SII-SWORD/CoKE huggingface dataset:
Pfam PF01889: Membrane protein of unknown function DUF63 (family)
Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane 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 PF08107: Pleurocidin family (family)
This family consists of the pleurocidin family of antimicrobial peptides. Pleurocidins are found in the skin mucous secretions of the winter flounder (Pleuronectes americanus) and these peptides exhibit antimicrobial activity against Escherichia coli. Pleurocidin is predicted to assume an amphipathic alpha-helical conformation similar to other linear antimicrobial peptides and may play a role in innate host defense.
Wikipedia: Pleurocidin is an antimicrobial peptide found in the mucus secreted by the skin of the winter flounder. It exhibits broad-spectrum antimicrobial activity. Pleurocidin assumes an amphipathic alpha-helical conformation similar to other linear antimicrobial peptides and may play a role in innate host defence.
Pfam PF17057: Poxviridae B3 protein (family)
This is a viral protein. Its function is unknown.
Pfam PF00449: Urease alpha-subunit, N-terminal domain (domain)
The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit.
Pfam PF11265: Mediator complex subunit 25 von Willebrand factor type A (family)
The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex.
Pfam PF04899: MbeD/MobD like (family)
The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmids mobilisation and transfer in the presence of conjugative plasmids.
Pfam PF00150: Cellulase (glycosyl hydrolase family 5) (domain)
Glycoside hydrolase family 5 GH5 comprises enzymes with several known activities; endoglucanase (3.2.1.4); beta-mannanase (3.2.1.78); exo-1,3-glucanase (3.2.1.58); endo-1,6-glucanase (3.2.1.75); xylanase (3.2.1.8); endoglycoceramidase (3.2.1.123).

The microbial degradation of cellulose and xylans requires several types of enzymes. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family A  or as the glycosyl hydrolases family 5 . One of the conserved regions in this family contains a conserved glutamic acid residue which is potentially involved  in the catalytic mechanism.
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.
Wikipedia: In molecular biology, glycoside hydrolase family 5 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 PF01701: Photosystem I reaction centre subunit IX / PsaJ (family)
This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organisms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ [swissprot:P19443] is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood. PsaJ can be cross-linked to PsaF [swissprot:P12356] and has a single predicted transmembrane domain it has a proposed role in maintaining PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+.
Pfam PF07283: Conjugal transfer protein TrbH (family)
This family contains TrbH, a bacterial conjugal transfer protein approximately 150 residues long. This contains a putative membrane lipoprotein lipid attachment site.
Pfam PF08409: Protein O-mannosyl-transferase TMTC, DUF1736 (family)
This domain of unknown function is found in O-mannosyl -transferases TMTC1-4, and constitutes a loop between TM7 and TM8 located in the ER lumen that contains a small hydrophobic, but not membrane-embedded helix. This loop is critical for catalysis and binding of ligands, especially the lipid-linked sugar moiety. TMTCs transfers mannosyl residues to the hydroxyl group of serine or threonine residues. The 4 members of the TMTC family are O-mannosyl-transferases acting primarily on the cadherin superfamily; each member has distinct roles in decorating the cadherin domains with O-linked mannose glycans at specific regions. These proteins also act as O-mannosyl-transferase on other proteins such as PDIA3.
Pfam PF11856: Protein of unknown function (DUF3376) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 770 to 1142 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 PF08948: Bacteriophage PRD1, P5, spike N-terminal (domain)
The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. This domain is found at the N-terminal of bacteriophage PRD1 spike protein P5 and mediates the interaction with protein P31. The C-terminal domain appears to contain the residues responsible for the trimerization of the protein.
Pfam PF01739: CheR methyltransferase, SAM binding domain (domain)
CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase - the C-terminal domain (this one) binds SAM.
Wikipedia: In enzymology, a protein-glutamate O-methyltransferase is an enzyme that catalyzes the chemical reactionS-adenosyl-L-methionine + protein L-glutamate  S-adenosyl-L-homocysteine + protein L-glutamate methyl ester
Pfam PF09058: L27_1 (domain)
The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.
Wikipedia: The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein. The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices.
The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer.
Pfam PF03391: Nepovirus coat protein, central domain (domain)
The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.
