SII-SWORD/CoKE huggingface dataset:
Pfam PF14372: hAT-like transposase, RNase-H fold (domain)
This domain is part of an RNase-H fold section in a number of hAT-like transposases, such as protein DAYSLEEPER (At3g42170) from Arabidopsis. Protein DAYSLEEPER is essential for plant development and can also regulate global gene expression. This entry also includes some uncharacterised fungal proteins.
Pfam PF08670: MEKHLA domain (domain)
The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins.
Pfam PF06878: Pkip-1 protein (family)
This family consists of several Pkip-1 proteins which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection.
Pfam PF14659: Phage integrase, N-terminal SAM-like domain (domain)
This domain is found in a variety of phage integrase proteins.
Pfam PF13921: Myb-like DNA-binding domain (domain)
This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.
Pfam PF21275: Thiamin pyrophosphokinase, substrate-binding domain (domain)
This domain is found at the C-terminal end of a group of proteins predominantly found in Bacteroidetes, including Thiamin pyrophosphokinase from Bacteroides thetaiotaomicron. This protein consists of a N-terminal catalytic domain ([pfam:PF04263]) and a C- terminal domain (this entry), which shows an structure mainly composed of beta-strands.
Pfam PF20194: Family of unknown function (DUF6557) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 200 amino acids in length. There is a quite conserved EMTFxxG motif.
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 PF23945: Family of unknown function (DUF7279) (family)
This family represents a family of uncharacterised proteins from T even 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 PF09628: YvfG protein (domain)
Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer.
Pfam PF23877: Family of unknown function (DUF7231) (family)
This entry represents a family of unknown function found in phage proteins, typically 120-130 amino acids in length. Some members contain a C-terminal region enriched in basic residues that is predicted to be disordered.  The N-terminus of the proteins contain a small globular domain. These proteins are found in the Ackermannviridae family of phages that infect Enterobacteria such as Salmonella, Escherichia, Shigella, and Dickeya.
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 PF15117: Uncharacterised protein family UPF0697 (family)
This family of uncharacterised proteins is found in vertebrates. Proteins in this family are typically around 100 amino acids in length.
Pfam PF13572: Domain of unknown function (DUF4134) (family)
Based on Bacteroides thetaiotaomicron gene BT_0095, 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 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 PF23747: CATSPERD Ig-like domain (domain)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. These are multidomain proteins which share a similar domain organisation. This entry represents a Ig-like domain found in the central region of the delta subunit (CATSPERD).
Wikipedia: The cation channels of sperm also known as Catsper channels or CatSper, are ion channels that are related to the two-pore channels and distantly related to TRP channels. The four members of this family form voltage-gated Ca2+ channels that seem to be specific to sperm. As sperm encounter the more alkaline environment of the female reproductive tract, CatSper channels become activated by the altered ion concentration. These channels are required for proper fertilization. The study of these channels has been slow because they do not traffic to the cell membrane in many heterologous systems.
Pfam PF06785: Uncharacterised protein family (UPF0242) N-terminus (family)
This region includes an N-terminal transmembrane region and a C-terminal coiled-coil.
Pfam PF12318: Membrane bound FAD containing D-sorbitol dehydrogenase (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 189 amino acids in length. There is a conserved ALM sequence motif. This family is a membrane protein (FAD-SLDH) involved in oxidation of D-sorbitol to L-sorbose.
Pfam PF02581: Thiamine monophosphate synthase (domain)
Thiamine monophosphate synthase (TMP) ([ec:2.5.1.3]) catalyses the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate. This Pfam family also includes the regulatory protein TENI ([swissprot:P25053]), a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production. While TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase.
Pfam PF07724: AAA domain (Cdc48 subfamily) (domain)
This Pfam entry includes some of the AAA proteins not detected by the [pfam:PF00004] model.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF10653: Protein gp45 of Bacteriophage A118 (family)
This domain is found in bacteriophage and is thought to have a gp45 function within the phage tail-fibre system.
