found in numerous spliceosome associated proteins.
Pfam PF22645: Glucokinase regulatory protein N-terminal SIS domain (domain)
This domain is found N-terminal in glucokinase regulatory protein (GKRP) and related proteins. GKRP regulates glucokinase and it is activated by fructose 6-phosphate and inactivated by fructose 1-phosphate. It consists of two topologically identical SIS domains and and alpha-helical lid domain.
Pfam PF19767: Family of unknown function (DUF6254) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 39 and 59 amino acids in length. This family contains a highly conserved sequence HGKV/IKS/T.
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 PF19007: Domain of unknown function (DUF5736) (repeat)
A highly conserved domain of unknown function found in various Platyhelminthes. This domain adopts a 6-bladed beta propeller 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 PF05005: Janus/Ocnus family (Ocnus) (family)
This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster.
Pfam PF24124: YphA-like integral membrane protein (domain)
This entry represents a family of proteins related to B. subtilis YphA protein. These proteins are predicted as integral membrane proteins and are structurally related to [pfam:PF07758].
Pfam PF05861: Bacterial phosphonate metabolism protein (PhnI) (family)
This family consists of several Proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex.
Pfam PF22971: VEGFR-1-like, immunoglobulin-like domain (domain)
This is the fifth immunoglobulin-like domain of human Vascular endothelial growth factor receptor 1 (VEGFR-1) and similar sequences mainly found in animals. VEGFR-1 is a tyrosine-protein kinase that plays an essential role in the development of embryonic vasculature, the regulation of angiogenesis, cell survival, cell migration, macrophage function, chemotaxis, and cancer cell invasion.
Pfam PF02429: Peridinin-chlorophyll A binding protein (domain)
Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. These proteins are composed of two similar repeated domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules.
Wikipedia: The peridinin-chlorophyll-protein complex is a soluble molecular complex consisting of the peridinin-chlorophyll a-protein bound to peridinin, chlorophyll, and lipids. The peridinin molecules absorb light in the blue-green wavelengths and transfer energy to the chlorophyll molecules with extremely high efficiency. PCP complexes are found in many photosynthetic dinoflagellates, in which they may be the primary light-harvesting complexes.
Pfam PF04616: Glycosyl hydrolases family 43 (repeat)
The glycosyl hydrolase family 43 contains members that are arabinanases. Arabinanases hydrolyse the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans.  The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.
Wikipedia: In molecular biology, glycoside hydrolase family 43 is a family of glycoside hydrolases.
Pfam PF24069: Family of unknown function (DUF7364) (family)
This entry represents a small uncharacterised family of Pseudomonas phage proteins. Structure prediction suggests that these proteins adopt a pair of alpha helices. These proteins are predicted to dimerise to form a four helical bundle. In the predicted dimer there is a short C-terminal beta strand that forms an anti parallel cap at one end of the helical bundle.
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 PF14061: Polycomb-like MTF2 factor 2 (domain)
Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics.
Pfam PF23386: NPP-6, helical domain (domain)
This entry represents the helical domain present in NPP-6 found in Caenorhabditis elegans. These proteins are components of the Nuclear Pore Complex (NPC). NPP-6 and NUP133 are part of the cytoplasmic and nucleoplasmic rings, while NUP155 is part of the inner ring. The NPC plays a role in the export of mRNA from the nucleus and the import of transcription factors and other proteins.
Pfam PF14728: PTHB1 GAE domain (domain)
This entry represents the gamma-adaptin ear (GAE) domain of PTHB1 protein (also known as Bardet-Biedl syndrome 9 protein, BBS9). This protein forms a part of the BBSome complex, which is required for ciliogenesis. PTHB1 is the major binding subunit of IFT38 C-terminal domain, which assists the BBSome in some of its roles.
Pfam PF25107: VWA7 N-terminal domain (domain)
This domain is found N-terminal in the human von Willebrand factor A domain-containing protein 7 and related proteins. VWA7 is found in the major histocompatibility complex class III region and may be implicated in susceptibility to lung tumors. This domain is usually followed by [pfam:PF25106].
Pfam PF13893: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) (domain)
The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins.
Pfam PF06707: Protein of unknown function (DUF1194) (family)
This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. 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 PF01895: PhoU domain (domain)
This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif.
Pfam PF10062: Predicted secreted protein (DUF2300) (family)
This domain, found in various bacterial hypothetical and putative signal peptide 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 PF04517: Microvirus lysis protein (E), C terminus (family)
E protein causes host cell lysis by inhibiting MraY, a peptidoglycan biosynthesis enzyme.  This leads to cell wall failure at septation. The N terminal transmembrane region matches the signal peptide model and must be omitted from the family.
Pfam PF11597: Mediator complex subunit 13 N-terminal (domain)
Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood.
Wikipedia: Mediator complex subunit 13 is a protein that in humans is encoded by the MED13 gene.