Pfam PF14141: YqzM-like protein (family)
The YqzM-like protein family includes the B. subtilis YqzM protein [swissprot:C0H453] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length.
Pfam PF12249: Arabinofuranosyltransferase A C terminal (family)
This domain family is found in bacteria, and is typically between 179 and 190 amino acids in length. This family is the C terminal region of AftA. The enzyme catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The C terminal region is predicted to be directed towards the periplasm.
Pfam PF01692: Paramyxovirus non-structural protein C (family)
This family consist of the C proteins (C', C, Y1, Y2) found in Paramyxovirinae; human parainfluenza, and sendai virus. The C proteins effect viral RNA synthesis having both a positive and negative effect during the course of infection. Paramyxovirus have a negative strand ssRNA genome of 15.3kb form which six mRNAs are transcribed, five of these are monocistronic. The P/C mRNA is polycistronic and has two overlapping open reading frames P and C, C encodes the nested C proteins C', C, Y1 and Y2.
Pfam PF08878: HamA (family)
Hachiman antiphage defense system has been described in Ralstonia solanacearum species complex (RSSC), and is composed of two genes, hamAB, which encode a protein of unknown function HamA, represented in this entry, and an helicase (HamB). Only one strain (KACC10722) from phylotype IV shows this system complete and both genes are organised in an operon.
Pfam PF24838: Octameric membrane protein family (8xMP) (domain)
This protein is an integral membrane protein composed of three integral membrane alpha helices. Structure prediction suggests that these proteins form an octameric complex (A0A0D0Q6W1 ipTM = 0.81 pTM = 0.82). This complex contains a central pore. The predicted complex has a flat face on the predicted extracellular face that suggests it may form a complex with another as yet unidentified partner. The alpha helices project into the cytoplasm.
Pfam PF23789: Pre-tape measure protein (domain)
This entry represents a conserved region found in bacteriophage pre-tape measure proteins, located just upstream of the tape measure protein. The region is typically around 140-160 amino acids in length. In some phages the pre-tape measure protein is produced by a programmed translational frameshift.
Pfam PF02772: S-adenosylmethionine synthetase, central domain (domain)
The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.
Wikipedia: S-Adenosylmethionine synthetase, also known as methionine adenosyltransferase (MAT), is an enzyme that creates S-adenosylmethionine by reacting methionine and ATP.
Pfam PF08037: Attractin family (family)
This family consists of the attractin family of water-borne pheromone. Mate attraction in Aplysia  involves a long-distance water-borne signal in  the form of the attractin peptide, that is released  during egg laying. These peptides contain 6 conserved  cysteines and are folded into 2 antiparallel helices. The second helix contains the IEECKTS sequence conserved in Aplysia attractins.
Pfam PF13115: YtkA-like (family)
This entry represents a domain found in protein YtkA from Bacillus subtilis. This domain can also be found in the C-terminal of the copper transport protein YcnJ. YcnJ is involved in uptake of extracellular oxidized copper under copper-limiting conditions .
Pfam PF08210: APOBEC-like N-terminal domain (domain)
A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes.  The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain.  RNA editing by APOBEC-1 requires homodimerisation and this  complex interacts with RNA binding proteins to from the editosome  (and references therein). This family also includes the functionally  homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea  lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like  role in the adaptive immune response of jawless vertebrates.  Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum.
Wikipedia: APOBEC is a family of evolutionarily conserved cytidine deaminases.
Pfam PF12198: Tuberculin-active protein (domain)
This entry represents the tuberculin-active protein from Mycobacterium tuberculosis.
Pfam PF14028: Lantibiotic biosynthesis dehydratase C-term (domain)
Lant_dehydr_C is the C-terminal domain of a family of dehydratases that are involved in the biosynthesis of lantibiotics. While the extensive N-terminal domain, [pfam:PF04738], is involved in the serine-threonine glutamylation step of the synthetic process, this C-terminal domain, once thought to be a separate domain from the dehydratase enzymic activity, is necessary for the final glutamate-elimination step in the generation of the lantibiotic. Lantibiotics are a class of peptide antibiotic that contains one or more thioether bonds.
Pfam PF19073: Family of unknown function (DUF5769) (family)
This is a family of uncharacterised proteins of unknown function found in Mimiviridae.