Pfam PF20549: Family of unknown function (DUF6763) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in proteobacteria. Proteins in this family are tipically between 95 and 160 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 PF18444: RNA recognition motif (domain)
The Mex67-Mtr2 complex (TAP-p15 or NXF1-NXT1 in metazoans) is the principal mRNA export factor in Saccharomyces cerevisiae. Mex67 is a member of the NXF family of proteins and has conserved homologs through eukaryotes from yeast to humans. Although sequence conservation is poor between S. cerevisiae Mex67 and Homo sapiens NXF1, they do show functional complementarity. Mex67 and TAP/NXF1 are modular proteins that contain four structural domains: an N-terminal RNA recognition motif (RRM), a leucine rich repeat (LRR) domain, a nuclear transport factor 2-like domain (NTF2L) and an ubiquitin-associated domain (UBA). This entry describes the N-terminal RNA recognition motif (RRM) found in Mex67 proteins.
Pfam PF22149: Type IV pilin Tt1219 (domain)
The founding member of this family is Tt1219 that is a type IV pilin. This protein is likely involved in the formation of polymers that extend from the surface of the bacterial cell and could mediate a wide variety of functions such as adhesion, motility and natural competence. This domain is closely related to type II secretion pseudopilins such as EpsJ, GspJ and XcpW. It consists of the canonical type IV pilin structural core comprising an alpha-helix packed against a four-stranded beta-sheet and a variable lobe comprising a beta-sheet that packs the helix on the side.
Pfam PF20802: Mastermind-like 1/3, transactivation domain 1 (domain)
This is the Transactivation domain 1 (TAD1) found in the central region of Mastermind-like proteins 1 and 3 (MAML1-3) which contains a nuclear localization sequence (NLS) and recruits CBP/p300 to promote nucleosome acetylation at Notch enhancers. This domain is essential for the formation of the ICN-CSL-MAML1 ternary complex, which binds the promoters of specific target genes and determines their transcriptional activation. It is required to sustain Notch-dependent transcription.
Pfam PF23981: Domain of unknown function (DUF7305) (domain)
This domain is found in uncharacterised prokaryotic proteins most of which likely associated with proteins located in pilBC operon. It is frequently found inserted in [[pfam:PF23960]]. This domain is predicted to adopt a single-stranded right-handed beta-helix with similarity to ice-binding proteins and other adhesive domains.
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 PF13810: Domain of unknown function (DUF4185) (repeat)
This presumed domain is functionally uncharacterised.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19874: Family of unknown function (DUF6347) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001130) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the fabclavine Ia biosynthetic gene  cluster from Xenorhabdus budapestensis.
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 PF21760: Protein translocase subunit SecDF, P1 domain, N-terminal (domain)
This domain is found in Protein translocase subunit SecDF from Thermus thermophilus, which belongs to the RND superfamily. SecDF shows 12 transmembrane (TM) regions and 6 periplasmic regions (P1-P6). This entry represents the N-terminal region of the base subdomain of the P1 domain that is located in the N- terminal half of the polypeptide, also known as SecD region. This domain folds into a a pseudo-symmetrical anti-parallel beta-sheet that rearranges to a beta-barrel architecture during ion transport. This domain, which covers the TM region, is related to [pfam:PF03176] and usually appears associated with [pfam:PF07549] and [pfam:PF02355].
Pfam PF11462: Protein of unknown function (DUF3203) (domain)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF20878: Helical region in REST corepressor (family)
This helical region is found in the REST corepressor protein.
Pfam PF16775: Target recognition domain of lytic exoenzyme (domain)
ZoocinA_TRD is domain found downstream of various lytic enzymes, such as peptidase M23 and phage lysins.  The domain is composed of strands of antiparallel beta sheet with one short alpha helix at the C-terminal end.
Pfam PF19140: Family of unknown function (DUF5823) (family)
This is a family of uncharacterised 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 PF11128: Plant viral coat protein nucleocapsid (family)
This family of nucleocapsid proteins is from ssRNA negative-strand viruses of plant origin.