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 PF04182: B-block binding subunit of TFIIIC (family)
Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding.
Pfam PF14813: NADH dehydrogenase 1 beta subcomplex subunit 2 (family)
This family represents an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF20083: Family of unknown function (DUF6477) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 96 and 116 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 PF07583: Protein of unknown function (DUF1549) (family)
A family of paralogues in the planctomyces.
Pfam PF21267: Ubiquitin-associated protein 1, UBA2 domain (domain)
This domain is found in Ubiquitin-associated protein 1 (UBAP-1) and similar proteins predominantly found in animals. UBAP-1 is involved in vesicular trafficking process, as it's a component of an endosome- specific endosomal sorting complex I (ESCRT-I). It is thought to play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). This protein contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and several tandem ubiquitin- associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This entry corresponds to UBA2 domain.
Pfam PF20067: Strictosidine synthase-like, N-terminal (repeat)
This domain is found at the N-terminal of strictosidine synthase-like (SSL) proteins including Adipocyte plasma membrane- associated proteins (APMAPs) from animals, Protein STRICTOSIDINE SYNTHASE-LIKE (SSLs) from Arabidopsis and SGL proteins, being also present in bacterial sequences. It is about 50 amino acids in length. It contains residues involved in metal coordination in the active site. This domain is also found in Gluconolactonase and Sugar lactone lactonase. These proteins share a six-bladed beta-propeller fold structure and have similar structural and mechanistic features to SS (strictosidine synthase) that involve nucleophilic attack on an electrophilic substrate, although they do not catalyse the SS reaction as they lack the catalytic glutamate required for SS activity; they catalyse hydrolytic reactions instead. APMAPs shows similarity with paraoxonases (PON) and has a strong arylesterase activity with beta-naphthyl acetate and phenyl acetate. They are involved in adipocyte differentiation.
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 PF00631: GGL domain (domain)
G-protein gamma like domains (GGL) are found in the gamma subunit of the heterotrimeric G protein complex and in regulators of G protein signaling (RGS) proteins. It is also found fused to an inactive  Galpha in the Dictyostelium protein gbqA. G-gamma likely shares a common origin with the helical N-terminal unit of G-beta. All organisms that posses a G-beta possess a G-gamma.
Wikipedia: GGL domain  is domain found in the gamma subunit of the heterotrimeric G protein complex and in regulators of G protein signaling RGS proteins.
Pfam PF06634: Protein of unknown function (DUF1156) (family)
This family represents a conserved region within hypothetical prokaryotic and archaeal proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids.
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 PF08397: IRSp53/MIM homology domain (family)
The N-terminal predicted helical stretch of the insulin receptor tyrosine kinase substrate p53 (IRSp53) is an evolutionary conserved F-actin bundling domain involved in filopodium formation. The domain has been named IMD after the IRSp53 and missing in metastasis (MIM) proteins in which it occurs. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent.
Wikipedia: In molecular biology, the IMD domain is a BAR-like domain of approximately 250 amino acids found at the N-terminus in the insulin receptor tyrosine kinase substrate p53 (IRSp53/BAIAP2) and in the evolutionarily related IRSp53/MIM (MTSS1) family. In IRSp53, a ubiquitous regulator of the actin cytoskeleton, the IMD domain acts as conserved F-actin bundling domain involved in filopodium formation. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent. The IRSp53/MIM family is a novel F-actin bundling protein family that includes invertebrate relatives:Vertebrate MIM (MTSS1), an actin-binding scaffold protein that may be involved in cancer metastasis.
Vertebrate ABBA-1 (MTSS1L), a MIM-related protein.
Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2 or insulin receptor tyrosine kinase substrate p53 (IRSp53), a multifunctional adaptor protein that links Rac1 with a Wiskott–Aldrich syndrome family verprolin-homologous protein 2 (WAVE2/WASF2) to induce lamellipodia or Cdc42 with Mena to induce filopodia.
Vertebrate brain-specific angiogenesis inhibitor 1-associated protein 2-like proteins 1 and 2.
Drosophila melanogaster CG32082-PA.
Caenorhabditis elegans M04F3.5 protein.
Pfam PF16013: Domain of unknown function (DUF4781) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and eukaryotes, and is typically between 288 and 306 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.