Pfam PF07577: Domain of Unknown Function (DUF1547) (domain)
This domain appears to be found only in a small family of Chlamydia species. It is usually found repeated. This domain can be found in translocated actin-recruiting phosphoprotein (Tarp) from Chlamydia trachomatis serovar L2. Tarp appears to initiate or participate in signalling events that regulate the actin recruitment, which ultimately leads to internalisation.
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 PF19154: Family of unknown function (DUF5836) (family)
This family represents the induction peptide AbpIP, which regulates the biosynthesis of the bacteriocin ABP-118 in Lactobacillus salivarius subsp. salivarius UCC118.
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 PF06920: DHR-2, Lobe A (repeat)
This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs), that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminus and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DHR-2 is a GEF catalytic domain organised into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe A, formed from an antiparallel array of alpha helices that adopts a tetratricopeptide repeat-like fold, which through extensive contacts with lobe B, stabilises DHR-2 domain.
Wikipedia: DOCK is a family of related proteins involved in intracellular signalling networks. DOCK family members contain a RhoGEF domain to function as guanine nucleotide exchange factors to promote GDP release and GTP binding to specific Small GTPases of the Rho family, leading to their activation since Rho proteins are inactive when bound to GDP but active when bound to GTP.
Pfam PF22890: EMC2 TPR-like repeat domain (repeat)
ER membrane protein complex subunit 2 (EMC2, also known as tetratricopeptide repeat protein 35) is a tetratricopeptide repeat-containing protein, and a component of the ER membrane protein complex (EMC), which is required for efficient folding of proteins in the endoplasmic reticulum (ER). EMC2 is a cytosolic component of the complex. Purified recombinant EMC2 formed a stable complex with either EMC8 or EMC9.
Pfam PF06531: Protein of unknown function (DUF1108) (family)
This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. 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 PF11926: Domain of unknown function (DUF3444) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 210 amino acids in length. This domain is found associated with [pfam:PF00226]. This domain has two conserved sequence motifs: FSH and FSH.
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 PF13254: Domain of unknown function (DUF4045) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 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 PF01487: Type I 3-dehydroquinase (domain)
Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see [pfam:PF01220].
Wikipedia: The enzyme 3-dehydroquinate dehydratase (EC 4.2.1.10) catalyzes the chemical reaction3-dehydroquinate  3-dehydroshikimate + H2O
Pfam PF06252: Bacteriophage Mu, GemA protein (family)
This family consists of several bacterial and phage proteins, including GemA (also known as gp16) protein from Bacteriophage Mu. GemA is an early protein responsible for decreasing host DNA gyrase activity, that promotes DNA relaxation of bacterial host genome. Modulates the expression of various host genes probably controlled by supercoiling of their promoters. Host genes affected include DNA replication and cell division determinants. This family also includes the Mu-like prophage FluMu protein gp16 from Haemophilus influenzae.
Pfam PF09577: Sporulation protein YpjB (SpoYpjB) (family)
These proteins are found in the endospore-forming bacteria which include Bacillus species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Pfam PF06324: Pigment-dispersing hormone (PDH) (family)
This family consists of several eukaryotic pigment-dispersing hormone (PDH) proteins. The pigment-dispersing hormone (PDH) is produced in the eyestalks of Crustacea where it induces light-adapting movements of pigment in the compound eye and regulates the pigment dispersion in the chromatophores.
Pfam PF14900: Domain of unknown function (DUF4493) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 264 and 710 amino acids in length. Many of these proteins have a lipid attachment site suggesting they are lipoproteins.
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 PF12464: Maltose acetyltransferase hexapeptide capping motif (conserved_site)
This family is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with [pfam:PF00132]. Mac uses acetyl-CoA as acetyl donor to acetylated cytoplasmic maltose. This region is a short capping motif.
Pfam PF10668: Phage terminase small subunit (domain)
This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.